Starting phenix.real_space_refine on Wed Sep 17 19:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq9_38570/09_2025/8xq9_38570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq9_38570/09_2025/8xq9_38570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xq9_38570/09_2025/8xq9_38570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq9_38570/09_2025/8xq9_38570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xq9_38570/09_2025/8xq9_38570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq9_38570/09_2025/8xq9_38570.map" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6976 2.51 5 N 1766 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5336 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 Chain: "B" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5336 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 23, 'TRANS': 659} Chain breaks: 2 Time building chain proxies: 2.92, per 1000 atoms: 0.27 Number of scatterers: 10672 At special positions: 0 Unit cell: (102.6, 115.56, 115.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1870 8.00 N 1766 7.00 C 6976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 455.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.943A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.854A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 413 Proline residue: A 408 - end of helix removed outlier: 3.889A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.986A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.285A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.655A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 573 through 601 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 639 through 653 removed outlier: 4.034A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 853 Processing helix chain 'A' and resid 853 through 858 removed outlier: 4.335A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'B' and resid 76 through 95 Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.028A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'B' and resid 134 through 153 removed outlier: 3.592A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 223 through 253 Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.847A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 318 removed outlier: 3.900A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 4.230A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 376 Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 432 through 445 Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.438A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.910A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 573 through 600 Processing helix chain 'B' and resid 604 through 620 Processing helix chain 'B' and resid 639 through 653 removed outlier: 3.893A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 853 removed outlier: 3.809A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 removed outlier: 4.228A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.537A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 918 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.577A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3357 1.34 - 1.46: 2018 1.46 - 1.58: 5393 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10880 Sorted by residual: bond pdb=" CA PRO B 949 " pdb=" C PRO B 949 " ideal model delta sigma weight residual 1.517 1.503 0.014 6.70e-03 2.23e+04 4.43e+00 bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.548 -0.014 6.80e-03 2.16e+04 4.20e+00 bond pdb=" CA ILE A 488 " pdb=" C ILE A 488 " ideal model delta sigma weight residual 1.520 1.536 -0.016 8.80e-03 1.29e+04 3.29e+00 bond pdb=" C ILE B 818 " pdb=" N PRO B 819 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.28e-02 6.10e+03 2.79e+00 bond pdb=" C LEU B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.71e+00 ... (remaining 10875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 14447 2.02 - 4.05: 273 4.05 - 6.07: 18 6.07 - 8.09: 17 8.09 - 10.11: 7 Bond angle restraints: 14762 Sorted by residual: angle pdb=" C GLU A 337 " pdb=" N LYS A 338 " pdb=" CA LYS A 338 " ideal model delta sigma weight residual 126.32 134.30 -7.98 1.74e+00 3.30e-01 2.10e+01 angle pdb=" C PHE A 294 " pdb=" N ASN A 295 " pdb=" CA ASN A 295 " ideal model delta sigma weight residual 122.08 128.75 -6.67 1.47e+00 4.63e-01 2.06e+01 angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 123.07 -2.83 6.30e-01 2.52e+00 2.02e+01 angle pdb=" C GLU B 337 " pdb=" N LYS B 338 " pdb=" CA LYS B 338 " ideal model delta sigma weight residual 126.32 133.64 -7.32 1.74e+00 3.30e-01 1.77e+01 angle pdb=" C SER B 487 " pdb=" N ILE B 488 " pdb=" CA ILE B 488 " ideal model delta sigma weight residual 120.33 123.35 -3.02 8.00e-01 1.56e+00 1.43e+01 ... (remaining 14757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5903 17.58 - 35.16: 431 35.16 - 52.74: 147 52.74 - 70.32: 22 70.32 - 87.90: 3 Dihedral angle restraints: 6506 sinusoidal: 2554 harmonic: 3952 Sorted by residual: dihedral pdb=" CA GLU A 337 " pdb=" C GLU A 337 " pdb=" N LYS A 338 " pdb=" CA LYS A 338 " ideal model delta harmonic sigma weight residual -180.00 -156.11 -23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA LYS B 338 " pdb=" C LYS B 338 " pdb=" N THR B 339 " pdb=" CA THR B 339 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS A 338 " pdb=" C LYS A 338 " pdb=" N THR A 339 " pdb=" CA THR A 339 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 6503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1323 0.047 - 0.093: 358 0.093 - 0.140: 91 0.140 - 0.186: 9 0.186 - 0.233: 1 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CB ILE A 488 " pdb=" CA ILE A 488 " pdb=" CG1 ILE A 488 " pdb=" CG2 ILE A 488 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN A 295 " pdb=" N ASN A 295 " pdb=" C ASN A 295 " pdb=" CB ASN A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA SER B 407 " pdb=" N SER B 407 " pdb=" C SER B 407 " pdb=" CB SER B 407 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1779 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 818 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 819 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 819 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 819 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 467 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C LEU B 467 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU B 467 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 468 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 271 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C VAL A 271 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL A 271 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 272 " 0.010 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2922 2.81 - 3.34: 10555 3.34 - 3.86: 18370 3.86 - 4.38: 19514 4.38 - 4.90: 34749 Nonbonded interactions: 86110 Sorted by model distance: nonbonded pdb=" OD1 ASN A 194 " pdb=" OG SER A 196 " model vdw 2.293 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.298 3.040 nonbonded pdb=" O ILE B 462 " pdb=" OG1 THR B 466 " model vdw 2.309 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASN B 194 " pdb=" OG SER B 196 " model vdw 2.334 3.040 ... (remaining 86105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10880 Z= 0.183 Angle : 0.712 10.113 14762 Z= 0.393 Chirality : 0.045 0.233 1782 Planarity : 0.006 0.055 1816 Dihedral : 14.170 87.897 3946 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.48 % Allowed : 11.29 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.20), residues: 1354 helix: -0.46 (0.13), residues: 1138 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 887 TYR 0.012 0.001 TYR B 392 PHE 0.011 0.001 PHE B 455 TRP 0.007 0.001 TRP B 643 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00327 (10880) covalent geometry : angle 0.71195 (14762) hydrogen bonds : bond 0.10310 ( 905) hydrogen bonds : angle 5.60384 ( 2715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 474 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8031 (mt) cc_final: 0.7609 (mm) REVERT: A 112 ILE cc_start: 0.8065 (mt) cc_final: 0.7770 (mt) REVERT: A 113 LEU cc_start: 0.8152 (tt) cc_final: 0.7861 (tp) REVERT: A 124 GLU cc_start: 0.6952 (tt0) cc_final: 0.6404 (tt0) REVERT: A 134 ASP cc_start: 0.8102 (t70) cc_final: 0.7717 (t0) REVERT: A 155 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6526 (p0) REVERT: A 158 THR cc_start: 0.8144 (m) cc_final: 0.7579 (p) REVERT: A 180 LEU cc_start: 0.8496 (mt) cc_final: 0.8215 (mm) REVERT: A 197 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 199 MET cc_start: 0.7636 (tpt) cc_final: 0.7416 (tpt) REVERT: A 204 ILE cc_start: 0.8625 (mt) cc_final: 0.8342 (tt) REVERT: A 211 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7890 (p) REVERT: A 216 LEU cc_start: 0.8573 (mp) cc_final: 0.8325 (mp) REVERT: A 226 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8092 (pp) REVERT: A 233 GLU cc_start: 0.7841 (tt0) cc_final: 0.6420 (tt0) REVERT: A 234 SER cc_start: 0.7897 (p) cc_final: 0.7276 (p) REVERT: A 236 LEU cc_start: 0.8257 (mt) cc_final: 0.7978 (mp) REVERT: A 237 ASN cc_start: 0.8115 (t0) cc_final: 0.7562 (t0) REVERT: A 238 ASP cc_start: 0.7323 (m-30) cc_final: 0.6891 (m-30) REVERT: A 240 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 248 PHE cc_start: 0.8077 (m-80) cc_final: 0.7526 (m-10) REVERT: A 251 MET cc_start: 0.7609 (ttm) cc_final: 0.7241 (ttm) REVERT: A 294 PHE cc_start: 0.7990 (m-80) cc_final: 0.7725 (m-80) REVERT: A 312 TYR cc_start: 0.8166 (t80) cc_final: 0.7784 (t80) REVERT: A 316 ASP cc_start: 0.7348 (m-30) cc_final: 0.6962 (m-30) REVERT: A 350 HIS cc_start: 0.8552 (m-70) cc_final: 0.7938 (m90) REVERT: A 351 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7888 (tpp80) REVERT: A 364 ILE cc_start: 0.8197 (mt) cc_final: 0.7791 (mt) REVERT: A 384 ASP cc_start: 0.8037 (t0) cc_final: 0.7718 (t0) REVERT: A 393 LEU cc_start: 0.8772 (mp) cc_final: 0.8463 (mp) REVERT: A 396 THR cc_start: 0.8366 (m) cc_final: 0.8097 (p) REVERT: A 399 ARG cc_start: 0.8068 (ttt90) cc_final: 0.7488 (tpt170) REVERT: A 401 MET cc_start: 0.7685 (ttm) cc_final: 0.7399 (ttm) REVERT: A 427 TRP cc_start: 0.8403 (t-100) cc_final: 0.8152 (t-100) REVERT: A 443 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 444 ASN cc_start: 0.8440 (t0) cc_final: 0.8114 (t0) REVERT: A 445 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 465 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 480 ILE cc_start: 0.8475 (mt) cc_final: 0.8138 (mm) REVERT: A 485 ASP cc_start: 0.8121 (t0) cc_final: 0.7763 (t0) REVERT: A 499 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7752 (ttp80) REVERT: A 502 HIS cc_start: 0.8042 (t70) cc_final: 0.7529 (t70) REVERT: A 505 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 506 ASN cc_start: 0.8401 (m-40) cc_final: 0.7848 (m-40) REVERT: A 507 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7881 (ptp-110) REVERT: A 511 MET cc_start: 0.8154 (ttm) cc_final: 0.7409 (tmm) REVERT: A 533 SER cc_start: 0.8522 (p) cc_final: 0.8223 (p) REVERT: A 534 ASP cc_start: 0.7617 (t0) cc_final: 0.7384 (t0) REVERT: A 586 MET cc_start: 0.7756 (ptm) cc_final: 0.7305 (ptm) REVERT: A 587 LEU cc_start: 0.8808 (pp) cc_final: 0.8487 (pp) REVERT: A 590 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 591 LYS cc_start: 0.8759 (pttp) cc_final: 0.8497 (pttp) REVERT: A 610 LEU cc_start: 0.8873 (tt) cc_final: 0.8038 (tp) REVERT: A 613 GLN cc_start: 0.8428 (pp30) cc_final: 0.7866 (pp30) REVERT: A 832 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 833 LEU cc_start: 0.8859 (tp) cc_final: 0.8599 (mm) REVERT: A 844 ILE cc_start: 0.9028 (mm) cc_final: 0.8392 (pt) REVERT: A 848 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 875 ARG cc_start: 0.7513 (ttp80) cc_final: 0.6826 (ttp80) REVERT: A 897 LYS cc_start: 0.8724 (pttt) cc_final: 0.8509 (pttt) REVERT: A 899 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7382 (mtt90) REVERT: A 900 GLN cc_start: 0.8128 (tt0) cc_final: 0.7885 (tt0) REVERT: A 906 LEU cc_start: 0.8474 (mt) cc_final: 0.8092 (mm) REVERT: A 909 SER cc_start: 0.8696 (t) cc_final: 0.8153 (p) REVERT: A 911 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 938 MET cc_start: 0.8282 (tpp) cc_final: 0.7879 (tpp) REVERT: B 90 ILE cc_start: 0.8238 (mt) cc_final: 0.7956 (mm) REVERT: B 118 SER cc_start: 0.8190 (t) cc_final: 0.7778 (p) REVERT: B 155 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6266 (p0) REVERT: B 161 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7653 (ptp-170) REVERT: B 162 SER cc_start: 0.8908 (t) cc_final: 0.8578 (t) REVERT: B 163 PHE cc_start: 0.7970 (t80) cc_final: 0.7739 (t80) REVERT: B 165 GLN cc_start: 0.8177 (pt0) cc_final: 0.7899 (pt0) REVERT: B 166 VAL cc_start: 0.8682 (t) cc_final: 0.8367 (p) REVERT: B 189 PHE cc_start: 0.7893 (m-10) cc_final: 0.7402 (m-10) REVERT: B 191 TYR cc_start: 0.8355 (m-80) cc_final: 0.7953 (m-80) REVERT: B 199 MET cc_start: 0.7330 (tpt) cc_final: 0.6810 (tpp) REVERT: B 218 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8054 (ptmm) REVERT: B 237 ASN cc_start: 0.8049 (t0) cc_final: 0.7593 (t0) REVERT: B 248 PHE cc_start: 0.8077 (m-80) cc_final: 0.7349 (m-80) REVERT: B 249 MET cc_start: 0.7658 (tmm) cc_final: 0.7311 (tmm) REVERT: B 251 MET cc_start: 