Starting phenix.real_space_refine on Tue Sep 15 11:08:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.cif Found real_map, /net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.map" model { file = "/net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6puu_20482/09_2026/6puu_20482.cif" } resolution = 3.7 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Br 4 7.06 5 P 8 5.49 5 S 148 5.16 5 C 24796 2.51 5 N 6768 2.21 5 O 6764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 9586 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PTRANS': 63, 'TRANS': 1245} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1012 Unresolved non-hydrogen angles: 1276 Unresolved non-hydrogen dihedrals: 839 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 18, 'GLU:plan': 44, 'PHE:plan': 9, 'ASP:plan': 29, 'HIS:plan': 11, 'TRP:plan': 5, 'ARG:plan': 20, 'TYR:plan': 5, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 642 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'CV1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 13.07, per 1000 atoms: 0.34 Number of scatterers: 38492 At special positions: 0 Unit cell: (175.062, 175.062, 167.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 4 34.99 Ca 4 19.99 S 148 16.00 P 8 15.00 O 6764 8.00 N 6768 7.00 C 24796 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: 3.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9888 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 36 sheets defined 55.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.734A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.578A pdb=" N GLN A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.670A pdb=" N THR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 removed outlier: 3.632A pdb=" N ASN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.850A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.791A pdb=" N ASP A 453 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.699A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.542A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.713A pdb=" N SER A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.062A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.884A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.537A pdb=" N ALA A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 665 removed outlier: 3.508A pdb=" N ALA A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 697 removed outlier: 3.543A pdb=" N GLU A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.873A pdb=" N ALA A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.690A pdb=" N VAL A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 745 Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.723A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.762A pdb=" N VAL A 781 " --> pdb=" O ARG A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 794 through 819 Processing helix chain 'A' and resid 826 through 849 removed outlier: 3.631A pdb=" N ILE A 832 " --> pdb=" O CYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 866 removed outlier: 4.026A pdb=" N ASP A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.830A pdb=" N ILE A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 909 removed outlier: 3.585A pdb=" N ARG A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.508A pdb=" N ILE A 916 " --> pdb=" O ILE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 3.501A pdb=" N ILE A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 980 removed outlier: 3.527A pdb=" N ARG A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1038 through 1067 removed outlier: 3.553A pdb=" N GLN A1054 " --> pdb=" O TYR A1050 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU A1057 " --> pdb=" O GLN A1053 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS A1058 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP A1060 " --> pdb=" O GLN A1056 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A1065 " --> pdb=" O GLN A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1077 removed outlier: 3.880A pdb=" N ILE A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 removed outlier: 4.202A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1092 " --> pdb=" O SER A1088 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1099 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 4.033A pdb=" N ALA A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A1134 " --> pdb=" O GLU A1130 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1165 Processing helix chain 'A' and resid 1279 through 1282 removed outlier: 3.854A pdb=" N ASP A1282 " --> pdb=" O GLU A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1282' Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 4.333A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1292 " --> pdb=" O MET A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1288 through 1292' Processing helix chain 'A' and resid 1397 through 1403 Processing helix chain 'A' and resid 1409 through 1418 removed outlier: 4.021A pdb=" N SER A1413 " --> pdb=" O GLU A1409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A1414 " --> pdb=" O HIS A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1463 removed outlier: 4.087A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1496 removed outlier: 3.729A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.734A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.578A pdb=" N GLN B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.670A pdb=" N THR B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 347 removed outlier: 3.632A pdb=" N ASN B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.850A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.791A pdb=" N ASP B 453 " --> pdb=" O HIS B 449 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 456 " --> pdb=" O TRP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.699A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 removed outlier: 3.542A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.712A pdb=" N SER B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 557 through 570 removed outlier: 4.063A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.883A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.537A pdb=" N ALA B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.508A pdb=" N ALA B 651 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 665 " --> pdb=" O GLU B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 697 removed outlier: 3.542A pdb=" N GLU B 673 " --> pdb=" O THR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 707 removed outlier: 3.873A pdb=" N ALA B 701 " --> pdb=" O ASP B 697 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 707 " --> pdb=" O LYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 724 Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.690A pdb=" N VAL B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 745 Processing helix chain 'B' and resid 752 through 762 removed outlier: 3.724A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.763A pdb=" N VAL B 781 " --> pdb=" O ARG B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 794 through 819 Processing helix chain 'B' and resid 826 through 849 removed outlier: 3.631A pdb=" N ILE B 832 " --> pdb=" O CYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 866 removed outlier: 4.026A pdb=" N ASP B 866 " --> pdb=" O LEU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 888 removed outlier: 3.830A pdb=" N ILE B 888 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 909 removed outlier: 3.585A pdb=" N ARG B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.508A pdb=" N ILE B 916 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 3.501A pdb=" N ILE B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 980 removed outlier: 3.527A pdb=" N ARG B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 980 " --> pdb=" O LEU B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1037 Processing helix chain 'B' and resid 1038 through 1067 removed outlier: 3.553A pdb=" N GLN