Starting phenix.real_space_refine on Tue Aug 26 15:00:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eu2_3957/08_2025/6eu2_3957.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eu2_3957/08_2025/6eu2_3957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6eu2_3957/08_2025/6eu2_3957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eu2_3957/08_2025/6eu2_3957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6eu2_3957/08_2025/6eu2_3957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eu2_3957/08_2025/6eu2_3957.map" } resolution = 3.4 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 207 5.16 5 C 24312 2.51 5 N 6585 2.21 5 O 7218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38329 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 10980 Classifications: {'peptide': 1402} Link IDs: {'PTRANS': 63, 'TRANS': 1338} Chain breaks: 3 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 558 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "O" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4315 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 17, 'TRANS': 519} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "Q" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 510 SG CYS A 70 78.753 66.943 79.309 1.00 66.93 S ATOM 795 SG CYS A 107 61.364 111.694 95.439 1.00 48.48 S ATOM 1184 SG CYS A 154 62.664 114.580 93.523 1.00 68.31 S ATOM 1208 SG CYS A 157 58.803 114.034 93.724 1.00 70.16 S ATOM 19341 SG CYS B1095 82.241 82.925 76.225 1.00 37.65 S ATOM 19430 SG CYS B1107 79.320 81.301 74.903 1.00 46.23 S ATOM 28552 SG CYS I 8 61.485 104.888 159.568 1.00 81.51 S ATOM 28703 SG CYS I 29 59.675 107.936 160.450 1.00 90.89 S ATOM 28892 SG CYS J 10 131.323 38.271 125.391 1.00 24.11 S ATOM 29172 SG CYS J 45 129.207 41.878 128.080 1.00 29.06 S ATOM 29178 SG CYS J 46 129.442 38.035 128.413 1.00 23.95 S ATOM 30215 SG CYS L 31 86.293 24.890 124.388 1.00 46.89 S ATOM 30235 SG CYS L 34 86.320 21.438 125.514 1.00 58.37 S ATOM 30362 SG CYS L 51 83.267 23.842 126.230 1.00 62.35 S Time building chain proxies: 7.69, per 1000 atoms: 0.20 Number of scatterers: 38329 At special positions: 0 Unit cell: (190.05, 159.6, 207.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 207 16.00 Mg 1 11.99 O 7218 8.00 N 6585 7.00 C 24312 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: 2.33 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 80 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9114 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 50 sheets defined 34.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 removed outlier: 3.669A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.506A pdb=" N ARG A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.560A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 191 through 208 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.604A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.502A pdb=" N ILE A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 303 removed outlier: 3.603A pdb=" N THR A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.806A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.626A pdb=" N GLN A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.550A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 456' Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.169A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.794A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 533' Processing helix chain 'A' and resid 554 through 565 removed outlier: 3.678A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.532A pdb=" N MET A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 4.102A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 685 through 709 removed outlier: 4.295A pdb=" N GLU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 740 removed outlier: 3.653A pdb=" N LYS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 removed outlier: 3.588A pdb=" N ASN A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 777 removed outlier: 3.718A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 removed outlier: 3.960A pdb=" N ASN A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 784' Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 857 through 877 removed outlier: 3.535A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.778A pdb=" N THR A 882 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.579A pdb=" N ASN A 944 " --> pdb=" O ASP A 940 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.898A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 removed outlier: 3.903A pdb=" N ARG A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A1015 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.539A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1080 removed outlier: 3.526A pdb=" N GLU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1102 removed outlier: 3.629A pdb=" N ILE A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1122 through 1131 removed outlier: 3.508A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 4.370A pdb=" N SER A1167 " --> pdb=" O THR A1164 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A1169 " --> pdb=" O LEU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1255 through 1266 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.692A pdb=" N VAL A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.711A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A1339 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 removed outlier: 3.807A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1402 removed outlier: 4.074A pdb=" N ASP A1398 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1399 " --> pdb=" O HIS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1418 removed outlier: 3.748A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.683A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1423 through 1427' Processing helix chain 'A' and resid 1449 through 1455 removed outlier: 3.937A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 removed outlier: 3.567A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.597A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.361A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 4.373A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.563A pdb=" N LEU B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.580A pdb=" N VAL B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 4.765A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.603A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 4.017A pdb=" N ILE B 319 " --> pdb=" O LYS B 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 320 " --> pdb=" O LEU B 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 316 through 320' Processing helix chain 'B' and resid 322 through 329 removed outlier: 4.330A pdb=" N ALA B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 362 removed outlier: 3.775A pdb=" N ALA B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 404 removed outlier: 4.108A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.999A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.602A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.646A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 526 through 537 removed outlier: 4.201A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.806A pdb=" N ILE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 583 removed outlier: 3.884A pdb=" N THR B 581 " --> pdb=" O HIS B 577 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.862A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 630 " --> pdb=" O HIS B 626 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.898A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 680' Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.992A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.204A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.733A pdb=" N GLN B 822 " --> pdb=" O TRP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.665A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 949 " --> pdb=" O PRO B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 945 through 949' Processing helix chain 'B' and resid 955 through 970 removed outlier: 3.515A pdb=" N GLU B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 967 " --> pdb=" O SER B 963 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 970 " --> pdb=" O ALA B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 993 removed outlier: 3.543A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 990 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.616A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1084 removed outlier: 3.765A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 Processing helix chain 'B' and resid 1123 through 1135 removed outlier: 