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I want to calculate the relaxed structure of 4 Pd atoms on top of a rutile TiO2 surface (110) using DFT+U calculations, with the U value applied for Ti only. The calculations converged and below are the INCAR, KPOINTS and CONTCAR files. If you'd visualize the CONTCAR file you'd notice straightaway that there is a high degree of assynnertry in the relaxed structure. I know that calculated structures need not be in the end completely symmetric but this one looks way too distorted. Could you please suggest what going wrong, if at all something is going wrong?

INCAR
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SYSTEM = TiO2_Pd
#======Accuracy&Speed======
ENCUT=500
ISMEAR= -5
ALGO=FAST
LREAL=AUTO
ADDGRID=.TRUE.
IDIPOL=3 # dipole correcion in the z direction
LDIPOL=.TRUE. # use after preconverging
NPAR=7
KPAR=2

#======Relaxation==========
ISIF=2
IBRION=2
NSW=1000
ISPIN=2
NELM=200
NBANDS=420

#======Verbosity===========
LWAVE=.FALSE.
LCHARGE=.TRUE. # .TRUE. for CHGCAR
LAECHG=.TRUE. # for Bader Charge Analysis

#======DFT+U===============
LASPH=.TRUE.
LDAU=.TRUE.
LDAUTYPE= 3 # some kind of thing everyone uses, no one explains
LDAUL= -1 2 -1 # for Pd,Ti(d),O
LDAUU= 0 5.2 0 # for Pd,Ti(d),O
LDAUJ= 0 1 0 # for Pd,Ti(d),O
LMAXMIX=4 # 4 for writing CHGCAR to include at least d electrons, 6 for f electrons
NSIM=4
LPLANE=.TRUE.
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KPOINTS
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Automatic mesh
0
Gamma
11 10 1
0 0 0
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CONTCAR
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TiO2(110)_Slab_4Pd
1.00000000000000
5.9180002212999998 0.0000000000000000 0.0000000000000000
0.0000000000000000 6.4969000815999998 0.0000000000000000
0.0000000000000000 0.0000000000000000 27.2817001342999994
Pd Ti O
4 16 32
Selective dynamics
Direct
0.1858294521090943 0.2983240554776972 0.4900009440651765 T T T
0.1912520495392255 0.6922224901740929 0.4916128501949542 T T T
0.6728809986761233 0.7006623730652624 0.4871303871419154 T T T
0.6921751669677573 0.3130705175368061 0.4895614208738577 T T T
0.9338256994893398 0.0333804093198772 0.0575697384904556 T T T
0.4338281493454132 0.0327529626007242 0.0574782536892628 T T T
0.9421536035129336 0.5413684211538597 0.1537357070142507 T T T
0.4427993944775946 0.5413857771239161 0.1536801858702429 T T T
0.9378723963317510 0.0055409726259982 0.2944542190037528 T T T
0.4374708293436624 0.9986562373155207 0.2945023944114822 T T T
0.0341911773782960 0.4962605570572513 0.3996249746208678 T T T
0.5007632389811018 0.4981208276180678 0.3994635615191754 T T T
0.2785830084899647 0.5408919674514626 0.0327413251601615 T T T
0.7786845146395130 0.5411081506661991 0.0327605096242828 T T T
0.2727255685459439 0.0475039770243869 0.1785249242014155 T T T
0.7723688296307784 0.0478328375862940 0.1784357348291208 T T T
0.2158423511566194 0.5057338401470473 0.2818967716507825 T T T
0.7156033746025128 0.5054312454684089 0.2828046556516923 T T T
0.2032025191227995 0.0084281921463188 0.4093509561030810 T T T
0.7065587470552653 0.9771185480940848 0.4084407220977908 T T T
0.9311698461990511 0.0032469280155202 0.1163656010168919 T T T
0.4305720158101369 0.0029505403888250 0.1162644151696770 T T T
0.0068632172099681 0.5044483881312499 0.2456594842083914 T T T
0.5085259746725203 0.5072491532443475 0.2460387202895735 T T T
0.9884303052236333 0.0082524876493915 0.3686458947686239 T T T
0.4936344648198929 0.9905837685307131 0.3680317701569863 T T T
0.9431593786210314 0.5026092823669389 0.0953839106325992 T T T
0.4431817527855698 0.5025834887917400 0.0953722182092939 T T T
-0.0017311936034102 0.0109097416178500 0.2139125114183992 T T T
0.4988104616821336 0.0081091659880431 0.2138803450364772 T T T
0.0455449671921270 0.4993446231749819 0.3410599643157731 T T T
0.5416033517603188 0.5009417259261796 0.3413834278100736 T T T
0.0953774814292299 0.9929749005258974 0.4672575053658909 T T T
0.5989272275932124 0.0093922819512133 0.4670085798272016 T T T
0.2102044166738682 0.1755682344391427 0.0448815861633208 T T T
0.7100924918338000 0.1759473201047329 0.0450123499652260 T T T
0.2176126587693890 0.6859719983979079 0.1634875298529508 T T T
0.7174302248114014 0.6866819648212956 0.1633366109311853 T T T
0.2680199394192587 0.1960054589792153 0.2907370744714202 T T T
0.7638825070495037 0.1991326750525741 0.2902619141366246 T T T
0.2656919387544532 0.6979331284463750 0.4144826867948500 T T T
0.7767445538623622 0.7034292394284603 0.4132605722842455 T T T
0.2805654273526881 0.7927034878396385 0.0380985738543658 T T T
0.7807589650669677 0.7930027516209931 0.0382035327004519 T T T
0.2737823731848890 0.2933582704312049 0.1705559249267962 T T T
0.7713706119628377 0.2937758308548660 0.1702089377863268 T T T
0.2593714514393552 0.8064975678941458 0.2896808577952940 T T T
0.7645986506130562 0.8094052354959062 0.2905573045568385 T T T
0.2775602823911044 0.2947310637711446 0.4118016430018864 T T T
0.7664781623774347 0.3151662739726207 0.4174952639381250 T T T
0.0000000000000000 0.5000000000000000 0.0000000000000000 F F F
0.5000000000000000 0.5000000000000000 0.0000000000000000 F F F

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<span class='smallblacktext'>[ Edited ]</span>

please check if each of the ionic steps have converged electronically below the EDIFF limit

Yeah, I checked thart, every step actually converges below the defualt EDIFF .

Is starting POSCAR OK? No disconnected Ti--O bonds? CONTCAR shows that the structure is too reconstructed. You need to fix positions of larger number of atoms, not just two of them.