B1054 " --> pdb=" O TYR B1050 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B1057 " --> pdb=" O GLN B1053 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS B1058 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP B1060 " --> pdb=" O GLN B1056 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B1065 " --> pdb=" O GLN B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1077 removed outlier: 3.880A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1099 removed outlier: 4.202A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B1092 " --> pdb=" O SER B1088 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B1097 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B1098 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B1099 " --> pdb=" O LYS B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 4.033A pdb=" N ALA B1120 " --> pdb=" O ASN B1116 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B1134 " --> pdb=" O GLU B1130 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1165 Processing helix chain 'B' and resid 1279 through 1282 removed outlier: 3.854A pdb=" N ASP B1282 " --> pdb=" O GLU B1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1279 through 1282' Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 4.334A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B1292 " --> pdb=" O MET B1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1288 through 1292' Processing helix chain 'B' and resid 1397 through 1403 Processing helix chain 'B' and resid 1409 through 1418 removed outlier: 4.020A pdb=" N SER B1413 " --> pdb=" O GLU B1409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B1414 " --> pdb=" O HIS B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1463 removed outlier: 4.087A pdb=" N ARG B1459 " --> pdb=" O VAL B1455 " (cutoff:3.500A) Processing helix chain 'B' and resid 1487 through 1496 removed outlier: 3.729A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.734A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 202 Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.578A pdb=" N GLN C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.671A pdb=" N THR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 304 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 347 removed outlier: 3.632A pdb=" N ASN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.850A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.792A pdb=" N ASP C 453 " --> pdb=" O HIS C 449 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.700A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 507 removed outlier: 3.542A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 525 Processing helix chain 'C' and resid 530 through 542 removed outlier: 3.713A pdb=" N SER C 534 " --> pdb=" O CYS C 530 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 557 through 570 removed outlier: 4.062A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.884A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.537A pdb=" N ALA C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 665 removed outlier: 3.508A pdb=" N ALA C 651 " --> pdb=" O ASP C 647 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 665 " --> pdb=" O GLU C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 697 removed outlier: 3.543A pdb=" N GLU C 673 " --> pdb=" O THR C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 707 removed outlier: 3.873A pdb=" N ALA C 701 " --> pdb=" O ASP C 697 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 707 " --> pdb=" O LYS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.690A pdb=" N VAL C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.723A pdb=" N VAL C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 781 removed outlier: 3.762A pdb=" N VAL C 781 " --> pdb=" O ARG C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 Processing helix chain 'C' and resid 794 through 819 Processing helix chain 'C' and resid 826 through 849 removed outlier: 3.632A pdb=" N ILE C 832 " --> pdb=" O CYS C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 866 removed outlier: 4.027A pdb=" N ASP C 866 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 888 removed outlier: 3.830A pdb=" N ILE C 888 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 909 removed outlier: 3.585A pdb=" N ARG C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.508A pdb=" N ILE C 916 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 3.501A pdb=" N ILE C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 980 removed outlier: 3.527A pdb=" N ARG C 968 " --> pdb=" O ASP C 964 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 980 " --> pdb=" O LEU C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1037 Processing helix chain 'C' and resid 1038 through 1067 removed outlier: 3.553A pdb=" N GLN C1054 " --> pdb=" O TYR C1050 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU C1057 " --> pdb=" O GLN C1053 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS C1058 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP C1060 " --> pdb=" O GLN C1056 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN C1061 " --> pdb=" O GLU C1057 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C1065 " --> pdb=" O GLN C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1077 removed outlier: 3.881A pdb=" N ILE C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1099 removed outlier: 4.202A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C1092 " --> pdb=" O SER C1088 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C1097 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C1098 " --> pdb=" O ILE C1094 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C1099 " --> pdb=" O LYS C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 4.033A pdb=" N ALA C1120 " --> pdb=" O ASN C1116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C1134 " --> pdb=" O GLU C1130 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1165 Processing helix chain 'C' and resid 1279 through 1282 removed outlier: 3.853A pdb=" N ASP C1282 " --> pdb=" O GLU C1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1279 through 1282' Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 4.333A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C1292 " --> pdb=" O MET C1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1288 through 1292' Processing helix chain 'C' and resid 1397 through 1403 Processing helix chain 'C' and resid 1409 through 1418 removed outlier: 4.021A pdb=" N SER C1413 " --> pdb=" O GLU C1409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C1414 " --> pdb=" O HIS C1410 " (cutoff:3.500A) Processing helix chain 'C' and resid 1455 through 1463 removed outlier: 4.087A pdb=" N ARG C1459 " --> pdb=" O VAL C1455 " (cutoff:3.500A) Processing helix chain 'C' and resid 1487 through 1496 removed outlier: 3.729A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.734A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.577A pdb=" N GLN D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.670A pdb=" N THR D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.632A pdb=" N ASN D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.850A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 449 through 462 removed outlier: 3.791A pdb=" N ASP D 453 " --> pdb=" O HIS D 449 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 456 " --> pdb=" O TRP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.699A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 removed outlier: 3.542A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 525 Processing helix chain 'D' and resid 530 through 542 removed outlier: 3.713A pdb=" N SER D 534 " --> pdb=" O CYS D 530 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 557 through 570 removed outlier: 4.062A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.884A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 642 removed outlier: 3.537A pdb=" N ALA D 638 " --> pdb=" O ARG D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 665 removed outlier: 3.508A pdb=" N ALA