3.742A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.588A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.699A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.562A pdb=" N ILE C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.643A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.590A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.865A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.579A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 4.035A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 327 removed outlier: 3.565A pdb=" N ILE C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.739A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.758A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 100 through 113 removed outlier: 4.062A pdb=" N PHE D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.360A pdb=" N LEU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.712A pdb=" N SER D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 4.051A pdb=" N GLU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE D 157 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.807A pdb=" N GLU E 6 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 26 removed outlier: 3.617A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 4.510A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.821A pdb=" N MET E 121 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.631A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.861A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.708A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.645A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.580A pdb=" N ASN G 32 " --> pdb=" O HIS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 removed outlier: 3.659A pdb=" N MET G 114 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.985A pdb=" N GLU G 167 " --> pdb=" O LYS G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.626A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.882A pdb=" N ALA K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 50 through 54' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.724A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.759A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.613A pdb=" N GLU M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 193 removed outlier: 3.611A pdb=" N THR M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 236 Processing helix chain 'M' and resid 251 through 256 removed outlier: 3.608A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 282 removed outlier: 3.759A pdb=" N LEU N 282 " --> pdb=" O ALA N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 295 removed outlier: 3.772A pdb=" N HIS N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN N 288 " --> pdb=" O ASN N 284 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 55 removed outlier: 3.610A pdb=" N VAL O 53 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.553A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU O 68 " --> pdb=" O VAL O 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 3.912A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.860A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER O 97 " --> pdb=" O THR O 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 133 removed outlier: 3.618A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 155 through 167 removed outlier: 3.934A pdb=" N GLN O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 176 removed outlier: 3.830A pdb=" N SER O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 195 removed outlier: 3.802A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS O 195 " --> pdb=" O PHE O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 222 removed outlier: 3.520A pdb=" N LEU O 214 " --> pdb=" O PRO O 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 254 removed outlier: 3.724A pdb=" N GLN O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA O 245 " --> pdb=" O ALA O 241 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS O 246 " --> pdb=" O LYS O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 304 removed outlier: 3.751A pdb=" N LYS O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 293 " --> pdb=" O LYS O 289 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 338 through 344 Processing helix chain 'O' and resid 345 through 355 removed outlier: 3.501A pdb=" N GLU O 350 " --> pdb=" O GLN O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 369 Processing helix chain 'O' and resid 451 through 462 Processing helix chain 'O' and resid 483 through 497 removed outlier: 3.755A pdb=" N VAL O 491 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR O 492 " --> pdb=" O LYS O 488 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL O 495 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE O 496 " --> pdb=" O TYR O 492 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA O 497 " --> pdb=" O GLU O 493 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.989A pdb=" N ILE O 511 " --> pdb=" O LEU O 507 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 523 removed outlier: 3.930A pdb=" N ASN O 523 " --> pdb=" O GLU O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 532 through 543 Processing helix chain 'O' and resid 572 through 591 removed outlier: 3.569A pdb=" N PHE O 576 " --> pdb=" O HIS O 572 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE O 590 " --> pdb=" O ALA O 586 " (cutoff:3.500A) Processing helix chain 'O' and resid 629 through 649 removed outlier: 4.107A pdb=" N ARG O 633 " --> pdb=" O MET O 629 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL O 637 " --> pdb=" O ARG O 633 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 650 through 653 removed outlier: 3.744A pdb=" N MET O 653 " --> pdb=" O VAL O 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 650 through 653' Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.941A pdb=" N ASN P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 219 through 227 Processing helix chain 'P' and resid 239 through 248 Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.621A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 68 removed outlier: 3.673A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.386A pdb=" N GLU A 3 " --> pdb=" O ILE G 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.138A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.882A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 90 removed outlier: 12.023A pdb=" N LEU A 88 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TYR A 260 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 4.110A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.591A pdb=" N LYS A 491 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 499 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.198A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.210A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 3.752A pdb=" N SER A 897 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1281 through 1285 removed outlier: 3.648A pdb=" N THR A1315 " --> pdb=" O ASN A1142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1176 through 1178 Processing sheet with id=AB5, first strand: chain 'F' and resid 132 through 135 Processing sheet with id=AB6, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.582A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE B 133 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 135 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS B 144 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.067A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.617A pdb=" N ILE B 206 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC2, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC3, first strand: chain 'B' and resid 560 through 561 removed outlier: 5.952A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.529A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.529A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 4.016A pdb=" N GLN B1025 " --> pdb=" O SER B 913 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 772 " --> pdb=" O ILE B 943 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 943 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 758 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.235A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC9, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD1, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.776A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 230 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.632A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.878A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AD5, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.505A pdb=" N GLU D 5 " --> pdb=" O LYS G 6 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 