0.6824 (tmm) cc_final: 0.6474 (tmm) REVERT: B 263 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 280 TYR cc_start: 0.7621 (t80) cc_final: 0.7133 (t80) REVERT: B 293 ILE cc_start: 0.8354 (mt) cc_final: 0.8123 (tp) REVERT: B 319 LEU cc_start: 0.7447 (mp) cc_final: 0.7239 (mt) REVERT: B 321 VAL cc_start: 0.6720 (OUTLIER) cc_final: 0.6298 (t) REVERT: B 335 ASN cc_start: 0.8419 (t0) cc_final: 0.8008 (t0) REVERT: B 339 THR cc_start: 0.8536 (p) cc_final: 0.8167 (p) REVERT: B 344 GLU cc_start: 0.7382 (pp20) cc_final: 0.7083 (pp20) REVERT: B 375 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7855 (ptpt) REVERT: B 377 LEU cc_start: 0.7622 (tp) cc_final: 0.7209 (tp) REVERT: B 383 MET cc_start: 0.7236 (tpp) cc_final: 0.5881 (tpp) REVERT: B 387 TYR cc_start: 0.7576 (m-10) cc_final: 0.7242 (m-80) REVERT: B 388 LEU cc_start: 0.8542 (tt) cc_final: 0.8305 (tp) REVERT: B 397 ILE cc_start: 0.8376 (mt) cc_final: 0.7444 (mm) REVERT: B 401 MET cc_start: 0.7735 (mtp) cc_final: 0.7094 (mtp) REVERT: B 413 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6275 (pt) REVERT: B 418 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 424 ILE cc_start: 0.8824 (tp) cc_final: 0.8621 (tp) REVERT: B 444 ASN cc_start: 0.8074 (t0) cc_final: 0.7865 (t0) REVERT: B 445 LEU cc_start: 0.8423 (tp) cc_final: 0.8139 (tp) REVERT: B 466 THR cc_start: 0.7743 (p) cc_final: 0.7491 (t) REVERT: B 470 ASN cc_start: 0.7791 (m-40) cc_final: 0.7447 (m110) REVERT: B 475 GLN cc_start: 0.8153 (tp40) cc_final: 0.7846 (tp40) REVERT: B 477 LEU cc_start: 0.8633 (mp) cc_final: 0.8206 (tp) REVERT: B 480 ILE cc_start: 0.7991 (mt) cc_final: 0.7789 (mt) REVERT: B 481 LEU cc_start: 0.8619 (mt) cc_final: 0.8075 (mm) REVERT: B 494 MET cc_start: 0.7574 (tpp) cc_final: 0.7159 (tpp) REVERT: B 500 ARG cc_start: 0.7861 (tmt-80) cc_final: 0.7477 (ttt-90) REVERT: B 512 LEU cc_start: 0.8777 (mp) cc_final: 0.8364 (mt) REVERT: B 517 PHE cc_start: 0.7302 (m-80) cc_final: 0.7086 (m-10) REVERT: B 580 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6654 (tp30) REVERT: B 583 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6485 (ttp-110) REVERT: B 586 MET cc_start: 0.7561 (tpt) cc_final: 0.7181 (tpt) REVERT: B 590 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 594 TYR cc_start: 0.8205 (m-10) cc_final: 0.8004 (m-80) REVERT: B 598 PHE cc_start: 0.8264 (t80) cc_final: 0.7797 (t80) REVERT: B 826 ASN cc_start: 0.8083 (t0) cc_final: 0.7166 (t0) REVERT: B 830 ASN cc_start: 0.8305 (m-40) cc_final: 0.7826 (m110) REVERT: B 832 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 848 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 877 GLN cc_start: 0.8184 (pp30) cc_final: 0.7709 (pp30) REVERT: B 880 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7813 (ptpp) REVERT: B 881 GLU cc_start: 0.7745 (pt0) cc_final: 0.7457 (pt0) REVERT: B 885 LEU cc_start: 0.8385 (tp) cc_final: 0.8154 (tp) REVERT: B 889 HIS cc_start: 0.7445 (m-70) cc_final: 0.6946 (m-70) REVERT: B 899 ARG cc_start: 0.7583 (tmm-80) cc_final: 0.6688 (tmm-80) REVERT: B 902 ILE cc_start: 0.8903 (tt) cc_final: 0.8552 (tp) REVERT: B 903 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7798 (ttm170) REVERT: B 921 LEU cc_start: 0.8762 (tt) cc_final: 0.8284 (mm) outliers start: 52 outliers final: 14 residues processed: 500 average time/residue: 0.1212 time to fit residues: 82.2719 Evaluate side-chains 478 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 453 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 264 ASN A 295 ASN A 374 GLN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN B 126 HIS B 157 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 421 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 826 ASN ** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103434 restraints weight = 23635.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106937 restraints weight = 12343.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109166 restraints weight = 7610.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110651 restraints weight = 5294.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.111647 restraints weight = 4055.448| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10880 Z= 0.157 Angle : 0.609 10.053 14762 Z= 0.322 Chirality : 0.040 0.236 1782 Planarity : 0.004 0.043 1816 Dihedral : 7.198 59.208 1499 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.88 % Allowed : 18.88 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.22), residues: 1354 helix: 1.00 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -1.25 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 887 TYR 0.016 0.001 TYR B 837 PHE 0.021 0.001 PHE A 598 TRP 0.023 0.001 TRP A 635 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00310 (10880) covalent geometry : angle 0.60888 (14762) hydrogen bonds : bond 0.04627 ( 905) hydrogen bonds : angle 4.33832 ( 2715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8118 (mt) cc_final: 0.7782 (mm) REVERT: A 113 LEU cc_start: 0.8240 (tt) cc_final: 0.7988 (tp) REVERT: A 134 ASP cc_start: 0.7916 (t70) cc_final: 0.7672 (t0) REVERT: A 155 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6123 (p0) REVERT: A 156 VAL cc_start: 0.8500 (t) cc_final: 0.8053 (m) REVERT: A 158 THR cc_start: 0.8297 (m) cc_final: 0.7367 (p) REVERT: A 161 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7120 (mmt180) REVERT: A 204 ILE cc_start: 0.8674 (mt) cc_final: 0.8360 (tt) REVERT: A 205 MET cc_start: 0.7814 (mmp) cc_final: 0.7530 (tpp) REVERT: A 206 SER cc_start: 0.8264 (t) cc_final: 0.7815 (p) REVERT: A 211 VAL cc_start: 0.8095 (m) cc_final: 0.7841 (p) REVERT: A 233 GLU cc_start: 0.7986 (tt0) cc_final: 0.7778 (tt0) REVERT: A 234 SER cc_start: 0.8205 (p) cc_final: 0.7412 (p) REVERT: A 238 ASP cc_start: 0.7370 (m-30) cc_final: 0.6872 (m-30) REVERT: A 248 PHE cc_start: 0.8113 (m-80) cc_final: 0.7494 (m-10) REVERT: A 251 MET cc_start: 0.7463 (ttm) cc_final: 0.7143 (ttm) REVERT: A 252 VAL cc_start: 0.7391 (t) cc_final: 0.6629 (m) REVERT: A 285 VAL cc_start: 0.8092 (t) cc_final: 0.7814 (p) REVERT: A 294 PHE cc_start: 0.8114 (m-80) cc_final: 0.7799 (m-80) REVERT: A 312 TYR cc_start: 0.8270 (t80) cc_final: 0.7865 (t80) REVERT: A 316 ASP cc_start: 0.7375 (m-30) cc_final: 0.6868 (m-30) REVERT: A 333 ILE cc_start: 0.8022 (mt) cc_final: 0.7806 (mm) REVERT: A 351 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7945 (tpp80) REVERT: A 364 ILE cc_start: 0.8230 (mt) cc_final: 0.7699 (tt) REVERT: A 384 ASP cc_start: 0.8037 (t0) cc_final: 0.7766 (t0) REVERT: A 393 LEU cc_start: 0.8852 (mp) cc_final: 0.8444 (mp) REVERT: A 396 THR cc_start: 0.8305 (m) cc_final: 0.8073 (p) REVERT: A 401 MET cc_start: 0.7522 (ttm) cc_final: 0.7305 (ttm) REVERT: A 425 MET cc_start: 0.7699 (tpt) cc_final: 0.7427 (tpt) REVERT: A 443 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 466 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 470 ASN cc_start: 0.8465 (m110) cc_final: 0.8262 (m-40) REVERT: A 485 ASP cc_start: 0.7972 (t0) cc_final: 0.7607 (t0) REVERT: A 494 MET cc_start: 0.7938 (tpp) cc_final: 0.7585 (tpp) REVERT: A 500 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7719 (ttt180) REVERT: A 502 HIS cc_start: 0.7972 (t70) cc_final: 0.7586 (t70) REVERT: A 505 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 506 ASN cc_start: 0.8399 (m-40) cc_final: 0.7848 (m110) REVERT: A 507 ARG cc_start: 0.7950 (ptp-110) cc_final: 0.7698 (ptp-110) REVERT: A 523 TRP cc_start: 0.7758 (m100) cc_final: 0.7339 (m100) REVERT: A 533 SER cc_start: 0.8628 (p) cc_final: 0.8350 (p) REVERT: A 534 ASP cc_start: 0.7615 (t0) cc_final: 0.7340 (t0) REVERT: A 578 MET cc_start: 0.8206 (ppp) cc_final: 0.8000 (ppp) REVERT: A 579 MET cc_start: 0.8587 (mmm) cc_final: 0.8360 (tpt) REVERT: A 581 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 586 MET cc_start: 0.7550 (ptm) cc_final: 0.7112 (ptm) REVERT: A 587 LEU cc_start: 0.8773 (pp) cc_final: 0.8472 (pp) REVERT: A 590 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 591 LYS cc_start: 0.8680 (pttp) cc_final: 0.8462 (pttp) REVERT: A 600 HIS cc_start: 0.7821 (t70) cc_final: 0.7525 (t70) REVERT: A 610 LEU cc_start: 0.8829 (tt) cc_final: 0.7986 (tp) REVERT: A 613 GLN cc_start: 0.8353 (pp30) cc_final: 0.7744 (pp30) REVERT: A 830 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7781 (t0) REVERT: A 832 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 844 ILE cc_start: 0.8977 (mm) cc_final: 0.8262 (tt) REVERT: A 848 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 875 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7005 (ttp80) REVERT: A 887 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7052 (mtm110) REVERT: A 888 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 899 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7274 (mtt90) REVERT: A 906 LEU cc_start: 0.8465 (mt) cc_final: 0.8138 (mm) REVERT: A 908 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: A 909 SER cc_start: 0.8793 (t) cc_final: 0.8572 (p) REVERT: A 911 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6894 (mt-10) REVERT: B 78 ILE cc_start: 0.8205 (tt) cc_final: 0.7660 (mt) REVERT: B 90 ILE cc_start: 0.8377 (mt) cc_final: 0.8055 (mm) REVERT: B 118 SER cc_start: 0.8460 (t) cc_final: 0.8224 (p) REVERT: B 156 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8403 (t) REVERT: B 162 SER cc_start: 0.8668 (t) cc_final: 0.8464 (p) REVERT: B 163 PHE cc_start: 0.8046 (t80) cc_final: 0.7712 (t80) REVERT: B 166 VAL cc_start: 0.8566 (t) cc_final: 0.8290 (p) REVERT: B 186 MET cc_start: 0.7739 (mmm) cc_final: 0.7363 (mmm) REVERT: B 189 PHE cc_start: 0.7666 (m-10) cc_final: 0.7365 (m-10) REVERT: B 194 ASN cc_start: 0.7712 (p0) cc_final: 0.7489 (p0) REVERT: B 197 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: B 218 LYS cc_start: 0.8465 (ptmm) cc_final: 0.8144 (ptmm) REVERT: B 237 ASN cc_start: 0.8022 (t0) cc_final: 0.7610 (t0) REVERT: B 242 ILE cc_start: 0.8588 (mt) cc_final: 0.8268 (mm) REVERT: B 248 PHE cc_start: 0.8071 (m-80) cc_final: 0.7447 (m-80) REVERT: B 251 MET cc_start: 0.6583 (tmm) cc_final: 0.6273 (tmm) REVERT: B 263 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 271 VAL cc_start: 0.8160 (t) cc_final: 0.7909 (t) REVERT: B 280 TYR cc_start: 0.7689 (t80) cc_final: 0.7278 (t80) REVERT: B 321 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6744 (t) REVERT: B 335 ASN cc_start: 0.8172 (t0) cc_final: 0.7924 (t0) REVERT: B 355 MET cc_start: 0.8104 (tmm) cc_final: 0.7877 (ttp) REVERT: B 375 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7829 (ptpt) REVERT: B 383 MET cc_start: 0.6751 (tpp) cc_final: 0.5653 (tpp) REVERT: B 387 TYR cc_start: 0.7538 (m-10) cc_final: 0.7225 (m-80) REVERT: B 393 LEU cc_start: 0.8535 (mp) cc_final: 0.8293 (mp) REVERT: B 397 ILE cc_start: 0.8548 (mt) cc_final: 0.7535 (mm) REVERT: B 399 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8583 (ttt90) REVERT: B 401 MET cc_start: 0.7747 (mtp) cc_final: 0.7192 (mtp) REVERT: B 406 PHE cc_start: 0.8002 (m-80) cc_final: 0.7688 (m-80) REVERT: B 425 MET cc_start: 0.8140 (mtt) cc_final: 0.7874 (mtp) REVERT: B 444 ASN cc_start: 0.8010 (t0) cc_final: 0.7767 (t0) REVERT: B 445 LEU cc_start: 0.8403 (tp) cc_final: 0.8100 (tp) REVERT: B 466 THR cc_start: 0.7777 (p) cc_final: 0.7486 (t) REVERT: B 470 ASN cc_start: 0.7737 (m-40) cc_final: 0.7447 (m110) REVERT: B 477 LEU cc_start: 0.8636 (mp) cc_final: 0.8250 (tp) REVERT: B 480 ILE cc_start: 0.8099 (mt) cc_final: 0.7868 (mt) REVERT: B 481 LEU cc_start: 0.8467 (mt) cc_final: 0.8243 (mm) REVERT: B 490 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8442 (ttmt) REVERT: B 494 MET cc_start: 0.7215 (tpp) cc_final: 0.7005 (tpp) REVERT: B 500 ARG cc_start: 0.7845 (tmt-80) cc_final: 0.7428 (ttt-90) REVERT: B 578 MET cc_start: 0.7415 (ppp) cc_final: 0.6852 (ppp) REVERT: B 580 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8123 (tp30) REVERT: B 586 MET cc_start: 0.7465 (tpt) cc_final: 0.7089 (tpt) REVERT: B 590 GLU cc_start: 0.7862 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 598 PHE cc_start: 0.8283 (t80) cc_final: 0.7931 (t80) REVERT: B 826 ASN cc_start: 0.8099 (t0) cc_final: 0.7289 (t0) REVERT: B 830 ASN cc_start: 0.8376 (m-40) cc_final: 0.7931 (m110) REVERT: B 832 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7272 (tp40) REVERT: B 848 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 877 GLN cc_start: 0.8261 (pp30) cc_final: 0.7749 (pp30) REVERT: B 878 VAL cc_start: 0.8401 (p) cc_final: 0.7933 (p) REVERT: B 881 GLU cc_start: 0.7877 (pt0) cc_final: 0.7478 (pt0) REVERT: B 885 LEU cc_start: 0.8320 (tp) cc_final: 0.8072 (tp) REVERT: B 889 HIS cc_start: 0.7327 (m-70) cc_final: 0.6882 (m-70) REVERT: B 899 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.6881 (tmm-80) REVERT: B 902 ILE cc_start: 0.8955 (tt) cc_final: 0.8454 (tp) REVERT: B 903 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7951 (ttm170) REVERT: B 921 LEU cc_start: 0.8747 (tt) cc_final: 0.8365 (mm) REVERT: B 942 MET cc_start: 0.7712 (tpp) cc_final: 0.7497 (tpp) outliers start: 45 outliers final: 19 residues processed: 478 average time/residue: 0.1268 time to fit residues: 81.4450 Evaluate side-chains 477 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 451 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 165 GLN A 458 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN B 225 GLN B 421 ASN B 613 GLN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 860 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.107023 restraints weight = 23868.