D 651 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 697 removed outlier: 3.543A pdb=" N GLU D 673 " --> pdb=" O THR D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 707 removed outlier: 3.873A pdb=" N ALA D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN D 702 " --> pdb=" O GLU D 698 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG D 707 " --> pdb=" O LYS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.690A pdb=" N VAL D 730 " --> pdb=" O ASP D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 745 Processing helix chain 'D' and resid 752 through 762 removed outlier: 3.724A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 781 removed outlier: 3.762A pdb=" N VAL D 781 " --> pdb=" O ARG D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'D' and resid 826 through 849 removed outlier: 3.631A pdb=" N ILE D 832 " --> pdb=" O CYS D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 866 removed outlier: 4.027A pdb=" N ASP D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 888 removed outlier: 3.830A pdb=" N ILE D 888 " --> pdb=" O THR D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 909 removed outlier: 3.585A pdb=" N ARG D 909 " --> pdb=" O LEU D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 916 removed outlier: 3.508A pdb=" N ILE D 916 " --> pdb=" O ILE D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 3.502A pdb=" N ILE D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 980 removed outlier: 3.526A pdb=" N ARG D 968 " --> pdb=" O ASP D 964 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY D 980 " --> pdb=" O LEU D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1037 Processing helix chain 'D' and resid 1038 through 1067 removed outlier: 3.553A pdb=" N GLN D1054 " --> pdb=" O TYR D1050 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU D1057 " --> pdb=" O GLN D1053 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS D1058 " --> pdb=" O GLN D1054 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP D1060 " --> pdb=" O GLN D1056 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN D1061 " --> pdb=" O GLU D1057 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D1065 " --> pdb=" O GLN D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1077 removed outlier: 3.880A pdb=" N ILE D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 4.202A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D1092 " --> pdb=" O SER D1088 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D1097 " --> pdb=" O PHE D1093 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D1098 " --> pdb=" O ILE D1094 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D1099 " --> pdb=" O LYS D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 4.033A pdb=" N ALA D1120 " --> pdb=" O ASN D1116 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN D1134 " --> pdb=" O GLU D1130 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1165 Processing helix chain 'D' and resid 1279 through 1282 removed outlier: 3.854A pdb=" N ASP D1282 " --> pdb=" O GLU D1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1279 through 1282' Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 4.333A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D1292 " --> pdb=" O MET D1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1288 through 1292' Processing helix chain 'D' and resid 1397 through 1403 Processing helix chain 'D' and resid 1409 through 1418 removed outlier: 4.021A pdb=" N SER D1413 " --> pdb=" O GLU D1409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D1414 " --> pdb=" O HIS D1410 " (cutoff:3.500A) Processing helix chain 'D' and resid 1455 through 1463 removed outlier: 4.088A pdb=" N ARG D1459 " --> pdb=" O VAL D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1487 through 1496 removed outlier: 3.728A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 7.645A pdb=" N TYR A 264 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 131 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 238 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 285 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY A 240 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 287 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 242 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 205 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 241 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR A 243 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU A 170 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 328 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER A 172 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316 removed outlier: 3.657A pdb=" N VAL A 319 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.863A pdb=" N THR A 715 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1275 through 1277 removed outlier: 3.603A pdb=" N ARG A1336 " --> pdb=" O TYR A1276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1303 through 1305 removed outlier: 3.567A pdb=" N ARG A1310 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A1308 " --> pdb=" O ASP A1305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA8, first strand: chain 'A' and resid 1343 through 1348 removed outlier: 6.205A pdb=" N GLY A1343 " --> pdb=" O TRP A1439 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A1441 " --> pdb=" O GLY A1343 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN A1345 " --> pdb=" O GLU A1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A1443 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A1347 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL A1445 " --> pdb=" O THR A1347 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A1440 " --> pdb=" O TYR A1428 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR A1428 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A1442 " --> pdb=" O LYS A1426 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A1426 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA A1444 " --> pdb=" O VAL A1424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1343 through 1348 removed outlier: 6.205A pdb=" N GLY A1343 " --> pdb=" O TRP A1439 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A1441 " --> pdb=" O GLY A1343 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN A1345 " --> pdb=" O GLU A1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A1443 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A1347 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL A1445 " --> pdb=" O THR A1347 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET A1351 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A1449 " --> pdb=" O MET A1351 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A1353 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AB2, first strand: chain 'B' and resid 263 through 264 removed outlier: 7.645A pdb=" N TYR B 264 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 131 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR B 238 " --> pdb=" O HIS B 283 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE B 285 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY B 240 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL B 287 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA B 242 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 205 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 241 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR B 207 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR B 243 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 170 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 328 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER B 172 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 316 removed outlier: 3.657A pdb=" N VAL B 319 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.863A pdb=" N THR B 715 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1275 through 1277 removed outlier: 3.603A pdb=" N ARG B1336 " --> pdb=" O TYR B1276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1303 