107 through 110 removed outlier: 3.626A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.110A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.912A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 86 Processing sheet with id=AE3, first strand: chain 'G' and resid 88 through 91 removed outlier: 7.972A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.833A pdb=" N VAL G 154 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA G 195 " --> pdb=" O VAL G 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'H' and resid 95 through 96 removed outlier: 6.825A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 14 through 17 removed outlier: 3.766A pdb=" N VAL I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 47 through 48 removed outlier: 3.611A pdb=" N GLN K 64 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.307A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE M 162 " --> pdb=" O TYR M 169 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 84 through 87 removed outlier: 4.608A pdb=" N SER M 84 " --> pdb=" O ILE N 399 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA N 396 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU N 408 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER N 398 " --> pdb=" O ALA N 406 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 119 through 122 removed outlier: 3.583A pdb=" N ILE M 121 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.643A pdb=" N VAL M 153 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL M 176 " --> pdb=" O VAL M 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 104 through 109 Processing sheet with id=AF4, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AF5, first strand: chain 'O' and resid 548 through 552 1094 hydrogen bonds defined for protein. 3063 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: 6.99 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12413 1.34 - 1.46: 7858 1.46 - 1.58: 18407 1.58 - 1.70: 0 1.70 - 1.82: 337 Bond restraints: 39015 Sorted by residual: bond pdb=" C PHE Q 36 " pdb=" N PRO Q 37 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.01e-02 9.80e+03 2.16e+01 bond pdb=" C LEU A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" C GLY P 201 " pdb=" N PRO P 202 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.38e+00 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 6.01e+00 bond pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.21e+00 ... (remaining 39010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 52073 4.03 - 8.06: 532 8.06 - 12.09: 74 12.09 - 16.11: 4 16.11 - 20.14: 2 Bond angle restraints: 52685 Sorted by residual: angle pdb=" N LEU N 409 " pdb=" CA LEU N 409 " pdb=" C LEU N 409 " ideal model delta sigma weight residual 110.80 90.66 20.14 2.13e+00 2.20e-01 8.94e+01 angle pdb=" C GLY O 198 " pdb=" N TYR O 199 " pdb=" CA TYR O 199 " ideal model delta sigma weight residual 120.82 129.53 -8.71 1.50e+00 4.44e-01 3.37e+01 angle pdb=" C SER B 889 " pdb=" N ASP B 890 " pdb=" CA ASP B 890 " ideal model delta sigma weight residual 120.82 129.43 -8.61 1.50e+00 4.44e-01 3.30e+01 angle pdb=" C GLY K 58 " pdb=" N THR K 59 " pdb=" CA THR K 59 " ideal model delta sigma weight residual 121.31 129.71 -8.40 1.49e+00 4.50e-01 3.18e+01 angle pdb=" C GLY N 410 " pdb=" N ARG N 411 " pdb=" CA ARG N 411 " ideal model delta sigma weight residual 121.54 132.29 -10.75 1.91e+00 2.74e-01 3.17e+01 ... (remaining 52680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 22547 17.29 - 34.57: 1132 34.57 - 51.86: 234 51.86 - 69.15: 18 69.15 - 86.44: 25 Dihedral angle restraints: 23956 sinusoidal: 9878 harmonic: 14078 Sorted by residual: dihedral pdb=" CA GLU P 308 " pdb=" C GLU P 308 " pdb=" N VAL P 309 " pdb=" CA VAL P 309 " ideal model delta harmonic sigma weight residual -180.00 -93.56 -86.44 0 5.00e+00 4.00e-02 2.99e+02 dihedral pdb=" CA LYS P 307 " pdb=" C LYS P 307 " pdb=" N GLU P 308 " pdb=" CA GLU P 308 " ideal model delta harmonic sigma weight residual -180.00 -113.62 -66.38 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CA LYS B 583 " pdb=" C LYS B 583 " pdb=" N VAL B 584 " pdb=" CA VAL B 584 " ideal model delta harmonic sigma weight residual -180.00 -123.56 -56.44 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 23953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5208 0.086 - 0.173: 689 0.173 - 0.259: 54 0.259 - 0.346: 8 0.346 - 0.432: 1 Chirality restraints: 5960 Sorted by residual: chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA LEU N 409 " pdb=" N LEU N 409 " pdb=" C LEU N 409 " pdb=" CB LEU N 409 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB VAL B 888 " pdb=" CA VAL B 888 " pdb=" CG1 VAL B 888 " pdb=" CG2 VAL B 888 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 5957 not shown) Planarity restraints: 6778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS O 236 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LYS O 236 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS O 236 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS O 237 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 28 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C LYS L 28 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS L 28 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR L 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O 43 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO O 44 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO O 44 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 44 " -0.039 5.00e-02 4.00e+02 ... (remaining 6775 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 56 2.41 - 3.03: 19200 3.03 - 3.65: 56018 3.65 - 4.28: 80136 4.28 - 4.90: 133566 Nonbonded interactions: 288976 Sorted by model distance: nonbonded pdb=" O GLU D 139 " pdb=" O GLU D 140 " model vdw 1.787 3.040 nonbonded pdb=" O ALA D 143 " pdb=" N PHE D 145 " model vdw 1.792 3.120 nonbonded pdb=" NZ LYS A 232 " pdb=" O TRP P 315 " model vdw 1.829 3.120 nonbonded pdb=" CE1 TYR D 135 " pdb=" CA ASP D 142 " model vdw 2.228 3.770 nonbonded pdb=" O LEU E 123 " pdb=" OG SER E 126 " model vdw 2.269 3.040 ... (remaining 288971 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 33.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0571 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 : 0.007 0.629 39030 Z= 0.276 Angle : 1.042 20.142 52685 Z= 0.546 Chirality : 0.059 0.432 5960 Planarity : 0.007 0.071 6778 Dihedral : 11.347 86.436 14842 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.97 % Favored : 86.51 % Rotamer: Outliers : 0.40 % Allowed : 6.28 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.96 % Twisted General : 0.57 % 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: -5.22 (0.09), residues: 4765 helix: -3.85 (0.07), residues: 1554 sheet: -2.18 (0.21), residues: 502 loop : -3.62 (0.09), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 915 TYR 0.028 0.002 TYR B1103 PHE 0.041 0.002 PHE D 145 TRP 0.024 0.002 TRP G 88 HIS 0.012 0.002 HIS B 947 Details of bonding type rmsd covalent geometry : bond 0.00428 (39015) covalent geometry : angle 1.04206 (52685) hydrogen bonds : bond 0.23678 ( 1073) hydrogen bonds : angle 8.35298 ( 3063) metal coordination : bond 0.26917 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 614 time to evaluate : 1.222 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 LEU cc_start: 0.0319 (pp) cc_final: -0.0177 (pp) REVERT: A 1032 LEU cc_start: 0.1190 (OUTLIER) cc_final: 0.0868 (tp) REVERT: B 269 MET cc_start: 0.0825 (tpt) cc_final: 0.0261 (ppp) REVERT: D 156 ILE cc_start: 0.4417 (OUTLIER) cc_final: 0.3378 (tt) REVERT: F 151 LEU cc_start: -0.0418 (mt) cc_final: -0.0779 (mt) REVERT: L 40 LEU cc_start: 0.4339 (pp) cc_final: 0.3167 (pp) REVERT: M 77 LYS cc_start: 0.5668 (mppt) cc_final: 0.5062 (tptt) REVERT: M 226 ARG cc_start: 0.3925 (pmm150) cc_final: 0.3675 (ptt-90) REVERT: P 263 VAL cc_start: -0.0018 (OUTLIER) cc_final: -0.0408 (p) REVERT: Q 66 LYS cc_start: 0.4236 (ttmm) cc_final: 0.3786 (mmtt) outliers start: 17 outliers final: 3 residues processed: 631 average time/residue: 0.2279 time to fit residues: 230.6684 Evaluate side-chains 343 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 337 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain N residue 409 LEU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 0.0970 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 109 ASN A 125 HIS A 229 ASN A 386 ASN A 427 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 566 HIS A 578 GLN A 589 HIS A 643 ASN A 805 ASN A 948 ASN A 990 ASN A1174 GLN A1254 ASN A1346 HIS A1354 HIS A1419 GLN A1453 ASN B 39 ASN B 197 GLN B 245 ASN B 286 ASN B 362 ASN B 396 ASN B 626 HIS B 774 ASN B 803 GLN B 861 ASN B 880 HIS B 893 GLN B 916 HIS ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN B1049 