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110471 restraints weight = 12425.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112729 restraints weight = 7661.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114204 restraints weight = 5325.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115238 restraints weight = 4078.255| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10880 Z= 0.157 Angle : 0.607 10.155 14762 Z= 0.320 Chirality : 0.040 0.176 1782 Planarity : 0.004 0.036 1816 Dihedral : 6.211 57.699 1475 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.69 % Allowed : 20.17 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.23), residues: 1354 helix: 1.44 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.019 0.001 TYR B 594 PHE 0.018 0.001 PHE B 457 TRP 0.029 0.002 TRP A 635 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00308 (10880) covalent geometry : angle 0.60736 (14762) hydrogen bonds : bond 0.04579 ( 905) hydrogen bonds : angle 4.24038 ( 2715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 459 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.7973 (mt) cc_final: 0.7746 (mm) REVERT: A 113 LEU cc_start: 0.8208 (tt) cc_final: 0.7968 (tp) REVERT: A 134 ASP cc_start: 0.7945 (t70) cc_final: 0.7672 (t0) REVERT: A 155 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.5971 (p0) REVERT: A 156 VAL cc_start: 0.8468 (t) cc_final: 0.7965 (m) REVERT: A 158 THR cc_start: 0.8160 (m) cc_final: 0.7244 (p) REVERT: A 161 ARG cc_start: 0.7530 (mmt180) cc_final: 0.7106 (mmt180) REVERT: A 195 PHE cc_start: 0.7922 (t80) cc_final: 0.7665 (t80) REVERT: A 204 ILE cc_start: 0.8685 (mt) cc_final: 0.8360 (tt) REVERT: A 206 SER cc_start: 0.8242 (t) cc_final: 0.7745 (p) REVERT: A 233 GLU cc_start: 0.8053 (tt0) cc_final: 0.7565 (tt0) REVERT: A 238 ASP cc_start: 0.7356 (m-30) cc_final: 0.6823 (m-30) REVERT: A 248 PHE cc_start: 0.8111 (m-80) cc_final: 0.7629 (m-10) REVERT: A 252 VAL cc_start: 0.7312 (t) cc_final: 0.6618 (m) REVERT: A 278 TRP cc_start: 0.8474 (t-100) cc_final: 0.8042 (t-100) REVERT: A 284 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7912 (mmmt) REVERT: A 303 ILE cc_start: 0.8039 (mt) cc_final: 0.7795 (mm) REVERT: A 312 TYR cc_start: 0.8277 (t80) cc_final: 0.7839 (t80) REVERT: A 316 ASP cc_start: 0.7382 (m-30) cc_final: 0.6893 (m-30) REVERT: A 345 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8031 (m) REVERT: A 364 ILE cc_start: 0.8212 (mt) cc_final: 0.7668 (tt) REVERT: A 384 ASP cc_start: 0.7941 (t0) cc_final: 0.7639 (t0) REVERT: A 393 LEU cc_start: 0.8829 (mp) cc_final: 0.8415 (mp) REVERT: A 396 THR cc_start: 0.8304 (m) cc_final: 0.8066 (p) REVERT: A 399 ARG cc_start: 0.7895 (ttt90) cc_final: 0.7514 (tpt170) REVERT: A 401 MET cc_start: 0.7485 (ttm) cc_final: 0.7280 (ttm) REVERT: A 425 MET cc_start: 0.7795 (tpt) cc_final: 0.6818 (tpp) REVERT: A 426 THR cc_start: 0.8376 (t) cc_final: 0.8130 (t) REVERT: A 443 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 449 ASP cc_start: 0.8443 (t0) cc_final: 0.8237 (t0) REVERT: A 466 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7896 (t) REVERT: A 480 ILE cc_start: 0.8327 (mt) cc_final: 0.8045 (mm) REVERT: A 485 ASP cc_start: 0.7999 (t0) cc_final: 0.7591 (t0) REVERT: A 486 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7509 (tp) REVERT: A 494 MET cc_start: 0.7886 (tpp) cc_final: 0.7370 (tpp) REVERT: A 500 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7731 (ttt180) REVERT: A 501 ILE cc_start: 0.8585 (tt) cc_final: 0.8381 (pt) REVERT: A 502 HIS cc_start: 0.7979 (t70) cc_final: 0.7617 (t70) REVERT: A 505 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 506 ASN cc_start: 0.8415 (m-40) cc_final: 0.7882 (m110) REVERT: A 507 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7700 (ptp-110) REVERT: A 511 MET cc_start: 0.8098 (ttm) cc_final: 0.7453 (tmm) REVERT: A 523 TRP cc_start: 0.7821 (m100) cc_final: 0.7491 (m100) REVERT: A 534 ASP cc_start: 0.7692 (t0) cc_final: 0.7433 (t0) REVERT: A 579 MET cc_start: 0.8654 (mmm) cc_final: 0.8078 (tpt) REVERT: A 581 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 586 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7079 (ptm) REVERT: A 587 LEU cc_start: 0.8744 (pp) cc_final: 0.8424 (pp) REVERT: A 590 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8029 (mt-10) REVERT: A 591 LYS cc_start: 0.8647 (pttp) cc_final: 0.8390 (pttp) REVERT: A 600 HIS cc_start: 0.7898 (t70) cc_final: 0.7499 (t70) REVERT: A 610 LEU cc_start: 0.8833 (tt) cc_final: 0.7987 (tp) REVERT: A 613 GLN cc_start: 0.8382 (pp30) cc_final: 0.7715 (pp30) REVERT: A 830 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 832 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 841 LYS cc_start: 0.8616 (mptt) cc_final: 0.7818 (tptt) REVERT: A 844 ILE cc_start: 0.8992 (mm) cc_final: 0.8460 (pt) REVERT: A 848 GLU cc_start: 0.8613 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 875 ARG cc_start: 0.7712 (ttp80) cc_final: 0.7047 (ttp80) REVERT: A 880 LYS cc_start: 0.8798 (pptt) cc_final: 0.8306 (pptt) REVERT: A 888 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 897 LYS cc_start: 0.8635 (pttt) cc_final: 0.8243 (pttt) REVERT: A 899 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7275 (mtt90) REVERT: A 906 LEU cc_start: 0.8453 (mt) cc_final: 0.8081 (mm) REVERT: A 908 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7453 (t-90) REVERT: A 909 SER cc_start: 0.8735 (t) cc_final: 0.8506 (p) REVERT: A 911 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 923 ASP cc_start: 0.5375 (p0) cc_final: 0.5166 (p0) REVERT: A 938 MET cc_start: 0.8299 (tpp) cc_final: 0.8014 (tpp) REVERT: B 90 ILE cc_start: 0.8359 (mt) cc_final: 0.8054 (mm) REVERT: B 92 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8554 (mmm-85) REVERT: B 109 LEU cc_start: 0.7860 (tp) cc_final: 0.7621 (tp) REVERT: B 163 PHE cc_start: 0.8073 (t80) cc_final: 0.7671 (t80) REVERT: B 166 VAL cc_start: 0.8526 (t) cc_final: 0.8231 (p) REVERT: B 186 MET cc_start: 0.7820 (mmm) cc_final: 0.7440 (mmm) REVERT: B 189 PHE cc_start: 0.7672 (m-10) cc_final: 0.7158 (m-10) REVERT: B 191 TYR cc_start: 0.8579 (m-80) cc_final: 0.8104 (m-80) REVERT: B 197 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: B 218 LYS cc_start: 0.8469 (ptmm) cc_final: 0.8141 (ptmm) REVERT: B 237 ASN cc_start: 0.8031 (t0) cc_final: 0.7644 (t0) REVERT: B 242 ILE cc_start: 0.8591 (mt) cc_final: 0.8276 (mm) REVERT: B 248 PHE cc_start: 0.8094 (m-80) cc_final: 0.7487 (m-80) REVERT: B 251 MET cc_start: 0.6516 (tmm) cc_final: 0.6217 (tmm) REVERT: B 263 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 293 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 303 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 321 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6928 (t) REVERT: B 375 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7823 (ptpt) REVERT: B 383 MET cc_start: 0.6817 (tpp) cc_final: 0.5384 (tpp) REVERT: B 387 TYR cc_start: 0.7521 (m-10) cc_final: 0.7258 (m-80) REVERT: B 393 LEU cc_start: 0.8571 (mp) cc_final: 0.8344 (mp) REVERT: B 397 ILE cc_start: 0.8563 (mt) cc_final: 0.7569 (mm) REVERT: B 399 ARG cc_start: 0.8871 (ttm-80) cc_final: 0.8622 (ttt90) REVERT: B 401 MET cc_start: 0.7769 (mtp) cc_final: 0.7215 (mtp) REVERT: B 406 PHE cc_start: 0.8031 (m-80) cc_final: 0.7718 (m-80) REVERT: B 444 ASN cc_start: 0.8022 (t0) cc_final: 0.7772 (t0) REVERT: B 445 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 466 THR cc_start: 0.7801 (p) cc_final: 0.7525 (t) REVERT: B 470 ASN cc_start: 0.7766 (m-40) cc_final: 0.7392 (m110) REVERT: B 477 LEU cc_start: 0.8617 (mp) cc_final: 0.8247 (tp) REVERT: B 480 ILE cc_start: 0.8153 (mt) cc_final: 0.7902 (mt) REVERT: B 481 LEU cc_start: 0.8520 (mt) cc_final: 0.8320 (mm) REVERT: B 490 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8366 (ttmt) REVERT: B 500 ARG cc_start: 0.7836 (tmt-80) cc_final: 0.7418 (ttt-90) REVERT: B 512 LEU cc_start: 0.8821 (mp) cc_final: 0.8474 (mm) REVERT: B 517 PHE cc_start: 0.7005 (m-10) cc_final: 0.6372 (m-10) REVERT: B 586 MET cc_start: 0.7505 (tpt) cc_final: 0.7085 (tpt) REVERT: B 590 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7391 (mt-10) REVERT: B 832 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7307 (tp40) REVERT: B 848 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 877 GLN cc_start: 0.8260 (pp30) cc_final: 0.7706 (pp30) REVERT: B 878 VAL cc_start: 0.8395 (p) cc_final: 0.7829 (p) REVERT: B 880 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7725 (ptpp) REVERT: B 885 LEU cc_start: 0.8328 (tp) cc_final: 0.7956 (tp) REVERT: B 888 GLU cc_start: 0.7502 (pt0) cc_final: 0.7293 (pt0) REVERT: B 889 HIS cc_start: 0.7387 (m-70) cc_final: 0.7130 (m-70) REVERT: B 899 ARG cc_start: 0.7741 (tmm-80) cc_final: 0.6993 (tmm-80) REVERT: B 902 ILE cc_start: 0.8932 (tt) cc_final: 0.8361 (tp) REVERT: B 903 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7976 (ttm170) REVERT: B 911 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 921 LEU cc_start: 0.8763 (tt) cc_final: 0.8417 (mm) REVERT: B 942 MET cc_start: 0.7753 (tpp) cc_final: 0.7505 (tpp) outliers start: 66 outliers final: 32 residues processed: 476 average time/residue: 0.1236 time to fit residues: 79.3196 Evaluate side-chains 492 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 448 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 458 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 421 ASN B 613 GLN B 826 ASN ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107070 restraints weight = 23991.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110519 restraints weight = 12396.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112799 restraints weight = 7604.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114301 restraints weight = 5246.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115289 restraints weight = 3980.606| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.147 Angle : 0.601 8.744 14762 Z= 0.315 Chirality : 0.040 0.271 1782 Planarity : 0.004 0.034 1816 Dihedral : 6.076 56.932 1471 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.34 % Allowed : 21.12 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.23), residues: 1354 helix: 1.65 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 491 TYR 0.016 0.001 TYR B 594 PHE 0.019 0.001 PHE A 457 TRP 0.029 0.001 TRP A 635 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00290 (10880) covalent geometry : angle 0.60072 (14762) hydrogen bonds : bond 0.04532 ( 905) hydrogen bonds : angle 4.17653 ( 2715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 460 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.7999 (mt) cc_final: 0.7792 (mm) REVERT: A 113 LEU cc_start: 0.8209 (tt) cc_final: 0.7971 (tp) REVERT: A 134 ASP cc_start: 0.7950 (t70) cc_final: 0.7693 (t0) REVERT: A 155 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.5832 (p0) REVERT: A 156 VAL cc_start: 0.8475 (t) cc_final: 0.7897 (m) REVERT: A 158 THR cc_start: 0.8163 (m) cc_final: 0.7173 (p) REVERT: A 161 ARG cc_start: 0.7528 (mmt180) cc_final: 0.7139 (mmt180) REVERT: A 204 ILE cc_start: 0.8674 (mt) cc_final: 0.8350 (tt) REVERT: A 206 SER cc_start: 0.8224 (t) cc_final: 0.7726 (p) REVERT: A 233 GLU cc_start: 0.8101 (tt0) cc_final: 0.7550 (tt0) REVERT: A 238 ASP cc_start: 0.7310 (m-30) cc_final: 0.6808 (m-30) REVERT: A 248 PHE cc_start: 0.8115 (m-80) cc_final: 0.7554 (m-10) REVERT: A 252 VAL cc_start: 0.7334 (t) cc_final: 0.6635 (m) REVERT: A 278 TRP cc_start: 0.8457 (t-100) cc_final: 0.8006 (t-100) REVERT: A 285 VAL cc_start: 0.8121 (t) cc_final: 0.7870 (p) REVERT: A 303 ILE cc_start: 0.8051 (mt) cc_final: 0.7781 (mm) REVERT: A 312 TYR cc_start: 0.8282 (t80) cc_final: 0.7795 (t80) REVERT: A 316 ASP cc_start: 0.7325 (m-30) cc_final: 0.6839 (m-30) REVERT: A 364 ILE cc_start: 0.8189 (mt) cc_final: 0.7711 (tt) REVERT: A 384 ASP cc_start: 0.7915 (t0) cc_final: 0.7652 (t0) REVERT: A 393 LEU cc_start: 0.8823 (mp) cc_final: 0.8391 (mp) REVERT: A 396 THR cc_start: 0.8291 (m) cc_final: 0.8042 (p) REVERT: A 399 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7433 (tpt170) REVERT: A 420 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7347 (mtm-85) REVERT: A 425 MET cc_start: 0.7816 (tpt) cc_final: 0.6801 (tpp) REVERT: A 426 THR cc_start: 0.8367 (t) cc_final: 0.8121 (t) REVERT: A 443 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 449 ASP cc_start: 0.8493 (t0) cc_final: 0.8285 (t0) REVERT: A 466 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7910 (t) REVERT: A 475 GLN cc_start: 0.8459 (tp40) cc_final: 0.8166 (mm-40) REVERT: A 480 ILE cc_start: 0.8310 (mt) cc_final: 0.7990 (mm) REVERT: A 485 ASP cc_start: 0.7997 (t0) cc_final: 0.7609 (t0) REVERT: A 486 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7500 (tp) REVERT: A 494 MET cc_start: 0.7893 (tpp) cc_final: 0.7352 (tpp) REVERT: A 500 ARG cc_start: 0.8032 (ttt90) cc_final: 0.7717 (ttt180) REVERT: A 505 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 506 ASN cc_start: 0.8397 (m-40) cc_final: 0.7967 (m110) REVERT: A 507 ARG cc_start: 0.7951 (ptp-110) cc_final: 0.7701 (ptp-110) REVERT: A 511 MET cc_start: 0.8075 (ttm) cc_final: 0.7479 (tmm) REVERT: A 523 TRP cc_start: 0.7800 (m100) cc_final: 0.7525 (m100) REVERT: A 578 MET cc_start: 0.8121 (ppp) cc_final: 0.7915 (ppp) REVERT: A 579 MET cc_start: 0.8657 (mmm) cc_final: 0.8157 (tpt) REVERT: A 581 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 586 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7098 (ptm) REVERT: A 587 LEU cc_start: 0.8746 (pp) cc_final: 0.8119 (pp) REVERT: A 590 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 591 LYS cc_start: 0.8633 (pttp) cc_final: 0.8255 (pttp) REVERT: A 600 HIS cc_start: 0.7808 (t70) cc_final: 0.7435 (t70) REVERT: A 610 LEU cc_start: 0.8820 (tt) cc_final: 0.7982 (tp) REVERT: A 613 GLN cc_start: 0.8360 (pp30) cc_final: 0.7669 (pp30) REVERT: A 830 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7767 (t0) REVERT: A 832 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 841 LYS cc_start: 0.8644 (mptt) cc_final: 0.8151 (tptt) REVERT: A 848 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 857 MET cc_start: 0.7751 (ppp) cc_final: 0.7181 (ppp) REVERT: A 875 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7021 (ttp80) REVERT: A 880 LYS cc_start: 0.8815 (pptt) cc_final: 0.8328 (pptt) REVERT: A 887 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7251 (mtm110) REVERT: A 888 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 897 LYS cc_start: 0.8567 (pttt) cc_final: 0.8152 (pttt) REVERT: A 899 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7332 (mtt90) REVERT: A 906 LEU cc_start: 0.8448 (mt) cc_final: 0.8039 (mm) REVERT: A 908 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7429 (t-90) REVERT: A 909 SER cc_start: 0.8723 (t) cc_final: 0.8491 (p) REVERT: A 911 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 923 ASP cc_start: 0.5334 (p0) cc_final: 0.5108 (p0) REVERT: A 925 MET cc_start: 0.8448 (pmm) cc_final: 0.8227 (ppp) REVERT: A 938 MET cc_start: 0.8341 (tpp) cc_final: 0.8017 (tpp) REVERT: B 90 ILE cc_start: 0.8353 (mt) cc_final: 0.8038 (mm) REVERT: B 92 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8575 (mmm-85) REVERT: B 163 PHE cc_start: 0.8110 (t80) cc_final: 0.7697 (t80) REVERT: B 166 VAL cc_start: 0.8616 (t) cc_final: 0.8279 (p) REVERT: B 186 MET cc_start: 0.7804 (mmm) cc_final: 0.7436 (mmm) REVERT: B 189 PHE cc_start: 0.7629 (m-10) cc_final: 0.7126 (m-10) REVERT: B 191 TYR cc_start: 0.8566 (m-80) cc_final: 0.8175 (m-80) REVERT: B 199 MET cc_start: 0.7538 (tpp) cc_final: 0.6903 (tpp) REVERT: B 218 LYS cc_start: 0.8444 (ptmm) cc_final: 0.8130 (ptmm) REVERT: B 237 ASN cc_start: 0.8021 (t0) cc_final: 0.7641 (t0) REVERT: B 242 ILE cc_start: 0.8603 (mt) cc_final: 0.8294 (mm) REVERT: B 248 PHE cc_start: 0.8085 (m-80) cc_final: 0.7524 (m-80) REVERT: B 251 MET cc_start: 0.6344 (tmm) cc_final: 0.6099 (tmm) REVERT: B 263 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 293 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8298 (tt) REVERT: B 303 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8129 (mt) REVERT: B 321 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.6959 (t) REVERT: B 375 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7815 (ptpt) REVERT: B 383 MET cc_start: 0.6732 (tpp) cc_final: 0.5247 (tpp) REVERT: B 387 TYR cc_start: 0.7517 (m-10) cc_final: 0.7265 (m-80) REVERT: B 393 LEU cc_start: 0.8564 (mp) cc_final: 0.8338 (mp) REVERT: B 397 ILE cc_start: 0.8581 (mt) cc_final: 0.7563 (mm) REVERT: B 399 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8630 (ttt90) REVERT: B 401 MET cc_start: 0.7813 (mtp) cc_final: 0.7227 (mtp) REVERT: B 406 PHE cc_start: 0.8025 (m-80) cc_final: 0.7734 (m-80) REVERT: B 444 ASN cc_start: 0.8008 (t0) cc_final: 0.7778 (t0) REVERT: B 445 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8113 (tp) REVERT: B 466 THR cc_start: 0.7809 (p) cc_final: 0.7499 (t) REVERT: B 470 ASN cc_start: 0.7764 (m-40) cc_final: 0.7447 (m110) REVERT: B 477 LEU cc_start: 0.8611 (mp) cc_final: 0.8256 (tp) REVERT: B 480 ILE cc_start: 0.8156 (mt) cc_final: 0.7915 (mt) REVERT: B 490 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8365 (ttmt) REVERT: B 491 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8132 (ttp-110) REVERT: B 500 ARG cc_start: 0.7849 (tmt-80) cc_final: 0.7421 (ttt-90) REVERT: B 517 PHE cc_start: 0.7113 (m-10) cc_final: 0.6582 (m-10) REVERT: B 579 MET cc_start: 0.7401 (mmm) cc_final: 0.6926 (mmm) REVERT: B 580 GLU cc_start: 0.7765 (tp30) cc_final: 0.6821 (tp30) REVERT: B 583 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6811 (ttp-110) REVERT: B 586 MET cc_start: 0.7465 (tpt) cc_final: 0.7058 (tpt) REVERT: B 590 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7412 (mt-10) REVERT: B 832 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7112 (tp40) REVERT: B 848 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 877 GLN cc_start: 0.8245 (pp30) cc_final: 0.7702 (pp30) REVERT: B 880 LYS cc_start: 0.8245 (ptpp) cc_final: 0.7727 (ptpp) REVERT: B 885 LEU cc_start: 0.8292 (tp) cc_final: 0.7923 (tp) REVERT: B 889 HIS cc_start: 0.7388 (m-70) cc_final: 0.7122 (m-70) REVERT: B 899 ARG cc_start: 0.7745 (tmm-80) cc_final: 0.7010 (tmm-80) REVERT: B 902 ILE cc_start: 0.8917 (tt) cc_final: 0.8272 (tp) REVERT: B 903 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7998 (ttm170) REVERT: B 906 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8455 (mm) REVERT: B 911 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 921 LEU cc_start: 0.8742 (tt) cc_final: 0.8411 (mm) REVERT: B 942 MET cc_start: 0.7746 (tpp) cc_final: 0.7503 (tpp) outliers start: 62 outliers final: 34 residues processed: 478 average time/residue: 0.1209 time to fit residues: 78.0152 Evaluate side-chains 501 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 454 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.0040 chunk 40 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.125714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107683 restraints weight = 23676.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111053 restraints weight = 12252.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113319 restraints weight = 7589.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114774 restraints weight = 5237.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115834 restraints weight = 3990.870| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10880 Z= 0.135 Angle : 0.615 12.141 14762 Z= 0.317 Chirality : 0.040 0.223 1782 Planarity : 0.004 0.040 1816 Dihedral : 6.051 59.947 1471 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.86 % Allowed : 23.45 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.23), residues: 1354 helix: 1.76 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 491 TYR 0.020 0.001 TYR B 837 PHE 0.021 0.001 PHE B 294 TRP 0.030 0.002 TRP A 635 HIS 0.002 0.000 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00269 (10880) covalent geometry : angle 0.61483 (14762) hydrogen bonds : bond 0.04455 ( 905) hydrogen bonds : angle 4.12638 ( 2715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 463 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8195 (tt) cc_final: 0.7955 (tp) REVERT: A 134 ASP cc_start: 0.7993 (t70) cc_final: 0.7710 (t0) REVERT: A 154 MET cc_start: 0.7244 (mmm) cc_final: 0.6699 (tpp) REVERT: A 155 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.5706 (p0) REVERT: A 156 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.7759 (m) REVERT: A 158 THR cc_start: 0.8092 (m) cc_final: 0.7133 (p) REVERT: A 161 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7196 (mmt180) REVERT: A 204 ILE cc_start: 0.8663 (mt) cc_final: 0.8327 (tt) REVERT: A 206 SER cc_start: 0.8209 (t) cc_final: 0.7486 (p) REVERT: A 231 GLU cc_start: 0.7797 (tt0) cc_final: 0.6785 (tt0) REVERT: A 233 GLU cc_start: 0.8035 (tt0) cc_final: 0.7467 (tt0) REVERT: A 237 ASN cc_start: 0.8180 (t0) cc_final: 0.7637 (t0) REVERT: A 238 ASP cc_start: 0.7208 (m-30) cc_final: 0.6746 (m-30) REVERT: A 248 PHE cc_start: 0.8116 (m-80) cc_final: 0.7533 (m-10) REVERT: A 252 VAL cc_start: 0.7307 (t) cc_final: 0.6607 (m) REVERT: A 278 TRP cc_start: 0.8431 (t-100) cc_final: 0.7982 (t-100) REVERT: A 285 VAL cc_start: 0.8097 (t) cc_final: 0.7852 (p) REVERT: A 303 ILE cc_start: 0.8058 (mt) cc_final: 0.7817 (mm) REVERT: A 312 TYR cc_start: 0.8281 (t80) cc_final: 0.7746 (t80) REVERT: A 316 ASP cc_start: 0.7335 (m-30) cc_final: 0.6826 (m-30) REVERT: A 345 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8048 (m) REVERT: A 364 ILE cc_start: 0.8168 (mt) cc_final: 0.7713 (tt) REVERT: A 384 ASP cc_start: 0.7937 (t0) cc_final: 0.7636 (t0) REVERT: A 393 LEU cc_start: 0.8803 (mp) cc_final: 0.8366 (mp) REVERT: A 396 THR cc_start: 0.8262 (m) cc_final: 0.8012 (p) REVERT: A 399 ARG cc_start: 0.7795 (ttt90) cc_final: 0.7413 (tpt170) REVERT: A 425 MET cc_start: 0.7818 (tpt) cc_final: 0.6742 (tpp) REVERT: A 426 THR cc_start: 0.8373 (t) cc_final: 0.8120 (t) REVERT: A 443 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 444 ASN cc_start: 0.8280 (t0) cc_final: 0.8001 (t0) REVERT: A 466 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 475 GLN cc_start: 0.8476 (tp40) cc_final: 0.8160 (mm-40) REVERT: A 485 ASP cc_start: 0.7931 (t0) cc_final: 0.7646 (t0) REVERT: A 486 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 494 MET cc_start: 0.7861 (tpp) cc_final: 0.7243 (tpp) REVERT: A 500 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7742 (ttt180) REVERT: A 501 ILE cc_start: 0.8596 (tt) cc_final: 0.8384 (pt) REVERT: A 502 HIS cc_start: 0.7993 (t70) cc_final: 0.7443 (t70) REVERT: A 505 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 506 ASN cc_start: 0.8393 (m-40) cc_final: 0.7760 (m-40) REVERT: A 507 ARG cc_start: 0.7993 (ptp-110) cc_final: 0.7695 (ptp-110) REVERT: A 523 TRP cc_start: 0.7766 (m100) cc_final: 0.7489 (m100) REVERT: A 579 MET cc_start: 0.8639 (mmm) cc_final: 0.8076 (tpt) REVERT: A 581 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 585 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.7951 (tmm-80) REVERT: A 586 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7078 (ptm) REVERT: A 587 LEU cc_start: 0.8721 (pp) cc_final: 0.8074 (pp) REVERT: A 590 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 591 LYS cc_start: 0.8622 (pttp) cc_final: 0.8242 (pttp) REVERT: A 600 HIS cc_start: 0.7752 (t70) cc_final: 0.7389 (t70) REVERT: A 610 LEU cc_start: 0.8836 (tt) cc_final: 0.8012 (tp) REVERT: A 613 GLN cc_start: 0.8345 (pp30) cc_final: 0.7632 (pp30) REVERT: A 832 GLN cc_start: 0.7399 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 841 LYS cc_start: 0.8628 (mptt) cc_final: 0.8159 (tptt) REVERT: A 848 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 857 MET cc_start: 0.7756 (ppp) cc_final: 0.7191 (ppp) REVERT: A 875 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7008 (ttp80) REVERT: A 897 LYS cc_start: 0.8617 (pttt) cc_final: 0.8225 (pttt) REVERT: A 899 ARG cc_start: 0.7711 (mtt90) cc_final: 0.7250 (mtt90) REVERT: A 906 LEU cc_start: 0.8427 (mt) cc_final: 0.8069 (mm) REVERT: A 908 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7431 (t-90) REVERT: A 909 SER cc_start: 0.8742 (t) cc_final: 0.8501 (p) REVERT: A 911 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 914 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7333 (m170) REVERT: A 923 ASP cc_start: 0.5322 (p0) cc_final: 0.5024 (p0) REVERT: A 925 MET cc_start: 0.8400 (pmm) cc_final: 0.8144 (pmm) REVERT: A 926 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 938 MET cc_start: 0.8345 (tpp) cc_final: 0.8002 (tpp) REVERT: B 163 PHE cc_start: 0.8085 (t80) cc_final: 0.7691 (t80) REVERT: B 166 VAL cc_start: 0.8608 (t) cc_final: 0.8265 (p) REVERT: B 189 PHE cc_start: 0.7632 (m-10) cc_final: 0.7196 (m-10) REVERT: B 191 TYR cc_start: 0.8522 (m-80) cc_final: 0.8251 (m-80) REVERT: B 197 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: B 199 MET cc_start: 0.7500 (tpp) cc_final: 0.6867 (tpp) REVERT: B 218 LYS cc_start: 0.8450 (ptmm) cc_final: 0.8121 (ptmm) REVERT: B 233 GLU cc_start: 0.7951 (tt0) cc_final: 0.7466 (tt0) REVERT: B 237 ASN cc_start: 0.8017 (t0) cc_final: 0.7634 (t0) REVERT: B 242 ILE cc_start: 0.8619 (mt) cc_final: 0.8308 (mm) REVERT: B 248 PHE cc_start: 0.8080 (m-80) cc_final: 0.7649 (m-80) REVERT: B 251 MET cc_start: 0.6443 (tmm) cc_final: 0.6230 (tmm) REVERT: B 263 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7362 (tm-30) REVERT: B 293 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 321 VAL cc_start: 0.7260 (OUTLIER) cc_final: 0.6972 (t) REVERT: B 375 LYS cc_start: 0.8204 (ptpt) cc_final: 0.7870 (ptpt) REVERT: B 377 LEU cc_start: 0.7613 (tp) cc_final: 0.7132 (tp) REVERT: B 383 MET cc_start: 0.6630 (tpp) cc_final: 0.5134 (tpp) REVERT: B 387 TYR cc_start: 0.7485 (m-10) cc_final: 0.7261 (m-80) REVERT: B 393 LEU cc_start: 0.8554 (mp) cc_final: 0.8332 (mp) REVERT: B 397 ILE cc_start: 0.8577 (mt) cc_final: 0.7535 (mm) REVERT: B 401 MET cc_start: 0.7757 (mtp) cc_final: 0.7195 (mtp) REVERT: B 406 PHE cc_start: 0.8022 (m-80) cc_final: 0.7744 (m-80) REVERT: B 413 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.3981 (mp) REVERT: B 425 MET cc_start: 0.7998 (mtt) cc_final: 0.7638 (mtp) REVERT: B 444 ASN cc_start: 0.8027 (t0) cc_final: 0.7811 (t0) REVERT: B 445 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8162 (tp) REVERT: B 466 THR cc_start: 0.7795 (p) cc_final: 0.7488 (t) REVERT: B 470 ASN cc_start: 0.7771 (m-40) cc_final: 0.7453 (m110) REVERT: B 477 LEU cc_start: 0.8615 (mp) cc_final: 0.8257 (tp) REVERT: B 480 ILE cc_start: 0.8150 (mt) cc_final: 0.7890 (mt) REVERT: B 490 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8407 (ttmt) REVERT: B 491 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8134 (ttp-110) REVERT: B 500 ARG cc_start: 0.7810 (tmt-80) cc_final: 0.7403 (ttt-90) REVERT: B 506 ASN cc_start: 0.8332 (m-40) cc_final: 0.8102 (m110) REVERT: B 512 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8453 (mm) REVERT: B 517 PHE cc_start: 0.7065 (m-10) cc_final: 0.6556 (m-10) REVERT: B 583 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6908 (ttp-110) REVERT: B 586 MET cc_start: 0.7370 (tpt) cc_final: 0.7072 (tpt) REVERT: B 590 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7057 (mt-10) REVERT: B 594 TYR cc_start: 0.7832 (m-80) cc_final: 0.7524 (m-80) REVERT: B 832 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7165 (tp40) REVERT: B 848 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 877 GLN cc_start: 0.8244 (pp30) cc_final: 0.7237 (pp30) REVERT: B 880 LYS cc_start: 0.8264 (ptpp) cc_final: 0.7753 (ptpp) REVERT: B 881 GLU cc_start: 0.7902 (pt0) cc_final: 0.7435 (pt0) REVERT: B 885 LEU cc_start: 0.8241 (tp) cc_final: 0.8023 (tp) REVERT: B 889 HIS cc_start: 0.7466 (m-70) cc_final: 0.7148 (m-70) REVERT: B 899 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7083 (tmm-80) REVERT: B 902 ILE cc_start: 0.8883 (tt) cc_final: 0.8202 (tp) REVERT: B 903 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8066 (ttm170) REVERT: B 904 THR cc_start: 0.8181 (m) cc_final: 0.7948 (p) REVERT: B 906 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8454 (mm) REVERT: B 911 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 921 LEU cc_start: 0.8719 (tt) cc_final: 0.8396 (mm) REVERT: B 942 MET cc_start: 0.7719 (tpp) cc_final: 0.7482 (tpp) outliers start: 68 outliers final: 39 residues processed: 482 average time/residue: 0.1236 time to fit residues: 80.6437 Evaluate side-chains 512 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 457 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 67 optimal weight: 0.0870 chunk 2 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108005 restraints weight = 23737.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111474 restraints weight = 12295.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113721 restraints weight = 7520.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115110 restraints weight = 5167.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116176 restraints weight = 3944.438| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.143 Angle : 0.639 12.329 14762 Z= 0.327 Chirality : 0.040 0.204 1782 Planarity : 0.004 0.042 1816 Dihedral : 5.937 56.198 1471 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.52 % Allowed : 23.79 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.23), residues: 1354 helix: 1.80 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.87 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 399 TYR 0.023 0.001 TYR B 837 PHE 0.021 0.001 PHE A 457 TRP 0.032 0.002 TRP A 643 HIS 0.001 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00283 (10880) covalent geometry : angle 0.63927 (14762) hydrogen bonds : bond 0.04476 ( 905) hydrogen bonds : angle 4.12428 ( 2715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 461 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8479 (p) cc_final: 0.8243 (p) REVERT: A 113 LEU cc_start: 0.8188 (tt) cc_final: 0.7952 (tp) REVERT: A 134 ASP cc_start: 0.8030 (t70) cc_final: 0.7762 (t0) REVERT: A 154 MET cc_start: 0.7097 (mmm) cc_final: 0.6692 (mmm) REVERT: A 155 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.5649 (p0) REVERT: A 156 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7941 (m) REVERT: A 158 THR cc_start: 0.8116 (m) cc_final: 0.7228 (p) REVERT: A 161 ARG cc_start: 0.7541 (mmt180) cc_final: 0.7089 (mmt-90) REVERT: A 199 MET cc_start: 0.7643 (tpt) cc_final: 0.7431 (tpp) REVERT: A 204 ILE cc_start: 0.8655 (mt) cc_final: 0.8319 (tt) REVERT: A 206 SER cc_start: 0.8218 (t) cc_final: 0.7505 (p) REVERT: A 231 GLU cc_start: 0.7792 (tt0) cc_final: 0.6996 (tt0) REVERT: A 233 GLU cc_start: 0.8030 (tt0) cc_final: 0.7439 (tt0) REVERT: A 237 ASN cc_start: 0.8160 (t0) cc_final: 0.7585 (t0) REVERT: A 238 ASP cc_start: 0.7212 (m-30) cc_final: 0.6775 (m-30) REVERT: A 248 PHE cc_start: 0.8115 (m-80) cc_final: 0.7542 (m-10) REVERT: A 252 VAL cc_start: 0.7295 (t) cc_final: 0.6612 (m) REVERT: A 278 TRP cc_start: 0.8445 (t-100) cc_final: 0.7973 (t-100) REVERT: A 303 ILE cc_start: 0.8063 (mt) cc_final: 0.7784 (mm) REVERT: A 312 TYR cc_start: 0.8283 (t80) cc_final: 0.7684 (t80) REVERT: A 316 ASP cc_start: 0.7334 (m-30) cc_final: 0.6752 (m-30) REVERT: A 345 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (m) REVERT: A 364 ILE cc_start: 0.8147 (mt) cc_final: 0.7687 (tt) REVERT: A 384 ASP cc_start: 0.7925 (t0) cc_final: 0.7629 (t0) REVERT: A 393 LEU cc_start: 0.8798 (mp) cc_final: 0.8364 (mp) REVERT: A 396 THR cc_start: 0.8237 (m) cc_final: 0.7979 (p) REVERT: A 399 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7454 (tpt170) REVERT: A 420 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7295 (mtm-85) REVERT: A 425 MET cc_start: 0.7814 (tpt) cc_final: 0.6687 (tpp) REVERT: A 426 THR cc_start: 0.8394 (t) cc_final: 0.8148 (t) REVERT: A 443 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 444 ASN cc_start: 0.8291 (t0) cc_final: 0.7995 (t0) REVERT: A 449 ASP cc_start: 0.8303 (t0) cc_final: 0.8034 (t0) REVERT: A 466 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 475 GLN cc_start: 0.8465 (tp40) cc_final: 0.8170 (mm-40) REVERT: A 485 ASP cc_start: 0.7934 (t0) cc_final: 0.7641 (t0) REVERT: A 486 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 494 MET cc_start: 0.7841 (tpp) cc_final: 0.7208 (tpp) REVERT: A 500 ARG cc_start: 0.8059 (ttt90) cc_final: 0.7763 (ttt180) REVERT: A 501 ILE cc_start: 0.8605 (tt) cc_final: 0.8399 (pt) REVERT: A 502 HIS cc_start: 0.7982 (t70) cc_final: 0.7440 (t70) REVERT: A 505 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 506 ASN cc_start: 0.8414 (m-40) cc_final: 0.7789 (m-40) REVERT: A 507 ARG cc_start: 0.8029 (ptp-110) cc_final: 0.7776 (ptp-110) REVERT: A 579 MET cc_start: 0.8673 (mmm) cc_final: 0.8150 (tpt) REVERT: A 581 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 586 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7106 (ptm) REVERT: A 587 LEU cc_start: 0.8730 (pp) cc_final: 0.8434 (pp) REVERT: A 590 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 591 LYS cc_start: 0.8624 (pttp) cc_final: 0.8389 (pttp) REVERT: A 600 HIS cc_start: 0.7747 (t70) cc_final: 0.7393 (t70) REVERT: A 610 LEU cc_start: 0.8843 (tt) cc_final: 0.8028 (tp) REVERT: A 613 GLN cc_start: 0.8354 (pp30) cc_final: 0.7876 (pp30) REVERT: A 647 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8437 (mtmm) REVERT: A 832 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7236 (tm-30) REVERT: A 841 LYS cc_start: 0.8642 (mptt) cc_final: 0.8229 (tptt) REVERT: A 848 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 857 MET cc_start: 0.7748 (ppp) cc_final: 0.7445 (ppp) REVERT: A 875 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7036 (ttp80) REVERT: A 897 LYS cc_start: 0.8592 (pttt) cc_final: 0.8235 (pttt) REVERT: A 899 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7250 (mtt90) REVERT: A 906 LEU cc_start: 0.8408 (mt) cc_final: 0.8021 (mm) REVERT: A 908 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7485 (t-90) REVERT: A 909 SER cc_start: 0.8749 (t) cc_final: 0.8516 (p) REVERT: A 911 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6952 (mt-10) REVERT: A 914 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7378 (m170) REVERT: A 923 ASP cc_start: 0.5447 (p0) cc_final: 0.5162 (p0) REVERT: A 926 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7746 (mm-30) REVERT: A 938 MET cc_start: 0.8346 (tpp) cc_final: 0.7988 (tpp) REVERT: B 154 MET cc_start: 0.6851 (ttm) cc_final: 0.6645 (mtp) REVERT: B 163 PHE cc_start: 0.8103 (t80) cc_final: 0.7657 (t80) REVERT: B 166 VAL cc_start: 0.8596 (t) cc_final: 0.8272 (p) REVERT: B 189 PHE cc_start: 0.7653 (m-10) cc_final: 0.7212 (m-10) REVERT: B 191 TYR cc_start: 0.8578 (m-80) cc_final: 0.8374 (m-80) REVERT: B 197 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: B 199 MET cc_start: 0.7516 (tpp) cc_final: 0.7084 (tpp) REVERT: B 218 LYS cc_start: 0.8461 (ptmm) cc_final: 0.8121 (ptmm) REVERT: B 237 ASN cc_start: 0.7998 (t0) cc_final: 0.7607 (t0) REVERT: B 242 ILE cc_start: 0.8612 (mt) cc_final: 0.8311 (mm) REVERT: B 248 PHE cc_start: 0.8111 (m-80) cc_final: 0.7678 (m-80) REVERT: B 251 MET cc_start: 0.6474 (tmm) cc_final: 0.6237 (tmm) REVERT: B 263 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 321 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.6999 (t) REVERT: B 337 GLU cc_start: 0.7330 (tp30) cc_final: 0.6893 (mp0) REVERT: B 375 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7835 (ptpt) REVERT: B 377 LEU cc_start: 0.7643 (tp) cc_final: 0.7152 (tp) REVERT: B 383 MET cc_start: 0.6638 (tpp) cc_final: 0.6162 (tpp) REVERT: B 393 LEU cc_start: 0.8565 (mp) cc_final: 0.8332 (mp) REVERT: B 397 ILE cc_start: 0.8534 (mt) cc_final: 0.8298 (mm) REVERT: B 406 PHE cc_start: 0.8068 (m-80) cc_final: 0.7798 (m-80) REVERT: B 413 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.4205 (mp) REVERT: B 425 MET cc_start: 0.8001 (mtt) cc_final: 0.7727 (mtp) REVERT: B 444 ASN cc_start: 0.8014 (t0) cc_final: 0.7798 (t0) REVERT: B 445 LEU cc_start: 0.8433 (tp) cc_final: 0.8183 (tp) REVERT: B 466 THR cc_start: 0.7798 (p) cc_final: 0.7485 (t) REVERT: B 470 ASN cc_start: 0.7783 (m-40) cc_final: 0.7462 (m110) REVERT: B 477 LEU cc_start: 0.8613 (mp) cc_final: 0.8259 (tp) REVERT: B 480 ILE cc_start: 0.8087 (mt) cc_final: 0.7839 (mt) REVERT: B 490 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8407 (ttmt) REVERT: B 491 ARG cc_start: 0.8431 (ttp-110) cc_final: 0.8123 (ttp-110) REVERT: B 500 ARG cc_start: 0.7781 (tmt-80) cc_final: 0.7375 (ttt-90) REVERT: B 506 ASN cc_start: 0.8368 (m-40) cc_final: 0.8161 (m110) REVERT: B 512 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8550 (mp) REVERT: B 517 PHE cc_start: 0.7042 (m-10) cc_final: 0.6614 (m-10) REVERT: B 578 MET cc_start: 0.7254 (ppp) cc_final: 0.7027 (ppp) REVERT: B 579 MET cc_start: 0.7779 (mmm) cc_final: 0.7483 (mmm) REVERT: B 583 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6991 (ttp-110) REVERT: B 586 MET cc_start: 0.7389 (tpt) cc_final: 0.7111 (tpt) REVERT: B 590 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7065 (mt-10) REVERT: B 594 TYR cc_start: 0.7862 (m-10) cc_final: 0.7540 (m-80) REVERT: B 646 ARG cc_start: 0.8363 (ptp-170) cc_final: 0.7903 (ptp-170) REVERT: B 832 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7220 (tp40) REVERT: B 833 LEU cc_start: 0.8676 (tt) cc_final: 0.8337 (pp) REVERT: B 848 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 877 GLN cc_start: 0.8203 (pp30) cc_final: 0.7190 (pp30) REVERT: B 880 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7761 (ptpp) REVERT: B 881 GLU cc_start: 0.7872 (pt0) cc_final: 0.7422 (pt0) REVERT: B 889 HIS cc_start: 0.7510 (m-70) cc_final: 0.7184 (m-70) REVERT: B 899 ARG cc_start: 0.7777 (tmm-80) cc_final: 0.7105 (tmm-80) REVERT: B 902 ILE cc_start: 0.8858 (tt) cc_final: 0.8132 (tp) REVERT: B 903 ARG cc_start: 0.8343 (ttm170) cc_final: 0.8090 (ttm170) REVERT: B 904 THR cc_start: 0.8193 (m) cc_final: 0.7961 (p) REVERT: B 906 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 911 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7773 (mt-10) REVERT: B 921 LEU cc_start: 0.8709 (tt) cc_final: 0.8395 (mm) REVERT: B 942 MET cc_start: 0.7729 (tpp) cc_final: 0.7482 (tpp) outliers start: 64 outliers final: 39 residues processed: 479 average time/residue: 0.1226 time to fit residues: 79.2258 Evaluate side-chains 513 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 459 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 421 ASN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 165 GLN B 421 ASN B 613 GLN ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.125170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107412 restraints weight = 23826.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110895 restraints weight = 12215.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113160 restraints weight = 7415.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114658 restraints weight = 5077.