through 1305 removed outlier: 3.567A pdb=" N ARG B1310 " --> pdb=" O VAL B1303 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B1308 " --> pdb=" O ASP B1305 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1319 through 1320 Processing sheet with id=AB8, first strand: chain 'B' and resid 1343 through 1348 removed outlier: 6.205A pdb=" N GLY B1343 " --> pdb=" O TRP B1439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B1441 " --> pdb=" O GLY B1343 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN B1345 " --> pdb=" O GLU B1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B1443 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL B1445 " --> pdb=" O THR B1347 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE B1440 " --> pdb=" O TYR B1428 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B1428 " --> pdb=" O ILE B1440 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B1442 " --> pdb=" O LYS B1426 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B1426 " --> pdb=" O THR B1442 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B1444 " --> pdb=" O VAL B1424 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1343 through 1348 removed outlier: 6.205A pdb=" N GLY B1343 " --> pdb=" O TRP B1439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU B1441 " --> pdb=" O GLY B1343 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN B1345 " --> pdb=" O GLU B1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B1443 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL B1445 " --> pdb=" O THR B1347 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N MET B1351 " --> pdb=" O VAL B1447 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE B1449 " --> pdb=" O MET B1351 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B1353 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AC2, first strand: chain 'C' and resid 263 through 264 removed outlier: 7.645A pdb=" N TYR C 264 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL C 131 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 238 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE C 285 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY C 240 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL C 287 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 242 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 205 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL C 241 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR C 207 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR C 243 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU C 170 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL C 328 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER C 172 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 313 through 316 removed outlier: 3.657A pdb=" N VAL C 319 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.862A pdb=" N THR C 715 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1275 through 1277 removed outlier: 3.603A pdb=" N ARG C1336 " --> pdb=" O TYR C1276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1303 through 1305 removed outlier: 3.567A pdb=" N ARG C1310 " --> pdb=" O VAL C1303 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C1308 " --> pdb=" O ASP C1305 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AC8, first strand: chain 'C' and resid 1343 through 1348 removed outlier: 6.206A pdb=" N GLY C1343 " --> pdb=" O TRP C1439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C1441 " --> pdb=" O GLY C1343 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN C1345 " --> pdb=" O GLU C1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C1443 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR C1347 " --> pdb=" O VAL C1443 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL C1445 " --> pdb=" O THR C1347 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE C1440 " --> pdb=" O TYR C1428 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR C1428 " --> pdb=" O ILE C1440 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C1442 " --> pdb=" O LYS C1426 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS C1426 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C1444 " --> pdb=" O VAL C1424 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1343 through 1348 removed outlier: 6.206A pdb=" N GLY C1343 " --> pdb=" O TRP C1439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C1441 " --> pdb=" O GLY C1343 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN C1345 " --> pdb=" O GLU C1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C1443 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR C1347 " --> pdb=" O VAL C1443 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL C1445 " --> pdb=" O THR C1347 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET C1351 " --> pdb=" O VAL C1447 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE C1449 " --> pdb=" O MET C1351 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C1353 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 68 through 71 Processing sheet with id=AD2, first strand: chain 'D' and resid 263 through 264 removed outlier: 7.645A pdb=" N TYR D 264 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL D 131 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR D 238 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE D 285 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY D 240 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL D 287 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA D 242 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE D 205 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL D 241 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR D 207 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR D 243 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU D 170 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL D 328 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER D 172 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 313 through 316 removed outlier: 3.657A pdb=" N VAL D 319 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 708 through 709 removed outlier: 3.863A pdb=" N THR D 715 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 3.603A pdb=" N ARG D1336 " --> pdb=" O TYR D1276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1303 through 1305 removed outlier: 3.567A pdb=" N ARG D1310 " --> pdb=" O VAL D1303 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D1308 " --> pdb=" O ASP D1305 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1319 through 1320 Processing sheet with id=AD8, first strand: chain 'D' and resid 1343 through 1348 removed outlier: 6.204A pdb=" N GLY D1343 " --> pdb=" O TRP D1439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU D1441 " --> pdb=" O GLY D1343 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN D1345 " --> pdb=" O GLU D1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL D1443 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N VAL D1445 " --> pdb=" O THR D1347 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE D1440 " --> pdb=" O TYR D1428 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR D1428 " --> pdb=" O ILE D1440 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR D1442 " --> pdb=" O LYS D1426 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS D1426 " --> pdb=" O THR D1442 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA D1444 " --> pdb=" O VAL D1424 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1343 through 1348 removed outlier: 6.204A pdb=" N GLY D1343 " --> pdb=" O TRP D1439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU D1441 " --> pdb=" O GLY D1343 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN D1345 " --> pdb=" O GLU D1441 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL D1443 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N VAL D1445 " --> pdb=" O THR D1347 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET D1351 " --> pdb=" O VAL D1447 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE D1449 " --> pdb=" O MET D1351 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D1353 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) 1973 hydrogen bonds defined for protein. 