GLN C 137 ASN C 143 ASN C 207 HIS D 56 GLN D 61 ASN D 71 ASN E 5 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN E 174 GLN H 128 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 ASN M 155 ASN M 158 GLN M 190 ASN N 298 ASN O 143 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 GLN O 225 ASN O 244 ASN O 254 ASN O 362 ASN O 464 ASN O 544 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.210663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178992 restraints weight = 59956.329| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.55 r_work: 0.3918 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0936 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.494 39030 Z= 0.290 Angle : 0.724 14.187 52685 Z= 0.373 Chirality : 0.046 0.475 5960 Planarity : 0.005 0.084 6778 Dihedral : 6.477 83.706 5237 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.73 % Favored : 87.95 % Rotamer: Outliers : 1.69 % Allowed : 9.68 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.39 % 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: -4.13 (0.10), residues: 4765 helix: -2.40 (0.11), residues: 1567 sheet: -1.75 (0.22), residues: 500 loop : -3.29 (0.10), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 561 TYR 0.030 0.001 TYR P 249 PHE 0.023 0.002 PHE O 287 TRP 0.016 0.001 TRP M 119 HIS 0.015 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00277 (39015) covalent geometry : angle 0.72373 (52685) hydrogen bonds : bond 0.04161 ( 1073) hydrogen bonds : angle 5.45145 ( 3063) metal coordination : bond 0.38583 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 393 time to evaluate : 1.411 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: -0.0156 (OUTLIER) cc_final: -0.1519 (mt) REVERT: A 145 LEU cc_start: 0.2112 (mp) cc_final: 0.1085 (mp) REVERT: A 325 MET cc_start: 0.1064 (ppp) cc_final: -0.1234 (tpp) REVERT: A 599 LYS cc_start: 0.4374 (tptp) cc_final: 0.3777 (mttp) REVERT: A 735 TYR cc_start: 0.0277 (m-80) cc_final: -0.1537 (m-10) REVERT: A 884 TYR cc_start: -0.1827 (t80) cc_final: -0.2406 (t80) REVERT: A 946 THR cc_start: 0.2790 (m) cc_final: 0.2455 (m) REVERT: B 269 MET cc_start: 0.0842 (tpt) cc_final: -0.0013 (ppp) REVERT: B 283 PHE cc_start: 0.2185 (t80) cc_final: 0.1875 (t80) REVERT: B 317 LEU cc_start: 0.4283 (OUTLIER) cc_final: 0.3730 (tt) REVERT: B 320 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6336 (tp) REVERT: B 360 MET cc_start: 0.4331 (mmt) cc_final: 0.3899 (mmt) REVERT: B 396 ASN cc_start: 0.2517 (m-40) cc_final: 0.2262 (m-40) REVERT: B 958 MET cc_start: -0.0116 (tpp) cc_final: -0.0463 (mmp) REVERT: D 144 ARG cc_start: 0.6634 (mmp80) cc_final: 0.5972 (mpp80) REVERT: D 153 MET cc_start: 0.0834 (ppp) cc_final: 0.0269 (ttp) REVERT: E 50 MET cc_start: 0.2126 (ppp) cc_final: 0.1521 (ptt) REVERT: E 75 MET cc_start: 0.3195 (ppp) cc_final: 0.2408 (mtm) REVERT: H 146 ARG cc_start: -0.0487 (ttm110) cc_final: -0.2837 (ttm170) REVERT: I 1 MET cc_start: 0.1031 (ptm) cc_final: 0.0737 (tpp) REVERT: M 77 LYS cc_start: 0.5628 (mppt) cc_final: 0.4806 (tptp) REVERT: M 226 ARG cc_start: 0.3973 (pmm150) cc_final: 0.3677 (ptt-90) REVERT: N 305 MET cc_start: 0.5233 (mpp) cc_final: 0.3956 (mtm) REVERT: N 380 MET cc_start: 0.3785 (ttp) cc_final: 0.3029 (tpt) REVERT: N 421 GLN cc_start: 0.4257 (pm20) cc_final: 0.3454 (pt0) REVERT: O 368 ARG cc_start: 0.5357 (tpm170) cc_final: 0.4698 (tpt170) REVERT: P 263 VAL cc_start: 0.0378 (OUTLIER) cc_final: 0.0097 (p) REVERT: Q 56 VAL cc_start: 0.3953 (t) cc_final: 0.2849 (p) REVERT: Q 66 LYS cc_start: 0.4883 (ttmm) cc_final: 0.4237 (mmtt) outliers start: 72 outliers final: 32 residues processed: 448 average time/residue: 0.2183 time to fit residues: 163.7690 Evaluate side-chains 358 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 102 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 270 optimal weight: 0.0770 chunk 456 optimal weight: 0.3980 chunk 228 optimal weight: 0.6980 chunk 352 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 408 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 469 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 465 HIS ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 695 ASN A1095 GLN A1233 ASN B 61 HIS B 374 ASN B 699 ASN B 997 ASN E 32 GLN H 134 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.212885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181019 restraints weight = 59916.143| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.44 r_work: 0.3965 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1132 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 1.202 39030 Z= 0.235 Angle : 0.678 13.693 52685 Z= 0.344 Chirality : 0.044 0.243 5960 Planarity : 0.005 0.062 6778 Dihedral : 6.151 84.071 5231 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.96 % Favored : 87.76 % Rotamer: Outliers : 2.27 % Allowed : 10.97 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.37 % 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: -3.57 (0.11), residues: 4765 helix: -1.69 (0.12), residues: 1570 sheet: -1.54 (0.22), residues: 539 loop : -3.11 (0.10), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 241 TYR 0.028 0.001 TYR P 249 PHE 0.026 0.001 PHE G 72 TRP 0.012 0.001 TRP M 119 HIS 0.008 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00246 (39015) covalent geometry : angle 0.67764 (52685) hydrogen bonds : bond 0.03623 ( 1073) hydrogen bonds : angle 5.09913 ( 3063) metal coordination : bond 0.31029 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 353 time to evaluate : 1.582 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 145 LEU cc_start: 0.1998 (OUTLIER) cc_final: 0.1034 (mt) REVERT: A 325 MET cc_start: 0.1346 (ppp) cc_final: -0.0905 (tpp) REVERT: A 735 TYR cc_start: 0.0309 (m-80) cc_final: 0.0086 (t80) REVERT: A 946 THR cc_start: 0.3134 (m) cc_final: 0.2781 (m) REVERT: A 1114 VAL cc_start: 0.0145 (OUTLIER) cc_final: -0.0268 (t) REVERT: A 1260 MET cc_start: 0.1699 (mmt) cc_final: 0.0818 (tmm) REVERT: A 1362 MET cc_start: 0.1824 (mmt) cc_final: 0.1130 (ttm) REVERT: B 83 ILE cc_start: 0.0834 (pt) cc_final: -0.0251 (tp) REVERT: B 269 MET cc_start: 0.0875 (tpt) cc_final: 0.0036 (ppp) REVERT: B 317 LEU cc_start: 0.4298 (OUTLIER) cc_final: 0.4042 (tt) REVERT: B 360 MET cc_start: 0.4301 (mmt) cc_final: 0.4050 (mmt) REVERT: B 565 ILE cc_start: 0.4657 (tt) cc_final: 0.4298 (tt) REVERT: B 728 MET cc_start: 0.2275 (tpp) cc_final: 0.0805 (ttm) REVERT: B 958 MET cc_start: -0.0087 (tpp) cc_final: -0.0424 (mmp) REVERT: C 321 LEU cc_start: 0.3460 (OUTLIER) cc_final: 0.3210 (tm) REVERT: D 144 ARG cc_start: 0.6209 (mmp80) cc_final: 0.4536 (ptp90) REVERT: D 153 MET cc_start: 0.0758 (ppp) cc_final: 0.0091 (ttp) REVERT: E 52 ARG cc_start: 0.4134 (ptp-170) cc_final: 0.3439 (mtp180) REVERT: E 75 MET cc_start: 0.3375 (ppp) cc_final: 0.2579 (mtm) REVERT: H 146 ARG cc_start: -0.0289 (ttm110) cc_final: -0.2299 (ttm110) REVERT: I 1 MET cc_start: 0.1338 (ptm) cc_final: 0.0770 (tpp) REVERT: K 81 MET cc_start: 0.2150 (ttt) cc_final: 0.0486 (mmm) REVERT: M 77 LYS cc_start: 0.5539 (mppt) cc_final: 0.4866 (tptp) REVERT: M 190 ASN cc_start: 0.3213 (OUTLIER) cc_final: 0.2626 (m110) REVERT: M 226 ARG cc_start: 0.4007 (pmm150) cc_final: 0.3707 (ptt-90) REVERT: N 305 MET cc_start: 0.5319 (mpp) cc_final: 0.3965 (mtm) REVERT: N 421 GLN cc_start: 0.4139 (pm20) cc_final: 0.3882 (pm20) REVERT: O 368 ARG cc_start: 0.5367 (tpm170) cc_final: 0.4747 (tpt170) REVERT: P 174 PHE cc_start: 0.3222 (p90) cc_final: 0.2832 (p90) REVERT: P 263 VAL cc_start: 0.0210 (OUTLIER) cc_final: 0.0008 (p) REVERT: P 299 MET cc_start: 0.3386 (ppp) cc_final: 0.3108 (mmt) REVERT: Q 56 VAL cc_start: 0.4061 (t) cc_final: 0.2995 (p) REVERT: Q 66 LYS cc_start: 0.5061 (ttmm) cc_final: 0.4288 (mmtt) outliers start: 97 outliers final: 53 residues processed: 422 average time/residue: 0.2159 time to fit residues: 153.6189 Evaluate side-chains 375 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 316 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 239 SER Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 522 ILE Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 234 optimal weight: 5.9990 chunk 431 optimal weight: 0.0770 chunk 202 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 325 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 189 optimal weight: 0.1980 chunk 30 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 80 HIS A 208 ASN A 520 HIS A 618 HIS A 695 ASN A 815 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS B 519 HIS B 552 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 753 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN C 14 ASN C 161 HIS C 248 GLN D 61 ASN K 52 GLN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN O 143 GLN O 469 ASN P 193 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.222706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193992 