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115640 restraints weight = 3822.079| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.147 Angle : 0.656 13.126 14762 Z= 0.333 Chirality : 0.041 0.208 1782 Planarity : 0.004 0.042 1816 Dihedral : 5.739 55.149 1469 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.52 % Allowed : 25.60 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.23), residues: 1354 helix: 1.84 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.92 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 399 TYR 0.025 0.001 TYR B 837 PHE 0.025 0.001 PHE B 457 TRP 0.035 0.002 TRP A 643 HIS 0.002 0.000 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00291 (10880) covalent geometry : angle 0.65624 (14762) hydrogen bonds : bond 0.04494 ( 905) hydrogen bonds : angle 4.13422 ( 2715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 460 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8471 (p) cc_final: 0.8233 (p) REVERT: A 113 LEU cc_start: 0.8195 (tt) cc_final: 0.7956 (tp) REVERT: A 134 ASP cc_start: 0.8045 (t70) cc_final: 0.7748 (t0) REVERT: A 154 MET cc_start: 0.7096 (mmm) cc_final: 0.6646 (mmm) REVERT: A 155 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6298 (p0) REVERT: A 156 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 161 ARG cc_start: 0.7569 (mmt180) cc_final: 0.7069 (mmt-90) REVERT: A 199 MET cc_start: 0.7652 (tpt) cc_final: 0.7438 (tpp) REVERT: A 204 ILE cc_start: 0.8658 (mt) cc_final: 0.8314 (tt) REVERT: A 206 SER cc_start: 0.8239 (t) cc_final: 0.7497 (p) REVERT: A 231 GLU cc_start: 0.7762 (tt0) cc_final: 0.6808 (tt0) REVERT: A 233 GLU cc_start: 0.7992 (tt0) cc_final: 0.7413 (tt0) REVERT: A 237 ASN cc_start: 0.8132 (t0) cc_final: 0.7552 (t0) REVERT: A 238 ASP cc_start: 0.7175 (m-30) cc_final: 0.6752 (m-30) REVERT: A 248 PHE cc_start: 0.8118 (m-80) cc_final: 0.7533 (m-10) REVERT: A 252 VAL cc_start: 0.7268 (t) cc_final: 0.6603 (m) REVERT: A 278 TRP cc_start: 0.8441 (t-100) cc_final: 0.7949 (t-100) REVERT: A 285 VAL cc_start: 0.8125 (t) cc_final: 0.7881 (p) REVERT: A 303 ILE cc_start: 0.7995 (mt) cc_final: 0.7649 (mt) REVERT: A 312 TYR cc_start: 0.8273 (t80) cc_final: 0.7665 (t80) REVERT: A 316 ASP cc_start: 0.7346 (m-30) cc_final: 0.6718 (m-30) REVERT: A 345 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8042 (m) REVERT: A 364 ILE cc_start: 0.8125 (mt) cc_final: 0.7689 (tt) REVERT: A 384 ASP cc_start: 0.7933 (t0) cc_final: 0.7640 (t0) REVERT: A 393 LEU cc_start: 0.8798 (mp) cc_final: 0.8355 (mp) REVERT: A 396 THR cc_start: 0.8236 (m) cc_final: 0.7978 (p) REVERT: A 399 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7468 (tpt170) REVERT: A 420 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7428 (mtm-85) REVERT: A 425 MET cc_start: 0.7812 (tpt) cc_final: 0.6649 (tpp) REVERT: A 426 THR cc_start: 0.8381 (t) cc_final: 0.8132 (t) REVERT: A 443 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 444 ASN cc_start: 0.8292 (t0) cc_final: 0.7993 (t0) REVERT: A 449 ASP cc_start: 0.8259 (t0) cc_final: 0.7992 (t0) REVERT: A 466 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7960 (t) REVERT: A 475 GLN cc_start: 0.8481 (tp40) cc_final: 0.8199 (mm-40) REVERT: A 485 ASP cc_start: 0.7932 (t0) cc_final: 0.7627 (t0) REVERT: A 486 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7581 (mp) REVERT: A 494 MET cc_start: 0.7842 (tpp) cc_final: 0.7191 (tpp) REVERT: A 500 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7809 (ttt180) REVERT: A 501 ILE cc_start: 0.8617 (tt) cc_final: 0.8404 (pt) REVERT: A 505 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 506 ASN cc_start: 0.8437 (m-40) cc_final: 0.8008 (m-40) REVERT: A 507 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7757 (ptp-110) REVERT: A 511 MET cc_start: 0.7820 (tmm) cc_final: 0.7613 (tmm) REVERT: A 517 PHE cc_start: 0.8117 (m-10) cc_final: 0.7861 (m-80) REVERT: A 536 TYR cc_start: 0.7715 (m-10) cc_final: 0.7286 (m-10) REVERT: A 579 MET cc_start: 0.8668 (mmm) cc_final: 0.8146 (tpt) REVERT: A 581 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 586 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7226 (ptm) REVERT: A 587 LEU cc_start: 0.8727 (pp) cc_final: 0.8112 (pp) REVERT: A 590 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 591 LYS cc_start: 0.8616 (pttp) cc_final: 0.8287 (pttp) REVERT: A 600 HIS cc_start: 0.7793 (t70) cc_final: 0.7427 (t70) REVERT: A 610 LEU cc_start: 0.8842 (tt) cc_final: 0.8045 (tp) REVERT: A 613 GLN cc_start: 0.8416 (pp30) cc_final: 0.7828 (pp30) REVERT: A 832 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 841 LYS cc_start: 0.8682 (mptt) cc_final: 0.8257 (tptt) REVERT: A 844 ILE cc_start: 0.9012 (mm) cc_final: 0.8483 (mm) REVERT: A 848 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 875 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 897 LYS cc_start: 0.8597 (pttt) cc_final: 0.8286 (pttt) REVERT: A 899 ARG cc_start: 0.7730 (mtt90) cc_final: 0.7273 (mtt90) REVERT: A 906 LEU cc_start: 0.8403 (mt) cc_final: 0.8013 (mm) REVERT: A 908 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7511 (t-90) REVERT: A 909 SER cc_start: 0.8753 (t) cc_final: 0.8542 (p) REVERT: A 911 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 914 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7364 (m170) REVERT: A 923 ASP cc_start: 0.5398 (p0) cc_final: 0.5016 (p0) REVERT: A 926 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 938 MET cc_start: 0.8355 (tpp) cc_final: 0.7989 (tpp) REVERT: B 78 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7875 (mt) REVERT: B 163 PHE cc_start: 0.8106 (t80) cc_final: 0.7643 (t80) REVERT: B 166 VAL cc_start: 0.8592 (t) cc_final: 0.8259 (p) REVERT: B 189 PHE cc_start: 0.7628 (m-10) cc_final: 0.7219 (m-10) REVERT: B 197 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: B 199 MET cc_start: 0.7512 (tpp) cc_final: 0.7084 (tpp) REVERT: B 218 LYS cc_start: 0.8476 (ptmm) cc_final: 0.8118 (ptmm) REVERT: B 233 GLU cc_start: 0.7800 (tt0) cc_final: 0.7424 (tm-30) REVERT: B 237 ASN cc_start: 0.8007 (t0) cc_final: 0.7768 (t0) REVERT: B 242 ILE cc_start: 0.8599 (mt) cc_final: 0.8306 (mm) REVERT: B 248 PHE cc_start: 0.8133 (m-80) cc_final: 0.7663 (m-80) REVERT: B 251 MET cc_start: 0.6468 (tmm) cc_final: 0.6224 (tmm) REVERT: B 263 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 321 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.7000 (t) REVERT: B 375 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7842 (ptpt) REVERT: B 377 LEU cc_start: 0.7607 (tp) cc_final: 0.7122 (tp) REVERT: B 383 MET cc_start: 0.6663 (tpp) cc_final: 0.6067 (tpp) REVERT: B 392 TYR cc_start: 0.8462 (t80) cc_final: 0.8125 (t80) REVERT: B 393 LEU cc_start: 0.8572 (mp) cc_final: 0.8319 (mp) REVERT: B 397 ILE cc_start: 0.8629 (mt) cc_final: 0.8305 (mm) REVERT: B 406 PHE cc_start: 0.8105 (m-80) cc_final: 0.7853 (m-80) REVERT: B 413 ILE cc_start: 0.6088 (OUTLIER) cc_final: 0.4316 (mp) REVERT: B 425 MET cc_start: 0.8050 (mtt) cc_final: 0.7697 (mtp) REVERT: B 427 TRP cc_start: 0.8081 (t-100) cc_final: 0.7861 (t-100) REVERT: B 444 ASN cc_start: 0.8004 (t0) cc_final: 0.7798 (t0) REVERT: B 445 LEU cc_start: 0.8439 (tp) cc_final: 0.8189 (tp) REVERT: B 466 THR cc_start: 0.7786 (p) cc_final: 0.7441 (t) REVERT: B 470 ASN cc_start: 0.7710 (m-40) cc_final: 0.7231 (m110) REVERT: B 477 LEU cc_start: 0.8605 (mp) cc_final: 0.8249 (tp) REVERT: B 480 ILE cc_start: 0.8124 (mt) cc_final: 0.7877 (mt) REVERT: B 490 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8411 (ttmt) REVERT: B 491 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8112 (ttp-110) REVERT: B 500 ARG cc_start: 0.7796 (tmt-80) cc_final: 0.7414 (ttt-90) REVERT: B 506 ASN cc_start: 0.8406 (m-40) cc_final: 0.8194 (m110) REVERT: B 512 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8546 (mm) REVERT: B 517 PHE cc_start: 0.7042 (m-10) cc_final: 0.6620 (m-10) REVERT: B 531 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7508 (tp30) REVERT: B 578 MET cc_start: 0.7318 (ppp) cc_final: 0.6999 (ppp) REVERT: B 579 MET cc_start: 0.7920 (mmm) cc_final: 0.7587 (mmm) REVERT: B 586 MET cc_start: 0.7424 (tpt) cc_final: 0.6904 (tpt) REVERT: B 590 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6865 (mt-10) REVERT: B 594 TYR cc_start: 0.7863 (m-10) cc_final: 0.7527 (m-80) REVERT: B 646 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.7887 (ptp-170) REVERT: B 823 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 832 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7218 (tp40) REVERT: B 833 LEU cc_start: 0.8682 (tt) cc_final: 0.8356 (pp) REVERT: B 848 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 877 GLN cc_start: 0.8264 (pp30) cc_final: 0.7714 (tp40) REVERT: B 880 LYS cc_start: 0.8278 (ptpp) cc_final: 0.7773 (ptpp) REVERT: B 881 GLU cc_start: 0.7881 (pt0) cc_final: 0.7217 (pt0) REVERT: B 889 HIS cc_start: 0.7534 (m-70) cc_final: 0.7193 (m-70) REVERT: B 899 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.7136 (tmm-80) REVERT: B 902 ILE cc_start: 0.8844 (tt) cc_final: 0.8107 (tp) REVERT: B 903 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8015 (ttm170) REVERT: B 904 THR cc_start: 0.8187 (m) cc_final: 0.7974 (p) REVERT: B 906 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 911 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7791 (mt-10) REVERT: B 921 LEU cc_start: 0.8718 (tt) cc_final: 0.8429 (mm) REVERT: B 926 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: B 942 MET cc_start: 0.7718 (tpp) cc_final: 0.7493 (tpp) outliers start: 64 outliers final: 39 residues processed: 478 average time/residue: 0.1156 time to fit residues: 74.4399 Evaluate side-chains 511 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 455 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 0.0050 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 0.0030 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108095 restraints weight = 23701.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111628 restraints weight = 12219.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113938 restraints weight = 7442.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115382 restraints weight = 5089.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116478 restraints weight = 3864.001| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.138 Angle : 0.694 12.054 14762 Z= 0.346 Chirality : 0.041 0.213 1782 Planarity : 0.004 0.044 1816 Dihedral : 5.656 55.152 1469 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.09 % Allowed : 25.95 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.23), residues: 1354 helix: 1.87 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.95 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 399 TYR 0.021 0.001 TYR B 191 PHE 0.024 0.001 PHE A 457 TRP 0.035 0.002 TRP A 635 HIS 0.002 0.000 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00280 (10880) covalent geometry : angle 0.69365 (14762) hydrogen bonds : bond 0.04411 ( 905) hydrogen bonds : angle 4.14194 ( 2715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 461 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8455 (p) cc_final: 0.8209 (p) REVERT: A 113 LEU cc_start: 0.8164 (tt) cc_final: 0.7925 (tp) REVERT: A 134 ASP cc_start: 0.8012 (t70) cc_final: 0.7738 (t0) REVERT: A 154 MET cc_start: 0.7074 (mmm) cc_final: 0.6733 (mmm) REVERT: A 155 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6319 (p0) REVERT: A 156 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7881 (m) REVERT: A 161 ARG cc_start: 0.7586 (mmt180) cc_final: 0.7073 (mmt-90) REVERT: A 204 ILE cc_start: 0.8635 (mt) cc_final: 0.8307 (tt) REVERT: A 206 SER cc_start: 0.8209 (t) cc_final: 0.7446 (p) REVERT: A 231 GLU cc_start: 0.7754 (tt0) cc_final: 0.6887 (tt0) REVERT: A 233 GLU cc_start: 0.8014 (tt0) cc_final: 0.7399 (tt0) REVERT: A 237 ASN cc_start: 0.8111 (t0) cc_final: 0.7524 (t0) REVERT: A 238 ASP cc_start: 0.7157 (m-30) cc_final: 0.6743 (m-30) REVERT: A 248 PHE cc_start: 0.8095 (m-80) cc_final: 0.7462 (m-10) REVERT: A 252 VAL cc_start: 0.7233 (t) cc_final: 0.6567 (m) REVERT: A 278 TRP cc_start: 0.8401 (t-100) cc_final: 0.7894 (t-100) REVERT: A 285 VAL cc_start: 0.8083 (t) cc_final: 0.7836 (p) REVERT: A 295 ASN cc_start: 0.7308 (p0) cc_final: 0.7001 (p0) REVERT: A 303 ILE cc_start: 0.7923 (mt) cc_final: 0.7554 (mt) REVERT: A 312 TYR cc_start: 0.8248 (t80) cc_final: 0.7587 (t80) REVERT: A 316 ASP cc_start: 0.7359 (m-30) cc_final: 0.6678 (m-30) REVERT: A 345 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 364 ILE cc_start: 0.8114 (mt) cc_final: 0.7700 (tt) REVERT: A 384 ASP cc_start: 0.8006 (t0) cc_final: 0.7706 (t0) REVERT: A 393 LEU cc_start: 0.8789 (mp) cc_final: 0.8347 (mp) REVERT: A 396 THR cc_start: 0.8209 (m) cc_final: 0.7962 (p) REVERT: A 399 ARG cc_start: 0.7742 (ttt90) cc_final: 0.7462 (tpt170) REVERT: A 425 MET cc_start: 0.7804 (tpt) cc_final: 0.6661 (tpp) REVERT: A 426 THR cc_start: 0.8328 (t) cc_final: 0.8082 (t) REVERT: A 431 ARG cc_start: 0.8410 (mmt180) cc_final: 0.8136 (mpt180) REVERT: A 443 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 444 ASN cc_start: 0.8267 (t0) cc_final: 0.7975 (t0) REVERT: A 449 ASP cc_start: 0.8246 (t0) cc_final: 0.7964 (t0) REVERT: A 466 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7948 (t) REVERT: A 475 GLN cc_start: 0.8481 (tp40) cc_final: 0.8201 (mm-40) REVERT: A 485 ASP cc_start: 0.7976 (t0) cc_final: 0.7500 (t0) REVERT: A 486 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7647 (mp) REVERT: A 494 MET cc_start: 0.7839 (tpp) cc_final: 0.7238 (tpp) REVERT: A 500 ARG cc_start: 0.8050 (ttt90) cc_final: 0.7767 (ttt180) REVERT: A 505 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 506 ASN cc_start: 0.8425 (m-40) cc_final: 0.7984 (m-40) REVERT: A 507 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7771 (ptp-110) REVERT: A 511 MET cc_start: 0.7830 (tmm) cc_final: 0.7581 (tmm) REVERT: A 517 PHE cc_start: 0.8095 (m-10) cc_final: 0.7828 (m-80) REVERT: A 579 MET cc_start: 0.8669 (mmm) cc_final: 0.8128 (tpt) REVERT: A 581 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 586 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7223 (ptm) REVERT: A 587 LEU cc_start: 0.8724 (pp) cc_final: 0.8087 (pp) REVERT: A 590 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 591 LYS cc_start: 0.8599 (pttp) cc_final: 0.8285 (pttp) REVERT: A 600 HIS cc_start: 0.7729 (t70) cc_final: 0.7349 (t70) REVERT: A 610 LEU cc_start: 0.8831 (tt) cc_final: 0.8012 (tp) REVERT: A 613 GLN cc_start: 0.8435 (pp30) cc_final: 0.7772 (pp30) REVERT: A 647 LYS cc_start: 0.8837 (mttp) cc_final: 0.8530 (mtmt) REVERT: A 832 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 841 LYS cc_start: 0.8716 (mptt) cc_final: 0.8328 (tptt) REVERT: A 844 ILE cc_start: 0.9014 (mm) cc_final: 0.8374 (tt) REVERT: A 847 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7787 (mp0) REVERT: A 848 GLU cc_start: 0.8618 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 866 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: A 875 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7107 (ttp80) REVERT: A 888 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 897 LYS cc_start: 0.8605 (pttt) cc_final: 0.8275 (pttt) REVERT: A 899 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7232 (mtt90) REVERT: A 906 LEU cc_start: 0.8385 (mt) cc_final: 0.8050 (mm) REVERT: A 908 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7477 (t-90) REVERT: A 909 SER cc_start: 0.8760 (t) cc_final: 0.8537 (p) REVERT: A 911 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 914 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7370 (m170) REVERT: A 923 ASP cc_start: 0.5421 (p0) cc_final: 0.5011 (p0) REVERT: A 926 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7838 (mm-30) REVERT: A 938 MET cc_start: 0.8376 (tpp) cc_final: 0.8060 (tpp) REVERT: B 78 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7830 (mt) REVERT: B 92 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8596 (mmm-85) REVERT: B 163 PHE cc_start: 0.8095 (t80) cc_final: 0.7695 (t80) REVERT: B 166 VAL cc_start: 0.8569 (t) cc_final: 0.8238 (p) REVERT: B 189 PHE cc_start: 0.7571 (m-10) cc_final: 0.7232 (m-10) REVERT: B 197 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: B 199 MET cc_start: 0.7485 (tpp) cc_final: 0.7046 (tpp) REVERT: B 218 LYS cc_start: 0.8451 (ptmm) cc_final: 0.8099 (ptmm) REVERT: B 237 ASN cc_start: 0.7962 (t0) cc_final: 0.7760 (t0) REVERT: B 242 ILE cc_start: 0.8591 (mt) cc_final: 0.8288 (mm) REVERT: B 248 PHE cc_start: 0.8122 (m-80) cc_final: 0.7666 (m-80) REVERT: B 251 MET cc_start: 0.6438 (tmm) cc_final: 0.6189 (tmm) REVERT: B 263 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 321 VAL cc_start: 0.7240 (OUTLIER) cc_final: 0.6980 (t) REVERT: B 375 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7827 (ptpt) REVERT: B 377 LEU cc_start: 0.7542 (tp) cc_final: 0.7038 (tp) REVERT: B 383 MET cc_start: 0.6660 (tpp) cc_final: 0.6040 (tpp) REVERT: B 386 PHE cc_start: 0.7564 (t80) cc_final: 0.7137 (t80) REVERT: B 392 TYR cc_start: 0.8455 (t80) cc_final: 0.8112 (t80) REVERT: B 393 LEU cc_start: 0.8547 (mp) cc_final: 0.8294 (mp) REVERT: B 397 ILE cc_start: 0.8622 (mt) cc_final: 0.8290 (mm) REVERT: B 406 PHE cc_start: 0.8101 (m-80) cc_final: 0.7857 (m-80) REVERT: B 413 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.4193 (mp) REVERT: B 425 MET cc_start: 0.8059 (mtt) cc_final: 0.7724 (mtp) REVERT: B 427 TRP cc_start: 0.8047 (t-100) cc_final: 0.7826 (t-100) REVERT: B 444 ASN cc_start: 0.8025 (t0) cc_final: 0.7809 (t0) REVERT: B 445 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 466 THR cc_start: 0.7769 (p) cc_final: 0.7446 (t) REVERT: B 470 ASN cc_start: 0.7750 (m-40) cc_final: 0.7256 (m110) REVERT: B 475 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7693 (tp40) REVERT: B 477 LEU cc_start: 0.8588 (mp) cc_final: 0.8227 (tp) REVERT: B 480 ILE cc_start: 0.8044 (mt) cc_final: 0.7816 (mt) REVERT: B 490 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8445 (ttmt) REVERT: B 491 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.8079 (ttp-110) REVERT: B 500 ARG cc_start: 0.7767 (tmt-80) cc_final: 0.7349 (ttt-90) REVERT: B 506 ASN cc_start: 0.8408 (m-40) cc_final: 0.8187 (m110) REVERT: B 512 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8515 (mm) REVERT: B 517 PHE cc_start: 0.7013 (m-10) cc_final: 0.6555 (m-10) REVERT: B 578 MET cc_start: 0.7292 (ppp) cc_final: 0.6883 (ppp) REVERT: B 579 MET cc_start: 0.7990 (mmm) cc_final: 0.7582 (mmm) REVERT: B 586 MET cc_start: 0.7384 (tpt) cc_final: 0.7094 (tpt) REVERT: B 590 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 594 TYR cc_start: 0.7910 (m-10) cc_final: 0.7603 (m-80) REVERT: B 646 ARG cc_start: 0.8287 (ptp-170) cc_final: 0.7868 (ptp-170) REVERT: B 826 ASN cc_start: 0.8219 (p0) cc_final: 0.7916 (p0) REVERT: B 832 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7321 (tp40) REVERT: B 833 LEU cc_start: 0.8692 (tt) cc_final: 0.8413 (pp) REVERT: B 848 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 877 GLN cc_start: 0.8259 (pp30) cc_final: 0.7321 (pp30) REVERT: B 880 LYS cc_start: 0.8279 (ptpp) cc_final: 0.7769 (ptpp) REVERT: B 881 GLU cc_start: 0.7893 (pt0) cc_final: 0.7406 (pt0) REVERT: B 885 LEU cc_start: 0.8225 (tp) cc_final: 0.8009 (tp) REVERT: B 889 HIS cc_start: 0.7526 (m-70) cc_final: 0.7189 (m-70) REVERT: B 899 ARG cc_start: 0.7802 (tmm-80) cc_final: 0.7119 (tmm-80) REVERT: B 902 ILE cc_start: 0.8818 (tt) cc_final: 0.8072 (tp) REVERT: B 903 ARG cc_start: 0.8331 (ttm170) cc_final: 0.8075 (ttm170) REVERT: B 904 THR cc_start: 0.8198 (m) cc_final: 0.7983 (p) REVERT: B 906 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8409 (mm) REVERT: B 911 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 921 LEU cc_start: 0.8702 (tt) cc_final: 0.8396 (mm) REVERT: B 942 MET cc_start: 0.7726 (tpp) cc_final: 0.7497 (tpp) outliers start: 59 outliers final: 37 residues processed: 473 average time/residue: 0.1228 time to fit residues: 78.6409 Evaluate side-chains 508 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 455 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107678 restraints weight = 23663.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111127 restraints weight = 12143.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113395 restraints weight = 7422.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114834 restraints weight = 5092.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115882 restraints weight = 3862.805| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10880 Z= 0.151 Angle : 0.724 11.909 14762 Z= 0.363 Chirality : 0.043 0.337 1782 Planarity : 0.004 0.045 1816 Dihedral : 5.470 54.247 1465 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.74 % Allowed : 26.21 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.23), residues: 1354 helix: 1.84 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -0.93 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 887 TYR 0.017 0.001 TYR B 837 PHE 0.028 0.001 PHE A 457 TRP 0.038 0.002 TRP A 635 HIS 0.004 0.000 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00308 (10880) covalent geometry : angle 0.72363 (14762) hydrogen bonds : bond 0.04501 ( 905) hydrogen bonds : angle 4.16653 ( 2715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 459 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8425 (p) cc_final: 0.8178 (p) REVERT: A 113 LEU cc_start: 0.8197 (tt) cc_final: 0.7969 (tp) REVERT: A 134 ASP cc_start: 0.8037 (t70) cc_final: 0.7756 (t0) REVERT: A 138 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 154 MET cc_start: 0.7094 (mmm) cc_final: 0.6627 (mmm) REVERT: A 155 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6346 (p0) REVERT: A 156 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7692 (m) REVERT: A 161 ARG cc_start: 0.7580 (mmt180) cc_final: 0.7334 (mmt180) REVERT: A 204 ILE cc_start: 0.8665 (mt) cc_final: 0.8311 (tt) REVERT: A 206 SER cc_start: 0.8224 (t) cc_final: 0.7502 (p) REVERT: A 231 GLU cc_start: 0.7687 (tt0) cc_final: 0.6730 (tt0) REVERT: A 233 GLU cc_start: 0.8013 (tt0) cc_final: 0.7415 (tt0) REVERT: A 237 ASN cc_start: 0.8130 (t0) cc_final: 0.7547 (t0) REVERT: A 238 ASP cc_start: 0.7141 (m-30) cc_final: 0.6715 (m-30) REVERT: A 248 PHE cc_start: 0.8065 (m-80) cc_final: 0.7453 (m-10) REVERT: A 252 VAL cc_start: 0.7278 (t) cc_final: 0.6657 (m) REVERT: A 278 TRP cc_start: 0.8414 (t-100) cc_final: 0.7927 (t-100) REVERT: A 285 VAL cc_start: 0.8100 (t) cc_final: 0.7865 (p) REVERT: A 295 ASN cc_start: 0.7304 (p0) cc_final: 0.6986 (p0) REVERT: A 303 ILE cc_start: 0.7841 (mt) cc_final: 0.7463 (mt) REVERT: A 312 TYR cc_start: 0.8254 (t80) cc_final: 0.7570 (t80) REVERT: A 316 ASP cc_start: 0.7313 (m-30) cc_final: 0.6666 (m-30) REVERT: A 345 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8043 (m) REVERT: A 364 ILE cc_start: 0.8123 (mt) cc_final: 0.7704 (tt) REVERT: A 384 ASP cc_start: 0.7945 (t0) cc_final: 0.7677 (t0) REVERT: A 393 LEU cc_start: 0.8792 (mp) cc_final: 0.8353 (mp) REVERT: A 396 THR cc_start: 0.8219 (m) cc_final: 0.7960 (p) REVERT: A 399 ARG cc_start: 0.7759 (ttt90) cc_final: 0.7430 (tpt170) REVERT: A 425 MET cc_start: 0.7803 (tpt) cc_final: 0.6616 (tpp) REVERT: A 426 THR cc_start: 0.8332 (t) cc_final: 0.8061 (t) REVERT: A 443 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 444 ASN cc_start: 0.8285 (t0) cc_final: 0.8001 (t0) REVERT: A 449 ASP cc_start: 0.8358 (t0) cc_final: 0.8075 (t0) REVERT: A 466 THR cc_start: 0.8202 (m) cc_final: 0.7942 (t) REVERT: A 485 ASP cc_start: 0.7951 (t0) cc_final: 0.7585 (t0) REVERT: A 494 MET cc_start: 0.7780 (tpp) cc_final: 0.7210 (tpp) REVERT: A 500 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7812 (ttt180) REVERT: A 501 ILE cc_start: 0.8657 (tt) cc_final: 0.8452 (pt) REVERT: A 502 HIS cc_start: 0.8044 (t70) cc_final: 0.7462 (t70) REVERT: A 505 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 506 ASN cc_start: 0.8435 (m-40) cc_final: 0.7754 (m-40) REVERT: A 507 ARG cc_start: 0.8057 (ptp-110) cc_final: 0.7776 (ptp-110) REVERT: A 511 MET cc_start: 0.7833 (tmm) cc_final: 0.7576 (tmm) REVERT: A 579 MET cc_start: 0.8648 (mmm) cc_final: 0.8099 (tpt) REVERT: A 581 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 586 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7242 (ptm) REVERT: A 587 LEU cc_start: 0.8744 (pp) cc_final: 0.8145 (pp) REVERT: A 590 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 591 LYS cc_start: 0.8594 (pttp) cc_final: 0.8282 (pttp) REVERT: A 600 HIS cc_start: 0.7632 (t70) cc_final: 0.7260 (t70) REVERT: A 610 LEU cc_start: 0.8839 (tt) cc_final: 0.8025 (tp) REVERT: A 613 GLN cc_start: 0.8454 (pp30) cc_final: 0.7756 (pp30) REVERT: A 647 LYS cc_start: 0.8890 (mttp) cc_final: 0.8626 (mtmt) REVERT: A 832 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 841 LYS cc_start: 0.8703 (mptt) cc_final: 0.8279 (tptt) REVERT: A 844 ILE cc_start: 0.9010 (mm) cc_final: 0.8440 (mt) REVERT: A 847 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7816 (mp0) REVERT: A 848 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7916 (mm-30) REVERT: A 866 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.5558 (tm-30) REVERT: A 875 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7129 (ttp80) REVERT: A 897 LYS cc_start: 0.8619 (pttt) cc_final: 0.8256 (pttt) REVERT: A 899 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7232 (mtt90) REVERT: A 906 LEU cc_start: 0.8394 (mt) cc_final: 0.8062 (mm) REVERT: A 908 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7486 (t-90) REVERT: A 909 SER cc_start: 0.8765 (t) cc_final: 0.8551 (p) REVERT: A 911 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 914 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7354 (m170) REVERT: A 923 ASP cc_start: 0.5488 (p0) cc_final: 0.4855 (p0) REVERT: A 925 MET cc_start: 0.8362 (pmm) cc_final: 0.7846 (pmm) REVERT: A 938 MET cc_start: 0.8371 (tpp) cc_final: 0.8063 (tpp) REVERT: B 163 PHE cc_start: 0.8111 (t80) cc_final: 0.7693 (t80) REVERT: B 166 VAL cc_start: 0.8570 (t) cc_final: 0.8238 (p) REVERT: B 189 PHE cc_start: 0.7579 (m-10) cc_final: 0.7336 (m-10) REVERT: B 197 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: B 199 MET cc_start: 0.7504 (tpp) cc_final: 0.7065 (tpp) REVERT: B 218 LYS cc_start: 0.8517 (ptmm) cc_final: 0.8141 (ptmm) REVERT: B 237 ASN cc_start: 0.7966 (t0) cc_final: 0.7752 (t0) REVERT: B 242 ILE cc_start: 0.8601 (mt) cc_final: 0.8301 (mm) REVERT: B 248 PHE cc_start: 0.8123 (m-80) cc_final: 0.7664 (m-80) REVERT: B 251 MET cc_start: 0.6477 (tmm) cc_final: 0.6212 (tmm) REVERT: B 263 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 321 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.6996 (t) REVERT: B 375 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7808 (ptpt) REVERT: B 383 MET cc_start: 0.6647 (tpp) cc_final: 0.6054 (tpp) REVERT: B 392 TYR cc_start: 0.8453 (t80) cc_final: 0.8103 (t80) REVERT: B 393 LEU cc_start: 0.8561 (mp) cc_final: 0.8296 (mp) REVERT: B 397 ILE cc_start: 0.8646 (mt) cc_final: 0.8304 (mm) REVERT: B 406 PHE cc_start: 0.8138 (m-80) cc_final: 0.7910 (m-80) REVERT: B 413 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.4197 (mp) REVERT: B 425 MET cc_start: 0.8057 (mtt) cc_final: 0.7731 (mtp) REVERT: B 444 ASN cc_start: 0.8034 (t0) cc_final: 0.7814 (t0) REVERT: B 445 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 466 THR cc_start: 0.7731 (p) cc_final: 0.7120 (t) REVERT: B 470 ASN cc_start: 0.7754 (m-40) cc_final: 0.7036 (m110) REVERT: B 477 LEU cc_start: 0.8606 (mp) cc_final: 