5763 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: 9.19 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12487 1.34 - 1.47: 9497 1.47 - 1.60: 17200 1.60 - 1.73: 16 1.73 - 1.85: 224 Bond restraints: 39424 Sorted by residual: bond pdb=" N ASN A1453 " pdb=" CA ASN A1453 " ideal model delta sigma weight residual 1.458 1.489 -0.031 6.30e-03 2.52e+04 2.36e+01 bond pdb=" N ASN B1453 " pdb=" CA ASN B1453 " ideal model delta sigma weight residual 1.458 1.489 -0.031 6.30e-03 2.52e+04 2.36e+01 bond pdb=" N ASN C1453 " pdb=" CA ASN C1453 " ideal model delta sigma weight residual 1.458 1.489 -0.031 6.30e-03 2.52e+04 2.36e+01 bond pdb=" N ASN D1453 " pdb=" CA ASN D1453 " ideal model delta sigma weight residual 1.458 1.489 -0.031 6.30e-03 2.52e+04 2.36e+01 bond pdb=" N ILE D 771 " pdb=" CA ILE D 771 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 ... (remaining 39419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 51668 2.14 - 4.28: 1930 4.28 - 6.41: 203 6.41 - 8.55: 79 8.55 - 10.69: 32 Bond angle restraints: 53912 Sorted by residual: angle pdb=" C HIS C1465 " pdb=" N ALA C1466 " pdb=" CA ALA C1466 " ideal model delta sigma weight residual 120.82 129.16 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" C HIS B1465 " pdb=" N ALA B1466 " pdb=" CA ALA B1466 " ideal model delta sigma weight residual 120.82 129.16 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" C HIS A1465 " pdb=" N ALA A1466 " pdb=" CA ALA A1466 " ideal model delta sigma weight residual 120.82 129.16 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" C HIS D1465 " pdb=" N ALA D1466 " pdb=" CA ALA D1466 " ideal model delta sigma weight residual 120.82 129.13 -8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" C GLY A 85 " pdb=" N LYS A 86 " pdb=" CA LYS A 86 " ideal model delta sigma weight residual 120.38 127.89 -7.51 1.37e+00 5.33e-01 3.01e+01 ... (remaining 53907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 21532 21.51 - 43.02: 1420 43.02 - 64.53: 160 64.53 - 86.04: 44 86.04 - 107.55: 8 Dihedral angle restraints: 23164 sinusoidal: 7932 harmonic: 15232 Sorted by residual: dihedral pdb=" CA ILE D1038 " pdb=" C ILE D1038 " pdb=" N LEU D1039 " pdb=" CA LEU D1039 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ILE A1038 " pdb=" C ILE A1038 " pdb=" N LEU A1039 " pdb=" CA LEU A1039 " ideal model delta harmonic sigma weight residual 180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE C1038 " pdb=" C ILE C1038 " pdb=" N LEU C1039 " pdb=" CA LEU C1039 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 23161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4551 0.048 - 0.097: 1246 0.097 - 0.145: 392 0.145 - 0.194: 75 0.194 - 0.242: 20 Chirality restraints: 6284 Sorted by residual: chirality pdb=" CB ILE D 771 " pdb=" CA ILE D 771 " pdb=" CG1 ILE D 771 " pdb=" CG2 ILE D 771 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE A 771 " pdb=" CA ILE A 771 " pdb=" CG1 ILE A 771 " pdb=" CG2 ILE A 771 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE C 771 " pdb=" CA ILE C 771 " pdb=" CG1 ILE C 771 " pdb=" CG2 ILE C 771 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 6281 not shown) Planarity restraints: 6892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CV1 C1601 " -0.020 2.00e-02 2.50e+03 9.76e-02 3.09e+02 pdb=" C1D CV1 C1601 " -0.267 2.00e-02 2.50e+03 pdb=" C2 CV1 C1601 " 0.125 2.00e-02 2.50e+03 pdb=" C4 CV1 C1601 " 0.025 2.00e-02 2.50e+03 pdb=" C5 CV1 C1601 " 0.024 2.00e-02 2.50e+03 pdb=" C6 CV1 C1601 " 0.054 2.00e-02 2.50e+03 pdb=" C8 CV1 C1601 " -0.028 2.00e-02 2.50e+03 pdb=" N1 CV1 C1601 " -0.020 2.00e-02 2.50e+03 pdb=" N3 CV1 C1601 " 0.053 2.00e-02 2.50e+03 pdb=" N6 CV1 C1601 " 0.150 2.00e-02 2.50e+03 pdb=" N7 CV1 C1601 " -0.010 2.00e-02 2.50e+03 pdb=" N9 CV1 C1601 " -0.009 2.00e-02 2.50e+03 pdb="BR1 CV1 C1601 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CV1 B1601 " 0.020 2.00e-02 2.50e+03 9.76e-02 3.09e+02 pdb=" C1D CV1 B1601 " 0.267 2.00e-02 2.50e+03 pdb=" C2 CV1 B1601 " -0.125 2.00e-02 2.50e+03 pdb=" C4 CV1 B1601 " -0.024 2.00e-02 2.50e+03 pdb=" C5 CV1 B1601 " -0.024 2.00e-02 2.50e+03 pdb=" C6 CV1 B1601 " -0.054 2.00e-02 2.50e+03 pdb=" C8 CV1 B1601 " 0.028 2.00e-02 2.50e+03 pdb=" N1 CV1 B1601 " 0.020 2.00e-02 2.50e+03 pdb=" N3 CV1 B1601 " -0.053 2.00e-02 2.50e+03 pdb=" N6 CV1 B1601 " -0.150 2.00e-02 2.50e+03 pdb=" N7 CV1 B1601 " 0.010 2.00e-02 2.50e+03 pdb=" N9 CV1 B1601 " 0.009 2.00e-02 2.50e+03 pdb="BR1 CV1 B1601 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CV1 A1601 " 0.021 2.00e-02 2.50e+03 9.75e-02 3.09e+02 pdb=" C1D CV1 A1601 " 0.267 2.00e-02 2.50e+03 pdb=" C2 CV1 A1601 " -0.125 2.00e-02 2.50e+03 pdb=" C4 CV1 A1601 " -0.024 2.00e-02 2.50e+03 pdb=" C5 CV1 A1601 " -0.024 2.00e-02 2.50e+03 pdb=" C6 CV1 A1601 " -0.054 2.00e-02 2.50e+03 pdb=" C8 CV1 A1601 " 0.028 2.00e-02 2.50e+03 pdb=" N1 CV1 A1601 " 0.020 2.00e-02 2.50e+03 pdb=" N3 CV1 A1601 " -0.053 2.00e-02 2.50e+03 pdb=" N6 CV1 A1601 " -0.149 2.00e-02 2.50e+03 pdb=" N7 CV1 A1601 " 0.010 2.00e-02 2.50e+03 pdb=" N9 CV1 A1601 " 0.009 2.00e-02 2.50e+03 pdb="BR1 CV1 A1601 " 0.075 2.00e-02 2.50e+03 ... (remaining 6889 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 11746 2.82 - 3.34: 35761 3.34 - 3.86: 61816 3.86 - 4.38: 64802 4.38 - 4.90: 113850 Nonbonded interactions: 287975 Sorted by model distance: nonbonded pdb=" O TRP C 944 " pdb=" OG SER C 947 " model vdw 2.302 3.040 nonbonded pdb=" O TRP B 944 " pdb=" OG SER B 947 " model vdw 2.302 3.040 nonbonded pdb=" O TRP D 944 " pdb=" OG SER D 947 " model vdw 2.302 3.040 nonbonded pdb=" O TRP A 944 " pdb=" OG SER A 947 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU C 843 " pdb=" OH TYR C 863 " model vdw 2.311 3.040 ... (remaining 287970 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 39.110 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.006 0.065 39424 Z= 0.306 Angle : 0.960 10.691 53912 Z= 0.563 Chirality : 0.051 0.242 6284 Planarity : 0.008 0.098 6892 Dihedral : 14.474 107.548 13276 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.36 % Favored : 94.41 % Rotamer: Outliers : 1.13 % Allowed : 8.05 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.09), residues: 5204 helix: -1.94 (0.07), residues: 2624 sheet: -1.91 (0.20), residues: 488 loop : -2.79 (0.11), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 774 TYR 0.021 0.002 TYR D 682 PHE 0.034 0.002 PHE C 948 TRP 0.020 0.002 TRP C 462 HIS 0.004 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.31 (39424) covalent geometry : angle 0.96009 / 0.56 (53912) hydrogen bonds : bond 0.16486 / 11.11 ( 1973) hydrogen bonds : angle 5.90923 / 4.20 ( 5763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.8346 (mtm) cc_final: 0.8056 (mtm) REVERT: A 420 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7735 (mmp80) REVERT: B 215 MET cc_start: 0.8379 (mtm) cc_final: 0.8099 (mtm) REVERT: B 420 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7744 (mmp80) REVERT: C 215 MET cc_start: 0.8329 (mtm) cc_final: 0.8048 (mtm) REVERT: C 420 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7777 (mmp80) REVERT: D 215 MET cc_start: 0.8330 (mtm) cc_final: 0.8040 (mtm) REVERT: D 420 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7735 (mmp80) outliers start: 40 outliers final: 13 residues processed: 282 average time/residue: 0.1974 time to fit residues: 97.6536 Evaluate side-chains 214 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 ARG Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 40.0000 chunk 497 optimal weight: 0.0070 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 0.4980 chunk 223 optimal weight: 8.9990 chunk 516 optimal weight: 7.9990 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS A 380 GLN A 407 GLN A 414 GLN A 451 ASN A 495 ASN A 525 ASN A 684 HIS A 719 GLN A 802 ASN A1437 ASN A1488 HIS B 283 HIS B 380 GLN B 407 GLN B 414 GLN B 451 ASN B 495 ASN B 525 ASN B 684 HIS B 719 GLN B 802 ASN B1437 ASN B1488 HIS C 283 HIS C 380 GLN C 407 GLN C 414 GLN C 451 ASN C 495 ASN C 525 ASN C 684 HIS C 719 GLN C 802 ASN C1437 ASN C1488 HIS D 283 HIS D 380 GLN D 407 GLN D 414 GLN D 451 ASN D 495 ASN D 525 ASN D 684 HIS D 719 GLN D 802 ASN D1437 ASN D1488 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.050282 restraints weight = 174291.