restraints weight = 62546.295| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.66 r_work: 0.4119 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2240 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 2.246 39030 Z= 0.429 Angle : 0.845 14.968 52685 Z= 0.430 Chirality : 0.050 0.352 5960 Planarity : 0.006 0.074 6778 Dihedral : 6.430 80.376 5231 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.35 % Favored : 86.38 % Rotamer: Outliers : 3.00 % Allowed : 12.45 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.37 % 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: -3.31 (0.11), residues: 4765 helix: -1.42 (0.12), residues: 1551 sheet: -1.26 (0.23), residues: 471 loop : -2.98 (0.10), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 528 TYR 0.041 0.003 TYR B 279 PHE 0.052 0.003 PHE H 118 TRP 0.024 0.002 TRP A 495 HIS 0.013 0.002 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00446 (39015) covalent geometry : angle 0.84478 (52685) hydrogen bonds : bond 0.04151 ( 1073) hydrogen bonds : angle 5.42699 ( 3063) metal coordination : bond 0.57986 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 418 time to evaluate : 1.204 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: symmetry clash REVERT: A 27 VAL cc_start: 0.5471 (t) cc_final: 0.4008 (m) REVERT: A 141 LEU cc_start: 0.0989 (OUTLIER) cc_final: 0.0567 (mt) REVERT: A 145 LEU cc_start: 0.2202 (OUTLIER) cc_final: 0.1486 (mt) REVERT: A 295 THR cc_start: 0.5670 (t) cc_final: 0.5370 (m) REVERT: A 325 MET cc_start: 0.2243 (ppp) cc_final: 0.0311 (tpp) REVERT: A 416 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.3617 (mt) REVERT: A 551 ILE cc_start: 0.1039 (OUTLIER) cc_final: 0.0451 (tt) REVERT: A 694 MET cc_start: 0.1381 (mmm) cc_final: 0.0379 (ttm) REVERT: A 794 MET cc_start: 0.1496 (mmm) cc_final: 0.0867 (mmp) REVERT: A 946 THR cc_start: 0.2824 (m) cc_final: 0.2314 (p) REVERT: A 1114 VAL cc_start: 0.0206 (OUTLIER) cc_final: -0.0239 (t) REVERT: A 1293 LEU cc_start: 0.2526 (OUTLIER) cc_final: 0.1992 (mm) REVERT: A 1362 MET cc_start: 0.2599 (mmt) cc_final: 0.2046 (mmt) REVERT: B 73 LEU cc_start: 0.3439 (OUTLIER) cc_final: 0.2703 (tp) REVERT: B 123 MET cc_start: 0.3208 (mmm) cc_final: 0.2824 (mtt) REVERT: B 251 ILE cc_start: 0.4516 (OUTLIER) cc_final: 0.4049 (mp) REVERT: B 269 MET cc_start: 0.1818 (tpt) cc_final: 0.0782 (ppp) REVERT: B 317 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.3988 (tt) REVERT: B 320 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6541 (tp) REVERT: B 496 MET cc_start: 0.1401 (tpt) cc_final: 0.1140 (tpt) REVERT: B 597 MET cc_start: 0.5249 (tmm) cc_final: 0.5023 (tpp) REVERT: B 1030 MET cc_start: 0.1528 (OUTLIER) cc_final: -0.0181 (mmt) REVERT: C 112 MET cc_start: 0.6410 (tmm) cc_final: 0.5022 (ttt) REVERT: D 65 TYR cc_start: 0.5971 (t80) cc_final: 0.5653 (t80) REVERT: D 131 MET cc_start: -0.0030 (mmm) cc_final: -0.0285 (mmm) REVERT: E 52 ARG cc_start: 0.4102 (ptp-170) cc_final: 0.3308 (mmm160) REVERT: E 75 MET cc_start: 0.3410 (ppp) cc_final: 0.2138 (mtm) REVERT: E 215 MET cc_start: 0.3073 (mmp) cc_final: 0.2714 (mtt) REVERT: G 207 LEU cc_start: 0.0804 (OUTLIER) cc_final: 0.0520 (tt) REVERT: H 146 ARG cc_start: 0.0725 (ttm110) cc_final: -0.2083 (ttm170) REVERT: K 103 ILE cc_start: 0.3757 (tt) cc_final: 0.3524 (tt) REVERT: M 77 LYS cc_start: 0.5840 (mppt) cc_final: 0.5259 (tptp) REVERT: N 380 MET cc_start: 0.4491 (ttp) cc_final: 0.4197 (tpt) REVERT: O 263 LEU cc_start: 0.0795 (OUTLIER) cc_final: -0.0207 (tm) REVERT: O 359 LEU cc_start: 0.2441 (OUTLIER) cc_final: 0.1984 (tt) REVERT: O 368 ARG cc_start: 0.5264 (tpm170) cc_final: 0.4836 (tpt170) outliers start: 128 outliers final: 54 residues processed: 505 average time/residue: 0.2176 time to fit residues: 182.0692 Evaluate side-chains 403 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 335 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 359 LEU Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Chi-restraints excluded: chain Q residue 43 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 382 optimal weight: 6.9990 chunk 108 optimal weight: 0.2980 chunk 185 optimal weight: 0.0470 chunk 381 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 211 optimal weight: 0.0870 chunk 306 optimal weight: 0.9990 chunk 466 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 540 ASN A 555 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN B 61 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 695 GLN B 753 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** O 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.223688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.195516 restraints weight = 62303.579| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.76 r_work: 0.4136 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2266 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 39030 Z= 0.122 Angle : 0.691 20.282 52685 Z= 0.345 Chirality : 0.045 0.211 5960 Planarity : 0.005 0.072 6778 Dihedral : 5.900 76.434 5229 Min Nonbonded Distance : 1.268 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.08 % Favored : 88.67 % Rotamer: Outliers : 2.51 % Allowed : 14.26 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.37 % 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: -2.90 (0.11), residues: 4765 helix: -0.96 (0.13), residues: 1549 sheet: -1.19 (0.23), residues: 458 loop : -2.77 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 102 TYR 0.025 0.001 TYR P 249 PHE 0.023 0.001 PHE G 148 TRP 0.015 0.001 TRP G 88 HIS 0.014 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00260 (39015) covalent geometry : angle 0.69106 (52685) hydrogen bonds : bond 0.03243 ( 1073) hydrogen bonds : angle 4.95279 ( 3063) metal coordination : bond 0.02590 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 385 time to evaluate : 1.494 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 27 VAL cc_start: 0.5473 (t) cc_final: 0.4019 (m) REVERT: A 58 MET cc_start: 0.4888 (mmt) cc_final: 0.2967 (tpp) REVERT: A 145 LEU cc_start: 0.2271 (mp) cc_final: 0.1713 (mt) REVERT: A 295 THR cc_start: 0.5733 (t) cc_final: 0.5481 (m) REVERT: A 325 MET cc_start: 0.2150 (ppp) cc_final: 0.0321 (tpp) REVERT: A 416 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.4105 (mt) REVERT: A 551 ILE cc_start: 0.1287 (OUTLIER) cc_final: 0.0728 (tt) REVERT: A 599 LYS cc_start: 0.5467 (tptp) cc_final: 0.4294 (mttp) REVERT: A 626 LEU cc_start: 0.2478 (OUTLIER) cc_final: -0.0444 (tp) REVERT: A 694 MET cc_start: 0.1192 (mmm) cc_final: 0.0022 (ttm) REVERT: A 735 TYR cc_start: 0.0990 (m-10) cc_final: 0.0333 (m-80) REVERT: A 946 THR cc_start: 0.3162 (m) cc_final: 0.2661 (p) REVERT: A 1114 VAL cc_start: 0.0322 (OUTLIER) cc_final: -0.0109 (t) REVERT: A 1196 LEU cc_start: -0.2430 (OUTLIER) cc_final: -0.3660 (tp) REVERT: A 1293 LEU cc_start: 0.2491 (OUTLIER) cc_final: 0.1972 (mm) REVERT: A 1362 MET cc_start: 0.2136 (mmt) cc_final: 0.1547 (mmt) REVERT: B 123 MET cc_start: 0.3370 (mmm) cc_final: 0.3084 (mtm) REVERT: B 269 MET cc_start: 0.1868 (tpt) cc_final: 0.0772 (ppp) REVERT: B 289 GLU cc_start: 0.5404 (tm-30) cc_final: 0.4462 (pt0) REVERT: B 317 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.3877 (tt) REVERT: B 320 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.6633 (tp) REVERT: B 439 THR cc_start: 0.5803 (m) cc_final: 0.4499 (t) REVERT: B 470 MET cc_start: 0.4404 (mmp) cc_final: 0.4176 (mmt) REVERT: B 597 MET cc_start: 0.5233 (tmm) cc_final: 0.4999 (tpp) REVERT: B 896 ILE cc_start: 0.4862 (mt) cc_final: 0.4486 (mt) REVERT: D 65 TYR cc_start: 0.6074 (t80) cc_final: 0.5822 (t80) REVERT: D 153 MET cc_start: 0.1100 (ppp) cc_final: 0.0317 (ttp) REVERT: E 28 TYR cc_start: 0.3918 (m-10) cc_final: 0.3691 (m-10) REVERT: E 52 ARG cc_start: 0.3793 (ptp-170) cc_final: 0.3094 (mmm160) REVERT: E 75 MET cc_start: 0.3443 (ppp) cc_final: 0.2320 (mtm) REVERT: E 215 MET cc_start: 0.3936 (mmp) cc_final: 0.3082 (ttp) REVERT: F 103 MET cc_start: 0.3448 (tpt) cc_final: 0.3039 (tpp) REVERT: G 39 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5537 (tp) REVERT: H 146 ARG cc_start: 0.0285 (ttm110) cc_final: -0.2264 (ttm170) REVERT: J 2 ILE cc_start: 0.1125 (OUTLIER) cc_final: -0.0039 (mt) REVERT: K 81 MET cc_start: 0.2840 (ttt) cc_final: 0.2017 (ttp) REVERT: K 103 ILE cc_start: 0.4307 (tt) cc_final: 0.4095 (tt) REVERT: M 77 LYS cc_start: 0.5773 (mppt) cc_final: 0.5314 (tptp) REVERT: M 166 MET cc_start: 0.3832 (tpp) cc_final: 0.3600 (tpt) REVERT: N 380 MET cc_start: 0.4445 (ttp) cc_final: 0.4199 (tpt) REVERT: O 243 MET cc_start: 0.5812 (tpt) cc_final: 0.5610 (tpp) REVERT: O 263 LEU cc_start: 0.1183 (OUTLIER) cc_final: 0.0195 (tm) REVERT: O 343 LYS cc_start: 0.5171 (mttp) cc_final: 0.4962 (mttp) REVERT: O 368 ARG cc_start: 0.5443 (tpm170) cc_final: 0.5051 (tpt170) REVERT: P 299 MET cc_start: 0.3980 (ppp) cc_final: 0.3688 (mmm) outliers start: 107 outliers final: 61 residues processed: 466 average time/residue: 0.1849 time to fit residues: 147.6579 Evaluate side-chains 426 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 498 SER Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 150 optimal weight: 9.9990 chunk 421 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 chunk 464 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 381 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 307 optimal weight: 0.0970 chunk 204 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 648 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.228098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.200651 restraints weight = 64369.476| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.68 r_work: 0.4200 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3002 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 39030 Z= 0.168 Angle : 0.757 17.851 52685 Z= 0.385 Chirality : 0.047 0.356 5960 Planarity : 0.005 0.078 6778 Dihedral : 5.986 75.614 5229 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.78 % Favored : 86.97 % Rotamer: Outliers : 2.77 % Allowed : 14.98 % Favored : 82.