0.8253 (tp) REVERT: B 480 ILE cc_start: 0.8094 (mt) cc_final: 0.7858 (mt) REVERT: B 490 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8431 (ttmt) REVERT: B 491 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8084 (ttp-110) REVERT: B 500 ARG cc_start: 0.7791 (tmt-80) cc_final: 0.7219 (ttt-90) REVERT: B 512 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8521 (mm) REVERT: B 517 PHE cc_start: 0.6950 (m-10) cc_final: 0.6537 (m-10) REVERT: B 578 MET cc_start: 0.7251 (ppp) cc_final: 0.6836 (ppp) REVERT: B 579 MET cc_start: 0.7975 (mmm) cc_final: 0.7580 (mmm) REVERT: B 586 MET cc_start: 0.7436 (tpt) cc_final: 0.7073 (tpt) REVERT: B 590 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 594 TYR cc_start: 0.7937 (m-10) cc_final: 0.7636 (m-80) REVERT: B 646 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.7863 (ptp-170) REVERT: B 832 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7251 (tp40) REVERT: B 833 LEU cc_start: 0.8703 (tt) cc_final: 0.8417 (pp) REVERT: B 848 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 875 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7374 (ttp80) REVERT: B 877 GLN cc_start: 0.8259 (pp30) cc_final: 0.7761 (tp40) REVERT: B 880 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7779 (ptpp) REVERT: B 881 GLU cc_start: 0.7909 (pt0) cc_final: 0.7296 (pt0) REVERT: B 885 LEU cc_start: 0.8213 (tp) cc_final: 0.7999 (tp) REVERT: B 889 HIS cc_start: 0.7612 (m-70) cc_final: 0.7250 (m-70) REVERT: B 899 ARG cc_start: 0.7816 (tmm-80) cc_final: 0.7137 (tmm-80) REVERT: B 902 ILE cc_start: 0.8798 (tt) cc_final: 0.8052 (tp) REVERT: B 903 ARG cc_start: 0.8359 (ttm170) cc_final: 0.8093 (ttm170) REVERT: B 904 THR cc_start: 0.8205 (m) cc_final: 0.7991 (p) REVERT: B 906 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 911 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7788 (mt-10) REVERT: B 921 LEU cc_start: 0.8692 (tt) cc_final: 0.8466 (mm) REVERT: B 942 MET cc_start: 0.7711 (tpp) cc_final: 0.7486 (tpp) outliers start: 55 outliers final: 34 residues processed: 474 average time/residue: 0.1196 time to fit residues: 76.5144 Evaluate side-chains 507 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 459 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 458 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 600 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107179 restraints weight = 23612.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110645 restraints weight = 12076.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112893 restraints weight = 7325.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114308 restraints weight = 5021.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115413 restraints weight = 3815.390| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10880 Z= 0.163 Angle : 0.743 12.582 14762 Z= 0.376 Chirality : 0.043 0.218 1782 Planarity : 0.004 0.055 1816 Dihedral : 5.473 53.570 1465 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.48 % Allowed : 26.98 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.23), residues: 1354 helix: 1.82 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 887 TYR 0.026 0.001 TYR B 837 PHE 0.027 0.001 PHE A 457 TRP 0.040 0.002 TRP A 635 HIS 0.008 0.001 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00330 (10880) covalent geometry : angle 0.74263 (14762) hydrogen bonds : bond 0.04612 ( 905) hydrogen bonds : angle 4.25408 ( 2715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 457 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8427 (p) cc_final: 0.8183 (p) REVERT: A 113 LEU cc_start: 0.8245 (tt) cc_final: 0.8020 (tp) REVERT: A 128 ARG cc_start: 0.7102 (ttp-110) cc_final: 0.6779 (ttp-110) REVERT: A 134 ASP cc_start: 0.8052 (t70) cc_final: 0.7772 (t0) REVERT: A 154 MET cc_start: 0.7116 (mmm) cc_final: 0.6603 (mmm) REVERT: A 155 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 156 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7726 (m) REVERT: A 204 ILE cc_start: 0.8669 (mt) cc_final: 0.8314 (tt) REVERT: A 231 GLU cc_start: 0.7688 (tt0) cc_final: 0.6717 (tt0) REVERT: A 233 GLU cc_start: 0.8021 (tt0) cc_final: 0.7444 (tt0) REVERT: A 237 ASN cc_start: 0.8145 (t0) cc_final: 0.7587 (t0) REVERT: A 238 ASP cc_start: 0.7129 (m-30) cc_final: 0.6719 (m-30) REVERT: A 248 PHE cc_start: 0.8065 (m-80) cc_final: 0.7453 (m-10) REVERT: A 252 VAL cc_start: 0.7275 (t) cc_final: 0.6661 (m) REVERT: A 278 TRP cc_start: 0.8422 (t-100) cc_final: 0.7932 (t-100) REVERT: A 285 VAL cc_start: 0.8102 (t) cc_final: 0.7871 (p) REVERT: A 293 ILE cc_start: 0.8730 (mm) cc_final: 0.8254 (mm) REVERT: A 295 ASN cc_start: 0.7266 (p0) cc_final: 0.6963 (p0) REVERT: A 312 TYR cc_start: 0.8250 (t80) cc_final: 0.7556 (t80) REVERT: A 316 ASP cc_start: 0.7334 (m-30) cc_final: 0.6650 (m-30) REVERT: A 345 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8034 (m) REVERT: A 364 ILE cc_start: 0.8118 (mt) cc_final: 0.7701 (tt) REVERT: A 384 ASP cc_start: 0.7930 (t0) cc_final: 0.7673 (t0) REVERT: A 393 LEU cc_start: 0.8790 (mp) cc_final: 0.8345 (mp) REVERT: A 396 THR cc_start: 0.8217 (m) cc_final: 0.7962 (p) REVERT: A 399 ARG cc_start: 0.7778 (ttt90) cc_final: 0.7424 (tpt170) REVERT: A 425 MET cc_start: 0.7795 (tpt) cc_final: 0.6611 (tpp) REVERT: A 426 THR cc_start: 0.8342 (t) cc_final: 0.8051 (t) REVERT: A 443 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 444 ASN cc_start: 0.8274 (t0) cc_final: 0.7993 (t0) REVERT: A 449 ASP cc_start: 0.8415 (t0) cc_final: 0.8162 (t0) REVERT: A 466 THR cc_start: 0.8229 (m) cc_final: 0.7967 (t) REVERT: A 485 ASP cc_start: 0.7891 (t0) cc_final: 0.7473 (t0) REVERT: A 494 MET cc_start: 0.7750 (tpp) cc_final: 0.7187 (tpp) REVERT: A 500 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7821 (ttt90) REVERT: A 501 ILE cc_start: 0.8669 (tt) cc_final: 0.8466 (pt) REVERT: A 505 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 506 ASN cc_start: 0.8438 (m-40) cc_final: 0.7978 (m-40) REVERT: A 507 ARG cc_start: 0.8045 (ptp-110) cc_final: 0.7778 (ptp-110) REVERT: A 511 MET cc_start: 0.7841 (tmm) cc_final: 0.7579 (tmm) REVERT: A 532 ILE cc_start: 0.8030 (mm) cc_final: 0.7699 (mm) REVERT: A 579 MET cc_start: 0.8649 (mmm) cc_final: 0.8101 (tpt) REVERT: A 581 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 586 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7196 (ptm) REVERT: A 587 LEU cc_start: 0.8723 (pp) cc_final: 0.8106 (pp) REVERT: A 590 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 591 LYS cc_start: 0.8562 (pttp) cc_final: 0.8275 (pttp) REVERT: A 600 HIS cc_start: 0.7722 (t70) cc_final: 0.7335 (t70) REVERT: A 610 LEU cc_start: 0.8830 (tt) cc_final: 0.8012 (tp) REVERT: A 613 GLN cc_start: 0.8458 (pp30) cc_final: 0.7746 (pp30) REVERT: A 832 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 841 LYS cc_start: 0.8690 (mptt) cc_final: 0.8295 (tptt) REVERT: A 844 ILE cc_start: 0.9009 (mm) cc_final: 0.8448 (mt) REVERT: A 847 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7795 (mp0) REVERT: A 848 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 866 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6213 (tm-30) REVERT: A 875 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7141 (ttp80) REVERT: A 897 LYS cc_start: 0.8611 (pttt) cc_final: 0.8242 (pttt) REVERT: A 899 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7247 (mtt90) REVERT: A 906 LEU cc_start: 0.8391 (mt) cc_final: 0.8031 (mm) REVERT: A 908 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7489 (t-90) REVERT: A 909 SER cc_start: 0.8765 (t) cc_final: 0.8548 (p) REVERT: A 911 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 914 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7357 (m170) REVERT: A 923 ASP cc_start: 0.5557 (p0) cc_final: 0.4876 (p0) REVERT: A 925 MET cc_start: 0.8371 (pmm) cc_final: 0.7857 (pmm) REVERT: A 938 MET cc_start: 0.8385 (tpp) cc_final: 0.8018 (tpp) REVERT: A 947 SER cc_start: 0.6970 (t) cc_final: 0.6467 (p) REVERT: B 163 PHE cc_start: 0.8113 (t80) cc_final: 0.7684 (t80) REVERT: B 166 VAL cc_start: 0.8580 (t) cc_final: 0.8250 (p) REVERT: B 189 PHE cc_start: 0.7567 (m-10) cc_final: 0.7324 (m-10) REVERT: B 197 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: B 199 MET cc_start: 0.7516 (tpp) cc_final: 0.7080 (tpp) REVERT: B 218 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8163 (ptmm) REVERT: B 237 ASN cc_start: 0.7984 (t0) cc_final: 0.7767 (t0) REVERT: B 242 ILE cc_start: 0.8621 (mt) cc_final: 0.8317 (mm) REVERT: B 248 PHE cc_start: 0.8125 (m-80) cc_final: 0.7656 (m-80) REVERT: B 251 MET cc_start: 0.6459 (tmm) cc_final: 0.6200 (tmm) REVERT: B 263 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 321 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.7035 (t) REVERT: B 375 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7819 (ptpt) REVERT: B 383 MET cc_start: 0.6645 (tpp) cc_final: 0.6048 (tpp) REVERT: B 392 TYR cc_start: 0.8449 (t80) cc_final: 0.7982 (t80) REVERT: B 393 LEU cc_start: 0.8586 (mp) cc_final: 0.8249 (mp) REVERT: B 396 THR cc_start: 0.8440 (m) cc_final: 0.7978 (p) REVERT: B 397 ILE cc_start: 0.8656 (mt) cc_final: 0.8263 (mm) REVERT: B 406 PHE cc_start: 0.8121 (m-80) cc_final: 0.7918 (m-80) REVERT: B 413 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.4166 (mp) REVERT: B 444 ASN cc_start: 0.8035 (t0) cc_final: 0.7815 (t0) REVERT: B 445 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8251 (tp) REVERT: B 466 THR cc_start: 0.7786 (p) cc_final: 0.7171 (t) REVERT: B 470 ASN cc_start: 0.7822 (m-40) cc_final: 0.7316 (m110) REVERT: B 477 LEU cc_start: 0.8609 (mp) cc_final: 0.8289 (tp) REVERT: B 480 ILE cc_start: 0.8113 (mt) cc_final: 0.7887 (mt) REVERT: B 490 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8453 (ttmt) REVERT: B 491 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.8065 (ttp-110) REVERT: B 500 ARG cc_start: 0.7785 (tmt-80) cc_final: 0.7217 (ttt-90) REVERT: B 512 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8569 (mm) REVERT: B 517 PHE cc_start: 0.6948 (m-10) cc_final: 0.6577 (m-10) REVERT: B 534 ASP cc_start: 0.8481 (p0) cc_final: 0.7065 (t0) REVERT: B 578 MET cc_start: 0.7220 (ppp) cc_final: 0.6757 (ppp) REVERT: B 579 MET cc_start: 0.7789 (mmm) cc_final: 0.7404 (mmm) REVERT: B 586 MET cc_start: 0.7382 (tpt) cc_final: 0.7039 (tpt) REVERT: B 590 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 594 TYR cc_start: 0.7916 (m-10) cc_final: 0.7603 (m-80) REVERT: B 646 ARG cc_start: 0.8267 (ptp-170) cc_final: 0.7861 (ptp-170) REVERT: B 832 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7278 (tp40) REVERT: B 848 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 875 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7341 (ttp80) REVERT: B 877 GLN cc_start: 0.8258 (pp30) cc_final: 0.7327 (pp30) REVERT: B 880 LYS cc_start: 0.8290 (ptpp) cc_final: 0.7792 (ptpp) REVERT: B 881 GLU cc_start: 0.7912 (pt0) cc_final: 0.7478 (pt0) REVERT: B 885 LEU cc_start: 0.8211 (tp) cc_final: 0.7989 (tp) REVERT: B 889 HIS cc_start: 0.7573 (m-70) cc_final: 0.7220 (m-70) REVERT: B 899 ARG cc_start: 0.7835 (tmm-80) cc_final: 0.7188 (tmm-80) REVERT: B 902 ILE cc_start: 0.8795 (tt) cc_final: 0.8028 (tp) REVERT: B 903 ARG cc_start: 0.8360 (ttm170) cc_final: 0.8103 (ttm170) REVERT: B 904 THR cc_start: 0.8241 (m) cc_final: 0.8007 (p) REVERT: B 906 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 911 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 921 LEU cc_start: 0.8710 (tt) cc_final: 0.8479 (mm) REVERT: B 942 MET cc_start: 0.7745 (tpp) cc_final: 0.7475 (tpp) outliers start: 52 outliers final: 35 residues processed: 469 average time/residue: 0.1251 time to fit residues: 79.1731 Evaluate side-chains 504 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 456 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 830 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 908 HIS Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 641 TYR Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 908 HIS Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 335 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101202 restraints weight = 23909.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104569 restraints weight = 12119.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106751 restraints weight = 7322.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108199 restraints weight = 5026.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109137 restraints weight = 3798.234| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10880 Z= 0.166 Angle : 0.745 12.580 14762 Z= 0.379 Chirality : 0.044 0.321 1782 Planarity : 0.004 0.055 1816 Dihedral : 5.481 52.773 1465 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.22 % Allowed : 27.59 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.23), residues: 1354 helix: 1.80 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -0.93 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 887 TYR 0.022 0.001 TYR B 837 PHE 0.028 0.001 PHE A 457 TRP 0.049 0.002 TRP A 643 HIS 0.004 0.000 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00340 (10880) covalent geometry : angle 0.74455 (14762) hydrogen bonds : bond 0.04657 ( 905) hydrogen bonds : angle 4.30779 ( 2715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2215.76 seconds wall clock time: 38 minutes 55.94 seconds (2335.94 seconds total)