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051842 restraints weight = 88246.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052828 restraints weight = 59332.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.053436 restraints weight = 46817.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053742 restraints weight = 40654.924| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39424 Z= 0.130 Angle : 0.590 12.366 53912 Z= 0.303 Chirality : 0.039 0.156 6284 Planarity : 0.005 0.055 6892 Dihedral : 6.232 102.705 5602 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 1.70 % Allowed : 11.71 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5204 helix: 0.22 (0.10), residues: 2700 sheet: -1.58 (0.20), residues: 488 loop : -2.28 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1474 TYR 0.012 0.001 TYR A 682 PHE 0.013 0.001 PHE C 690 TRP 0.009 0.001 TRP A 868 HIS 0.005 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (39424) covalent geometry : angle 0.59023 / 0.30 (53912) hydrogen bonds : bond 0.04978 / 3.46 ( 1973) hydrogen bonds : angle 4.12331 / 2.92 ( 5763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 1.242 Fit side-chains REVERT: A 122 MET cc_start: 0.7855 (mpp) cc_final: 0.7486 (mpp) REVERT: A 747 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9050 (pp) REVERT: B 122 MET cc_start: 0.7920 (mpp) cc_final: 0.7581 (mpp) REVERT: B 747 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9050 (pp) REVERT: C 122 MET cc_start: 0.7805 (mpp) cc_final: 0.7467 (mpp) REVERT: C 747 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9071 (pp) REVERT: D 122 MET cc_start: 0.7843 (mpp) cc_final: 0.7502 (mpp) REVERT: D 747 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9103 (pp) outliers start: 60 outliers final: 44 residues processed: 249 average time/residue: 0.2007 time to fit residues: 90.2749 Evaluate side-chains 227 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 93 TYR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 52 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 487 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 467 optimal weight: 9.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 495 ASN C 495 ASN D 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049774 restraints weight = 173455.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051277 restraints weight = 90288.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.052214 restraints weight = 61719.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052797 restraints weight = 49171.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053164 restraints weight = 42972.875| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39424 Z= 0.138 Angle : 0.554 6.576 53912 Z= 0.285 Chirality : 0.039 0.143 6284 Planarity : 0.004 0.042 6892 Dihedral : 5.755 98.440 5584 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 2.47 % Allowed : 13.27 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 5204 helix: 1.07 (0.10), residues: 2680 sheet: -1.48 (0.22), residues: 416 loop : -1.98 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1474 TYR 0.012 0.001 TYR B 682 PHE 0.021 0.001 PHE D 939 TRP 0.007 0.001 TRP B 743 HIS 0.004 0.001 HIS A1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (39424) covalent geometry : angle 0.55401 / 0.28 (53912) hydrogen bonds : bond 0.04605 / 3.22 ( 1973) hydrogen bonds : angle 3.91244 / 2.77 ( 5763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 1.574 Fit side-chains REVERT: A 420 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7463 (mmp80) REVERT: A 680 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 684 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.7792 (m90) REVERT: A 747 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9079 (pp) REVERT: B 215 MET cc_start: 0.8450 (mpp) cc_final: 0.7843 (ptp) REVERT: B 420 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7466 (mmp80) REVERT: B 747 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9060 (pp) REVERT: B 1158 MET cc_start: 0.9214 (mmm) cc_final: 0.9004 (mmp) REVERT: C 420 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7433 (mmp80) REVERT: C 680 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7822 (tm-30) REVERT: C 684 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7784 (m90) REVERT: C 747 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9063 (pp) REVERT: D 420 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7460 (mmp80) REVERT: D 747 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9066 (pp) outliers start: 87 outliers final: 48 residues processed: 259 average time/residue: 0.1972 time to fit residues: 89.6459 Evaluate side-chains 244 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 93 TYR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 468 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 516 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 495 ASN C 495 ASN D 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.070319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048355 restraints weight = 173543.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049838 restraints weight = 89556.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050770 restraints weight = 60812.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051365 restraints weight = 48309.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051721 restraints weight = 41984.392| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 39424 Z= 0.220 Angle : 0.613 7.851 53912 Z= 0.315 Chirality : 0.041 0.151 6284 Planarity : 0.005 0.068 6892 Dihedral : 5.674 91.740 5584 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.95 % Allowed : 15.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 5204 helix: 1.32 (0.10), residues: 2684 sheet: -1.63 (0.21), residues: 448 loop : -1.92 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 411 TYR 0.015 0.001 TYR A 682 PHE 0.014 0.001 PHE A 617 TRP 0.011 0.001 TRP D 743 HIS 0.006 0.001 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (39424) covalent geometry : angle 0.61291 / 0.31 (53912) hydrogen bonds : bond 0.05241 / 3.68 ( 1973) hydrogen bonds : angle 4.10783 / 2.91 ( 5763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 186 time to evaluate : 1.537 Fit side-chains REVERT: A 420 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7387 (mmp80) REVERT: A 747 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9052 (pp) REVERT: B 215 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: B 420 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7387 (mmp80) REVERT: B 747 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9050 (pp) REVERT: C 420 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7383 (mmp80) REVERT: C 747 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9053 (pp) REVERT: D 420 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7406 (mmp80) REVERT: D 747 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9056 (pp) outliers start: 104 outliers final: 72 residues processed: 267 average time/residue: 0.1796 time to fit residues: 86.1691 Evaluate side-chains 263 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 186 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 93 TYR Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 124 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 355 optimal weight: 8.9990 chunk 496 optimal weight: 20.0000 chunk 480 optimal weight: 8.9990 chunk 108 optimal weight: 0.0270 chunk 315 optimal weight: 0.9990 chunk 428 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 495 ASN C 495 ASN D 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.071007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049159 restraints weight = 172840.