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.82 (0.11), residues: 4765 helix: -0.82 (0.13), residues: 1567 sheet: -0.99 (0.23), residues: 480 loop : -2.82 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 561 TYR 0.029 0.002 TYR P 249 PHE 0.039 0.002 PHE H 118 TRP 0.018 0.002 TRP C 115 HIS 0.017 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00355 (39015) covalent geometry : angle 0.75677 (52685) hydrogen bonds : bond 0.03606 ( 1073) hydrogen bonds : angle 5.07587 ( 3063) metal coordination : bond 0.01008 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 439 time to evaluate : 1.293 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 58 MET cc_start: 0.5381 (mmt) cc_final: 0.3155 (tpp) REVERT: A 291 GLU cc_start: 0.4085 (tm-30) cc_final: 0.3751 (tt0) REVERT: A 295 THR cc_start: 0.6589 (t) cc_final: 0.6282 (m) REVERT: A 325 MET cc_start: 0.2337 (ppp) cc_final: 0.0518 (tpp) REVERT: A 416 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.4373 (mt) REVERT: A 420 ILE cc_start: 0.4396 (OUTLIER) cc_final: 0.4180 (tt) REVERT: A 551 ILE cc_start: 0.2192 (OUTLIER) cc_final: 0.1845 (mm) REVERT: A 694 MET cc_start: 0.1900 (mmm) cc_final: 0.1192 (ttm) REVERT: A 946 THR cc_start: 0.3463 (m) cc_final: 0.2779 (p) REVERT: A 1114 VAL cc_start: 0.0580 (OUTLIER) cc_final: 0.0159 (t) REVERT: A 1328 ILE cc_start: 0.2126 (OUTLIER) cc_final: 0.1240 (pt) REVERT: A 1362 MET cc_start: 0.2027 (mmt) cc_final: 0.1759 (mmt) REVERT: B 73 LEU cc_start: 0.3911 (OUTLIER) cc_final: 0.3152 (tp) REVERT: B 75 LYS cc_start: 0.6817 (mtpt) cc_final: 0.6528 (mttt) REVERT: B 251 ILE cc_start: 0.4664 (OUTLIER) cc_final: 0.4221 (mp) REVERT: B 269 MET cc_start: 0.2104 (tpt) cc_final: 0.0864 (ppp) REVERT: B 317 LEU cc_start: 0.4675 (OUTLIER) cc_final: 0.4165 (tt) REVERT: B 320 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6307 (tp) REVERT: B 382 GLN cc_start: 0.6720 (tp40) cc_final: 0.6419 (mp10) REVERT: B 449 MET cc_start: 0.1129 (mmt) cc_final: 0.0822 (tpp) REVERT: B 470 MET cc_start: 0.5418 (mmp) cc_final: 0.4960 (mmt) REVERT: B 944 MET cc_start: 0.0183 (ttt) cc_final: -0.0293 (ptp) REVERT: C 5 VAL cc_start: -0.1595 (OUTLIER) cc_final: -0.1826 (m) REVERT: C 112 MET cc_start: 0.6403 (tmm) cc_final: 0.6043 (ttp) REVERT: E 52 ARG cc_start: 0.4274 (ptp-170) cc_final: 0.3518 (mmm160) REVERT: E 75 MET cc_start: 0.3445 (ppp) cc_final: 0.1731 (mtm) REVERT: E 121 MET cc_start: 0.2105 (mpp) cc_final: 0.1904 (mpp) REVERT: E 215 MET cc_start: 0.4719 (mmp) cc_final: 0.4058 (mtt) REVERT: F 103 MET cc_start: 0.4595 (tpt) cc_final: 0.4158 (tpp) REVERT: G 39 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6170 (tp) REVERT: G 114 MET cc_start: 0.6774 (mmt) cc_final: 0.5642 (ptt) REVERT: H 102 TYR cc_start: 0.2663 (p90) cc_final: 0.0975 (p90) REVERT: H 146 ARG cc_start: 0.0814 (ttm110) cc_final: -0.2107 (ttm170) REVERT: K 103 ILE cc_start: 0.5540 (tt) cc_final: 0.5228 (tt) REVERT: K 125 MET cc_start: 0.4432 (mmp) cc_final: 0.3812 (mmp) REVERT: N 283 LEU cc_start: 0.1711 (OUTLIER) cc_final: 0.1179 (pt) REVERT: O 243 MET cc_start: 0.5893 (tpt) cc_final: 0.5676 (tpp) REVERT: O 263 LEU cc_start: 0.1157 (OUTLIER) cc_final: 0.0049 (tm) REVERT: O 359 LEU cc_start: 0.2535 (OUTLIER) cc_final: 0.1888 (tp) REVERT: O 368 ARG cc_start: 0.5045 (tpm170) cc_final: 0.4545 (mmm160) outliers start: 118 outliers final: 61 residues processed: 522 average time/residue: 0.2086 time to fit residues: 183.3341 Evaluate side-chains 450 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 375 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1328 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain O residue 359 LEU Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 641 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 440 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 321 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 383 optimal weight: 0.0170 chunk 224 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 331 optimal weight: 0.0980 chunk 434 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN B 197 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN C 99 HIS C 323 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.229784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.204259 restraints weight = 64585.047| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.41 r_work: 0.4246 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3217 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 39030 Z= 0.131 Angle : 0.714 15.840 52685 Z= 0.357 Chirality : 0.045 0.201 5960 Planarity : 0.005 0.072 6778 Dihedral : 5.740 72.879 5229 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.72 % Favored : 89.05 % Rotamer: Outliers : 2.39 % Allowed : 16.32 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.28 % 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: -2.59 (0.11), residues: 4765 helix: -0.63 (0.13), residues: 1578 sheet: -0.77 (0.23), residues: 482 loop : -2.70 (0.11), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 780 TYR 0.037 0.001 TYR B1005 PHE 0.031 0.001 PHE H 118 TRP 0.014 0.001 TRP B 819 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00287 (39015) covalent geometry : angle 0.71403 (52685) hydrogen bonds : bond 0.03147 ( 1073) hydrogen bonds : angle 4.89818 ( 3063) metal coordination : bond 0.01272 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 421 time to evaluate : 1.373 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: A 219 MET cc_start: 0.0513 (ttt) cc_final: -0.1171 (mtp) REVERT: A 288 LYS cc_start: 0.6414 (mttt) cc_final: 0.5605 (mmmt) REVERT: A 295 THR cc_start: 0.6662 (t) cc_final: 0.6382 (m) REVERT: A 325 MET cc_start: 0.2399 (ppp) cc_final: 0.0529 (tpp) REVERT: A 416 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.5231 (mt) REVERT: A 450 MET cc_start: 0.4755 (ptt) cc_final: 0.2580 (mmm) REVERT: A 551 ILE cc_start: 0.2929 (OUTLIER) cc_final: 0.2566 (mm) REVERT: A 946 THR cc_start: 0.3611 (m) cc_final: 0.2844 (p) REVERT: A 1114 VAL cc_start: 0.0637 (OUTLIER) cc_final: 0.0187 (t) REVERT: A 1362 MET cc_start: 0.2497 (mmt) cc_final: 0.2064 (mmt) REVERT: A 1397 PHE cc_start: 0.4512 (m-80) cc_final: 0.2783 (m-10) REVERT: B 73 LEU cc_start: 0.3889 (OUTLIER) cc_final: 0.3310 (tp) REVERT: B 75 LYS cc_start: 0.6928 (mtpt) cc_final: 0.6664 (mttt) REVERT: B 251 ILE cc_start: 0.4823 (OUTLIER) cc_final: 0.4435 (mp) REVERT: B 269 MET cc_start: 0.2044 (tpt) cc_final: 0.0714 (ppp) REVERT: B 317 LEU cc_start: 0.4249 (OUTLIER) cc_final: 0.3724 (tt) REVERT: B 320 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.6542 (tp) REVERT: B 356 VAL cc_start: 0.3563 (OUTLIER) cc_final: 0.2262 (p) REVERT: B 358 MET cc_start: 0.0671 (pmm) cc_final: -0.0835 (mmp) REVERT: B 376 ARG cc_start: 0.5331 (tmm-80) cc_final: 0.4663 (mtp180) REVERT: B 470 MET cc_start: 0.5261 (mmp) cc_final: 0.4938 (mmt) REVERT: B 735 MET cc_start: 0.2715 (ttt) cc_final: 0.1496 (mmm) REVERT: D 153 MET cc_start: 0.0652 (ppp) cc_final: 0.0301 (ttt) REVERT: E 28 TYR cc_start: 0.3979 (m-10) cc_final: 0.3707 (m-10) REVERT: E 52 ARG cc_start: 0.4101 (ptp-170) cc_final: 0.3427 (mmm160) REVERT: E 215 MET cc_start: 0.4463 (mmp) cc_final: 0.4236 (mtt) REVERT: G 47 THR cc_start: 0.8156 (t) cc_final: 0.7914 (m) REVERT: G 114 MET cc_start: 0.6839 (mmt) cc_final: 0.5842 (ptt) REVERT: H 146 ARG cc_start: 0.0735 (ttm110) cc_final: -0.2218 (ttm170) REVERT: K 103 ILE cc_start: 0.5855 (tt) cc_final: 0.5568 (tt) REVERT: K 125 MET cc_start: 0.4486 (mmp) cc_final: 0.4132 (mmp) REVERT: M 119 TRP cc_start: 0.4681 (OUTLIER) cc_final: 0.3837 (m100) REVERT: N 421 GLN cc_start: 0.4526 (pm20) cc_final: 0.3848 (pm20) REVERT: O 243 MET cc_start: 0.5978 (tpt) cc_final: 0.5742 (tpp) REVERT: O 263 LEU cc_start: 0.1176 (OUTLIER) cc_final: 0.0161 (tm) REVERT: O 368 ARG cc_start: 0.5098 (tpm170) cc_final: 0.4578 (mmm160) REVERT: P 299 MET cc_start: 0.6742 (mmm) cc_final: 0.6082 (ptt) outliers start: 102 outliers final: 60 residues processed: 492 average time/residue: 0.2140 time to fit residues: 175.7346 Evaluate side-chains 442 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 271 optimal weight: 0.7980 chunk 423 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 276 optimal weight: 0.0060 chunk 113 optimal weight: 7.9990 chunk 330 optimal weight: 0.9980 chunk 304 optimal weight: 5.9990 chunk 121 optimal weight: 0.0770 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 695 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 456 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.233452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.213883 restraints weight = 64299.548| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 1.72 r_work: 0.4309 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3307 moved from start: 0.8266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39030 Z= 0.119 Angle : 0.697 16.022 52685 Z= 0.348 Chirality : 0.045 0.186 5960 Planarity : 0.004 0.067 6778 Dihedral : 5.631 73.584 5229 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.69 % Favored : 88.08 % Rotamer: Outliers : 2.04 % Allowed : 17.23 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.31 % 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: -2.44 (0.12), residues: 4765 helix: -0.39 (0.13), residues: 1548 sheet: -0.77 (0.23), residues: 489 loop : -2.66 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 262 TYR 0.027 0.001 TYR B 842 PHE 0.030 0.001 PHE H 118 TRP 0.042 0.001 TRP A 185 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00258 (39015) covalent geometry : angle 0.69669 (52685) hydrogen bonds : bond 0.03041 ( 1073) hydrogen bonds : angle 4.74642 ( 3063) metal coordination : bond 0.01154 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 404 time to evaluate : 1.365 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 219 MET cc_start: 0.1066 (ttt) cc_final: -0.0826 (mtp) REVERT: A 228 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5396 (tp) REVERT: A 288 LYS cc_start: 0.6522 (mttt) cc_final: 0.5758 (mmmt) REVERT: A 325 MET cc_start: 0.2307 (ppp) cc_final: 0.0475 (tpp) REVERT: A 416 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.5374 (mt) REVERT: A 519 LEU cc_start: 0.5011 (tt) cc_final: 0.4534 (tt) REVERT: A 809 MET cc_start: 0.3897 (tpp) cc_final: 0.3126 (tpp) REVERT: A 946 THR cc_start: 0.3715 (m) cc_final: 0.2940 (p) REVERT: A 1114 VAL cc_start: 0.0597 (OUTLIER) cc_final: 0.0167 (t) REVERT: A 1362 MET cc_start: 0.2339 (mmt) cc_final: 0.2037 (mmt) REVERT: A 1397 PHE cc_start: 0.4694 (m-80) cc_final: 0.2894 (m-10) REVERT: B 73 LEU cc_start: 0.3991 (OUTLIER) cc_final: 0.3252 (tp) REVERT: B 251 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4590 (mp) REVERT: B 269 MET cc_start: 0.2066 (tpt) cc_final: 0.0807 (ppp) REVERT: B 317 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.3785 (tt) REVERT: B 320 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6605 (tp) REVERT: B 358 MET cc_start: 0.0087 (pmm) cc_final: -0.1083 (mmp) REVERT: B 470 MET cc_start: 0.5138 (mmp) cc_final: 0.4755 (mmt) REVERT: B 729 THR cc_start: 0.5938 (m) cc_final: 0.5600 (m) REVERT: B 774 ASN cc_start: 0.6293 (t0) cc_final: 0.5858 (t0) REVERT: C 112 MET cc_start: 0.6902 (tmm) cc_final: 0.6414 (tmm) REVERT: C 124 GLU cc_start: 0.5777 (mm-30) cc_final: 0.3804 (pt0) REVERT: D 153 MET cc_start: 0.0564 (ppp) cc_final: 0.0176 (ttt) REVERT: E 52 ARG cc_start: 0.3828 (ptp-170) cc_final: 0.3202 (mmm160) REVERT: G 83 GLU cc_start: 0.4397 (pp20) cc_final: 0.3821 (pp20) REVERT: G 114 MET cc_start: 0.6842 (mmt) cc_final: 0.5876 (ptt) REVERT: H 102 TYR cc_start: 0.2060 (p90) cc_final: 0.0591 (p90) REVERT: H 146 ARG cc_start: 0.0568 (ttm110) cc_final: -0.2496 (ttm170) REVERT: K 81 MET cc_start: 0.4033 (mmm) cc_final: 0.1720 (tmm) REVERT: K 103 ILE cc_start: 0.5769 (tt) cc_final: 0.5477 (tt) REVERT: K 125 MET cc_start: 0.4562 (mmp) cc_final: 0.4217 (mmp) REVERT: M 119 TRP cc_start: 0.5003 (OUTLIER) cc_final: 0.4197 (m100) REVERT: N 421 GLN cc_start: 0.4587 (pm20) cc_final: 0.4043 (pm20) REVERT: O 263 LEU cc_start: 0.1188 (OUTLIER) cc_final: 0.0083 (tm) REVERT: O 368 ARG cc_start: 0.5049 (tpm170) cc_final: 0.4545 (mmm160) REVERT: O 605 LYS cc_start: 0.1330 (pttp) cc_final: 0.0401 (pttt) REVERT: P 265 LEU cc_start: 0.1283 (OUTLIER) cc_final: 0.1052 (tm) REVERT: P 299 MET cc_start: 0.6592 (mmm) cc_final: 0.6091 (ptt) outliers start: 87 outliers final: 54 residues processed: 468 average time/residue: 0.2190 time to fit residues: 171.6911 Evaluate side-chains 434 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 370 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain G residue 140 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 572 HIS Chi-restraints excluded: chain O residue 585 MET Chi-restraints excluded: chain O residue 589 LEU Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 253 optimal weight: 0.0010 chunk 43 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 465 optimal weight: 0.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 147 GLN A 233 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 805 ASN A 816 GLN A 864 HIS ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1197 GLN A1233 ASN A1318 HIS ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN C 161 HIS C 248 GLN D 27 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN N 284 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS O 143 GLN O 207 HIS O 337 GLN O 572 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.240169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.222134 restraints weight = 66511.742| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 1.50 r_work: 0.4387 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4301 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 1.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.278 39030 Z= 0.345 Angle : 1.228 20.845 52685 Z= 0.635 Chirality : 0.064 0.378 5960 Planarity : 0.010 0.200 6778 Dihedral : 7.765 63.860 5229 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.57 % Favored : 84.09 % Rotamer: Outliers : 2.42 % Allowed : 17.30 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.41 % 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: -3.63 (0.10), residues: 4765 helix: -1.80 (0.11), residues: 1502 sheet: -1.44 (0.22), residues: 493 loop : -3.10 (0.10), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.002 ARG O 238 TYR 0.058 0.004 TYR B1024 PHE 0.062 0.005 PHE G 72 TRP 0.032 0.003 TRP B 442 HIS 0.023 0.003 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00752 (39015) covalent geometry : angle 1.22825 (52685) hydrogen bonds : bond 0.05913 ( 1073) hydrogen bonds : angle 6.73404 ( 3063) metal coordination : bond 0.01015 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 703 time to evaluate : 1.603 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 30 SER cc_start: 0.8362 (t) cc_final: 0.7820 (p) REVERT: A 219 MET cc_start: 0.1370 (ttt) cc_final: 0.0204 (mtp) REVERT: A 288 LYS cc_start: 0.7290 (mttt) cc_final: 0.7004 (mmmt) REVERT: A 325 MET cc_start: 0.4432 (ppp) cc_final: 0.1918 (tpp) REVERT: A 390 ASP cc_start: 0.8070 (p0) cc_final: 0.7740 (p0) REVERT: A 450 MET cc_start: 0.7094 (ptt) cc_final: 0.6812 (ttp) REVERT: A 582 MET cc_start: 0.7837 (ttm) cc_final: 0.7568 (mtt) REVERT: A 664 MET cc_start: 0.6138 (ppp) cc_final: 0.5369 (ttp) REVERT: A 959 ILE cc_start: 0.2760 (OUTLIER) cc_final: 0.2109 (pt) REVERT: A 1415 ILE cc_start: 0.8669 (pt) cc_final: 0.8363 (mt) REVERT: B 61 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.6457 (t-90) REVERT: B 122 ASP cc_start: 0.7572 (m-30) cc_final: 0.7354 (m-30) REVERT: B 251 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4472 (mp) REVERT: B 320 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6129 (tp) REVERT: B 470 MET cc_start: 0.8268 (mmp) cc_final: 0.7977 (mmt) REVERT: B 597 MET cc_start: 0.7153 (tpp) cc_final: 0.6947 (tpt) REVERT: B 607 ARG cc_start: 0.4972 (tpt-90) cc_final: 0.3677 (tpt-90) REVERT: B 717 GLN cc_start: 0.8332 (pt0) cc_final: 0.8090 (pt0) REVERT: B 1061 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7505 (mmt-90) REVERT: B 1084 MET cc_start: 0.8441 (tpt) cc_final: 0.8154 (tmm) REVERT: C 112 MET cc_start: 0.7512 (tmm) cc_final: 0.6652 (ttp) REVERT: D 153 MET cc_start: 0.0874 (ppp) cc_final: 0.0389 (ttt) REVERT: E 52 ARG cc_start: 0.3739 (ptp-170) cc_final: 0.3401 (mmm-85) REVERT: E 75 MET cc_start: 0.2472 (tmm) cc_final: 0.2107 (mtm) REVERT: E 215 MET cc_start: 