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050700 restraints weight = 86580.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051686 restraints weight = 57845.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052302 restraints weight = 45397.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052688 restraints weight = 39220.879| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39424 Z= 0.152 Angle : 0.549 6.858 53912 Z= 0.280 Chirality : 0.039 0.132 6284 Planarity : 0.004 0.038 6892 Dihedral : 5.433 85.626 5584 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 3.03 % Allowed : 16.30 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 5204 helix: 1.63 (0.10), residues: 2668 sheet: -1.45 (0.21), residues: 420 loop : -1.87 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 411 TYR 0.012 0.001 TYR A 682 PHE 0.026 0.001 PHE C 939 TRP 0.009 0.001 TRP D 743 HIS 0.004 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (39424) covalent geometry : angle 0.54894 / 0.28 (53912) hydrogen bonds : bond 0.04559 / 3.20 ( 1973) hydrogen bonds : angle 3.87751 / 2.75 ( 5763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 193 time to evaluate : 1.508 Fit side-chains REVERT: A 420 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7703 (mmt-90) REVERT: A 747 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9058 (pp) REVERT: B 215 MET cc_start: 0.8507 (mpp) cc_final: 0.7927 (ptp) REVERT: B 420 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7518 (mmp80) REVERT: B 747 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9055 (pp) REVERT: C 420 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7697 (mmt-90) REVERT: C 747 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9058 (pp) REVERT: D 420 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7545 (mmp80) REVERT: D 747 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9062 (pp) outliers start: 107 outliers final: 65 residues processed: 276 average time/residue: 0.1850 time to fit residues: 91.5877 Evaluate side-chains 253 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 124 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 517 optimal weight: 50.0000 chunk 515 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 452 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 386 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 455 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 495 ASN B1042 ASN C 495 ASN C1042 ASN D 495 ASN D1042 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048184 restraints weight = 173753.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049674 restraints weight = 88708.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050634 restraints weight = 59935.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051233 restraints weight = 47256.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051598 restraints weight = 40974.721| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 39424 Z= 0.200 Angle : 0.587 6.826 53912 Z= 0.299 Chirality : 0.040 0.132 6284 Planarity : 0.004 0.038 6892 Dihedral : 5.475 85.064 5584 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 3.34 % Allowed : 17.01 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 5204 helix: 1.58 (0.10), residues: 2692 sheet: -1.44 (0.21), residues: 428 loop : -1.91 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 623 TYR 0.013 0.001 TYR A 682 PHE 0.013 0.001 PHE A 617 TRP 0.011 0.001 TRP A 743 HIS 0.004 0.001 HIS C1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (39424) covalent geometry : angle 0.58735 / 0.30 (53912) hydrogen bonds : bond 0.05078 / 3.57 ( 1973) hydrogen bonds : angle 4.03531 / 2.86 ( 5763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 183 time to evaluate : 1.551 Fit side-chains REVERT: A 215 MET cc_start: 0.8423 (mpp) cc_final: 0.8087 (ptp) REVERT: A 420 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7803 (mmt-90) REVERT: A 747 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9037 (pp) REVERT: B 420 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7766 (mmt-90) REVERT: B 747 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9036 (pp) REVERT: B 1158 MET cc_start: 0.9271 (mmm) cc_final: 0.9062 (mmp) REVERT: C 215 MET cc_start: 0.8435 (mpp) cc_final: 0.8074 (ptp) REVERT: C 420 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7768 (mmt-90) REVERT: C 747 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9037 (pp) REVERT: D 215 MET cc_start: 0.8404 (mpp) cc_final: 0.8069 (ptp) REVERT: D 420 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7799 (mmt-90) REVERT: D 747 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9038 (pp) outliers start: 118 outliers final: 86 residues processed: 282 average time/residue: 0.1866 time to fit residues: 94.5209 Evaluate side-chains 273 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 183 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1429 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1429 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 484 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN A1042 ASN B 495 ASN C 495 ASN D 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.069974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047774 restraints weight = 176235.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049257 restraints weight = 90767.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.050207 restraints weight = 61772.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050814 restraints weight = 48858.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051174 restraints weight = 42443.146| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 39424 Z= 0.207 Angle : 0.591 7.628 53912 Z= 0.301 Chirality : 0.041 0.144 6284 Planarity : 0.004 0.038 6892 Dihedral : 5.485 82.971 5584 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 5204 helix: 1.59 (0.10), residues: 2692 sheet: -1.41 (0.22), residues: 388 loop : -1.88 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 464 TYR 0.015 0.001 TYR A 682 PHE 0.012 0.001 PHE B 617 TRP 0.011 0.001 TRP A 743 HIS 0.004 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (39424) covalent geometry : angle 0.59128 / 0.30 (53912) hydrogen bonds : bond 0.05085 / 3.57 ( 1973) hydrogen bonds : angle 4.07339 / 2.88 ( 5763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 183 time to evaluate : 1.124 Fit side-chains REVERT: A 122 MET cc_start: 0.8270 (mpp) cc_final: 0.7788 (mpp) REVERT: A 215 MET cc_start: 0.8416 (mpp) cc_final: 0.8077 (ptp) REVERT: A 420 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7780 (mmt-90) REVERT: A 747 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9043 (pp) REVERT: B 122 MET cc_start: 0.8252 (mpp) cc_final: 0.7780 (mpp) REVERT: B 420 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7802 (mmt-90) REVERT: B 747 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9040 (pp) REVERT: C 122 MET cc_start: 0.8268 (mpp) cc_final: 0.7785 (mpp) REVERT: C 215 MET cc_start: 0.8432 (mpp) cc_final: 0.8096 (ptp) REVERT: C 420 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7790 (mmt-90) REVERT: C 747 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9038 (pp) REVERT: D 122 MET cc_start: 0.8268 (mpp) cc_final: 0.7788 (mpp) REVERT: D 215 MET cc_start: 0.8414 (mpp) cc_final: 0.8078 (ptp) REVERT: D 420 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7792 (mmt-90) REVERT: D 747 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9039 (pp) outliers start: 127 outliers final: 88 residues processed: 290 average time/residue: 0.1903 time to fit residues: 99.3094 Evaluate side-chains 273 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 181 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 37 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 133 optimal weight: 0.0770 chunk 369 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 chunk 395 optimal weight: 30.0000 chunk 253 optimal weight: 0.0060 chunk 408 optimal weight: 10.0000 chunk 21 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 474 optimal weight: 6.9990 overall best weight: 1.