0.5872 (mtt) cc_final: 0.5669 (ttp) REVERT: F 128 LYS cc_start: 0.7706 (tppt) cc_final: 0.7361 (mmtm) REVERT: F 137 TYR cc_start: 0.8027 (m-80) cc_final: 0.7699 (m-80) REVERT: G 22 THR cc_start: 0.8099 (m) cc_final: 0.7741 (t) REVERT: G 26 ILE cc_start: 0.9163 (mt) cc_final: 0.8895 (mt) REVERT: G 83 GLU cc_start: 0.4752 (pp20) cc_final: 0.4449 (pp20) REVERT: H 102 TYR cc_start: 0.3824 (p90) cc_final: 0.2473 (p90) REVERT: H 132 LEU cc_start: 0.3627 (OUTLIER) cc_final: 0.2801 (mt) REVERT: L 49 LYS cc_start: 0.7365 (mmmt) cc_final: 0.7000 (mttt) REVERT: M 77 LYS cc_start: 0.6978 (mppt) cc_final: 0.6683 (tptt) REVERT: M 119 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.3594 (m-10) REVERT: O 38 GLU cc_start: 0.6689 (pm20) cc_final: 0.6440 (mt-10) REVERT: O 368 ARG cc_start: 0.5561 (tpm170) cc_final: 0.5060 (tpt170) REVERT: P 176 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6714 (t0) REVERT: P 188 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7348 (mp0) outliers start: 103 outliers final: 41 residues processed: 765 average time/residue: 0.2484 time to fit residues: 311.9466 Evaluate side-chains 529 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 481 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain N residue 286 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain O residue 513 ASP Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 215 TYR Chi-restraints excluded: chain P residue 312 PHE Chi-restraints excluded: chain Q residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 469 optimal weight: 0.2980 chunk 181 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 453 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 408 optimal weight: 0.6980 chunk 455 optimal weight: 0.7980 chunk 326 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 HIS A 909 ASN A 913 GLN A 944 ASN B 270 GLN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN O 549 GLN O 572 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.235639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.209357 restraints weight = 67492.085| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.71 r_work: 0.4245 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 1.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39030 Z= 0.163 Angle : 0.861 24.677 52685 Z= 0.430 Chirality : 0.049 0.354 5960 Planarity : 0.006 0.078 6778 Dihedral : 6.614 71.690 5229 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.52 % Favored : 88.25 % Rotamer: Outliers : 1.34 % Allowed : 20.61 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.16 (0.11), residues: 4765 helix: -1.26 (0.12), residues: 1540 sheet: -1.15 (0.24), residues: 481 loop : -2.92 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 241 TYR 0.047 0.002 TYR O 208 PHE 0.027 0.002 PHE A 474 TRP 0.049 0.002 TRP G 130 HIS 0.024 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00363 (39015) covalent geometry : angle 0.86133 (52685) hydrogen bonds : bond 0.03913 ( 1073) hydrogen bonds : angle 5.61478 ( 3063) metal coordination : bond 0.00905 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 569 time to evaluate : 1.812 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 30 SER cc_start: 0.8292 (t) cc_final: 0.7975 (p) REVERT: A 219 MET cc_start: 0.0677 (ttt) cc_final: -0.0280 (mtp) REVERT: A 288 LYS cc_start: 0.7483 (mttt) cc_final: 0.6749 (mmmt) REVERT: A 291 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6692 (mp0) REVERT: A 325 MET cc_start: 0.4495 (ppp) cc_final: 0.2106 (tpp) REVERT: A 390 ASP cc_start: 0.8310 (p0) cc_final: 0.8029 (p0) REVERT: A 419 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 450 MET cc_start: 0.6718 (ptt) cc_final: 0.6361 (ttp) REVERT: A 467 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 591 ASP cc_start: 0.6065 (m-30) cc_final: 0.5585 (p0) REVERT: A 592 ILE cc_start: 0.6710 (mm) cc_final: 0.6389 (mm) REVERT: A 664 MET cc_start: 0.6461 (ppp) cc_final: 0.5975 (ttm) REVERT: A 1304 MET cc_start: 0.2370 (mmt) cc_final: 0.0062 (tpp) REVERT: B 122 ASP cc_start: 0.7842 (m-30) cc_final: 0.7632 (m-30) REVERT: B 155 MET cc_start: 0.7780 (ttm) cc_final: 0.7559 (ttm) REVERT: B 217 GLN cc_start: 0.6121 (tt0) cc_final: 0.5404 (tt0) REVERT: B 232 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: B 251 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.4928 (mp) REVERT: B 269 MET cc_start: 0.2282 (tpt) cc_final: 0.0363 (ppp) REVERT: B 320 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6042 (tp) REVERT: B 358 MET cc_start: 0.2161 (pmm) cc_final: 0.0265 (mmp) REVERT: B 496 MET cc_start: 0.4529 (tpp) cc_final: 0.4219 (tpp) REVERT: B 607 ARG cc_start: 0.4986 (tpt-90) cc_final: 0.4145 (tpt-90) REVERT: B 717 GLN cc_start: 0.8785 (pt0) cc_final: 0.8463 (pt0) REVERT: B 760 MET cc_start: 0.6218 (ppp) cc_final: 0.4099 (ppp) REVERT: B 931 MET cc_start: 0.7592 (mpp) cc_final: 0.5699 (mtm) REVERT: B 1067 ARG cc_start: 0.6685 (mmp80) cc_final: 0.6322 (mtm110) REVERT: C 81 GLU cc_start: 0.7569 (tp30) cc_final: 0.7287 (tp30) REVERT: C 112 MET cc_start: 0.7683 (tmm) cc_final: 0.7345 (ppp) REVERT: C 205 LYS cc_start: 0.8455 (mppt) cc_final: 0.8192 (mtmt) REVERT: D 69 ASN cc_start: 0.5133 (OUTLIER) cc_final: 0.4812 (t0) REVERT: D 153 MET cc_start: 0.0939 (ppp) cc_final: 0.0461 (ttt) REVERT: E 52 ARG cc_start: 0.4566 (ptp-170) cc_final: 0.3752 (mmm160) REVERT: E 75 MET cc_start: 0.3448 (tmm) cc_final: 0.2523 (mtm) REVERT: F 85 MET cc_start: 0.5564 (tpt) cc_final: 0.4879 (tpt) REVERT: G 22 THR cc_start: 0.8146 (m) cc_final: 0.7727 (t) REVERT: G 26 ILE cc_start: 0.9274 (mt) cc_final: 0.8965 (mt) REVERT: G 152 ARG cc_start: 0.5629 (mmm-85) cc_final: 0.5376 (mmm160) REVERT: H 1 MET cc_start: 0.1219 (ppp) cc_final: 0.0524 (ptp) REVERT: H 102 TYR cc_start: 0.3627 (p90) cc_final: 0.2859 (p90) REVERT: L 57 LEU cc_start: 0.8795 (mm) cc_final: 0.8575 (mt) REVERT: M 119 TRP cc_start: 0.4691 (OUTLIER) cc_final: 0.4192 (m-10) REVERT: O 67 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7384 (mmm) REVERT: O 144 MET cc_start: 0.0810 (pmm) cc_final: 0.0075 (pmm) REVERT: O 208 TYR cc_start: 0.4944 (m-80) cc_final: 0.4638 (m-10) REVERT: O 263 LEU cc_start: 0.1398 (OUTLIER) cc_final: 0.0459 (tm) REVERT: O 368 ARG cc_start: 0.5663 (tpm170) cc_final: 0.5004 (mmm160) REVERT: O 605 LYS cc_start: 0.2057 (pttp) cc_final: 0.1684 (pttt) REVERT: P 176 ASN cc_start: 0.7345 (OUTLIER) cc_final: 0.6772 (t0) REVERT: P 188 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7369 (mp0) REVERT: P 241 ARG cc_start: 0.4402 (mmp80) cc_final: 0.3921 (tpt-90) outliers start: 57 outliers final: 33 residues processed: 608 average time/residue: 0.2459 time to fit residues: 246.9861 Evaluate side-chains 507 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 465 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 119 TRP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 197 ASN Chi-restraints excluded: chain P residue 312 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 187 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 131 optimal weight: 0.0980 chunk 16 optimal weight: 7.9990 chunk 90 optimal weight: 0.0980 chunk 386 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 418 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 386 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 944 ASN A1354 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN B 880 HIS B 918 GLN ** B 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 997 ASN C 29 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.233569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.208087 restraints weight = 66806.826| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 2.21 r_work: 0.4257 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 1.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39030 Z= 0.142 Angle : 0.815 28.045 52685 Z= 0.403 Chirality : 0.047 0.222 5960 Planarity : 0.005 0.068 6778 Dihedral : 6.193 71.985 5229 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.18 % Favored : 86.59 % Rotamer: Outliers : 1.31 % Allowed : 21.50 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.02 % Twisted Proline : 0.48 % Twisted General : 0.28 % 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: -2.84 (0.11), residues: 4765 helix: -0.87 (0.13), residues: 1552 sheet: -0.88 (0.24), residues: 496 loop : -2.84 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 47 TYR 0.029 0.002 TYR E 211 PHE 0.073 0.002 PHE A 914 TRP 0.050 0.002 TRP G 130 HIS 0.041 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00314 (39015) covalent geometry : angle 0.81500 (52685) hydrogen bonds : bond 0.03558 ( 1073) hydrogen bonds : angle 5.23469 ( 3063) metal coordination : bond 0.00943 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9500.15 seconds wall clock time: 163 minutes 26.19 seconds (9806.19 seconds total)