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN A 560 HIS A 684 HIS B 495 ASN B 560 HIS C 495 ASN C 560 HIS C 684 HIS D 495 ASN D 560 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.050086 restraints weight = 172174.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051657 restraints weight = 85839.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052659 restraints weight = 57103.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053283 restraints weight = 44630.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053668 restraints weight = 38484.881| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 39424 Z= 0.104 Angle : 0.530 8.525 53912 Z= 0.265 Chirality : 0.039 0.145 6284 Planarity : 0.004 0.040 6892 Dihedral : 5.183 78.808 5584 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 2.64 % Allowed : 18.06 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 5204 helix: 1.89 (0.10), residues: 2672 sheet: -1.21 (0.23), residues: 380 loop : -1.75 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.012 0.001 TYR C1074 PHE 0.015 0.001 PHE B 948 TRP 0.011 0.001 TRP B 712 HIS 0.004 0.001 HIS C 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (39424) covalent geometry : angle 0.53013 / 0.26 (53912) hydrogen bonds : bond 0.03921 / 2.74 ( 1973) hydrogen bonds : angle 3.68641 / 2.61 ( 5763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 197 time to evaluate : 1.543 Fit side-chains REVERT: A 122 MET cc_start: 0.8308 (mpp) cc_final: 0.7831 (mpp) REVERT: A 215 MET cc_start: 0.8336 (mpp) cc_final: 0.8120 (ptp) REVERT: A 420 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7743 (mmt-90) REVERT: A 747 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9050 (pp) REVERT: B 122 MET cc_start: 0.8331 (mpp) cc_final: 0.7878 (mpp) REVERT: B 420 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7746 (mmt-90) REVERT: B 747 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9042 (pp) REVERT: C 122 MET cc_start: 0.8288 (mpp) cc_final: 0.7801 (mpp) REVERT: C 215 MET cc_start: 0.8373 (mpp) cc_final: 0.8170 (ptp) REVERT: C 420 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7564 (mmp80) REVERT: C 747 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9048 (pp) REVERT: D 122 MET cc_start: 0.8287 (mpp) cc_final: 0.7798 (mpp) REVERT: D 215 MET cc_start: 0.8344 (mpp) cc_final: 0.8139 (ptp) REVERT: D 420 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7720 (mmt-90) REVERT: D 747 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9050 (pp) outliers start: 93 outliers final: 71 residues processed: 276 average time/residue: 0.1825 time to fit residues: 90.2668 Evaluate side-chains 267 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 355 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 437 optimal weight: 0.6980 chunk 350 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 364 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 495 ASN C 495 ASN D 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048966 restraints weight = 174012.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050494 restraints weight = 89764.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051476 restraints weight = 60734.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052087 restraints weight = 47875.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052407 restraints weight = 41537.052| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 39424 Z= 0.158 Angle : 0.581 13.832 53912 Z= 0.286 Chirality : 0.041 0.378 6284 Planarity : 0.004 0.038 6892 Dihedral : 5.206 79.406 5584 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 2.55 % Allowed : 18.71 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 5204 helix: 1.87 (0.10), residues: 2700 sheet: -1.16 (0.23), residues: 380 loop : -1.75 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.012 0.001 TYR D 682 PHE 0.013 0.001 PHE B 948 TRP 0.010 0.001 TRP A 743 HIS 0.004 0.001 HIS D1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (39424) covalent geometry : angle 0.58133 / 0.29 (53912) hydrogen bonds : bond 0.04383 / 3.08 ( 1973) hydrogen bonds : angle 3.81521 / 2.70 ( 5763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 190 time to evaluate : 1.467 Fit side-chains REVERT: A 215 MET cc_start: 0.8331 (mpp) cc_final: 0.8071 (ptp) REVERT: A 420 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7755 (mmt-90) REVERT: A 747 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9028 (pp) REVERT: B 420 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7753 (mmt-90) REVERT: B 747 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9022 (pp) REVERT: C 215 MET cc_start: 0.8357 (mpp) cc_final: 0.8076 (ptp) REVERT: C 420 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7754 (mmt-90) REVERT: C 747 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9024 (pp) REVERT: D 215 MET cc_start: 0.8337 (mpp) cc_final: 0.8080 (ptp) REVERT: D 420 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7750 (mmt-90) REVERT: D 747 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9022 (pp) outliers start: 90 outliers final: 72 residues processed: 265 average time/residue: 0.1867 time to fit residues: 89.2967 Evaluate side-chains 268 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1137 GLN Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1137 GLN Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1137 GLN Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 79 optimal weight: 6.9990 chunk 495 optimal weight: 0.0980 chunk 263 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 424 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 239 optimal weight: 0.0030 chunk 343 optimal weight: 1.9990 chunk 179 optimal weight: 0.0270 chunk 478 optimal weight: 40.0000 overall best weight: 0.1046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 ASN A 495 ASN B 495 ASN C 451 ASN C 495 ASN D 451 ASN D 495 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.073377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052106 restraints weight = 171838.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053721 restraints weight = 84485.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054771 restraints weight = 55803.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055418 restraints weight = 43393.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055809 restraints weight = 37288.254| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39424 Z= 0.098 Angle : 0.548 10.216 53912 Z= 0.266 Chirality : 0.038 0.163 6284 Planarity : 0.004 0.041 6892 Dihedral : 4.899 75.428 5584 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 2.10 % Allowed : 18.74 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 5204 helix: 2.01 (0.10), residues: 2704 sheet: -1.01 (0.23), residues: 384 loop : -1.60 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 442 TYR 0.015 0.001 TYR C1074 PHE 0.016 0.001 PHE B 948 TRP 0.015 0.001 TRP B 516 HIS 0.003 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (39424) covalent geometry : angle 0.54754 / 0.27 (53912) hydrogen bonds : bond 0.03122 / 2.16 ( 1973) hydrogen bonds : angle 3.48678 / 2.47 ( 5763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 217 time to evaluate : 1.471 Fit side-chains REVERT: A 122 MET cc_start: 0.8136 (mpp) cc_final: 0.7765 (mpp) REVERT: A 215 MET cc_start: 0.8118 (mpp) cc_final: 0.7832 (ptp) REVERT: A 420 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7638 (mmt-90) REVERT: A 747 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9053 (pp) REVERT: A 1125 GLU cc_start: 0.9019 (tt0) cc_final: 0.8714 (tm-30) REVERT: A 1371 MET cc_start: 0.8494 (mmt) cc_final: 0.8283 (tpp) REVERT: B 122 MET cc_start: 0.8145 (mpp) cc_final: 0.7774 (mpp) REVERT: B 420 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7645 (mmt-90) REVERT: B 747 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9041 (pp) REVERT: B 1125 GLU cc_start: 0.9014 (tt0) cc_final: 0.8713 (tm-30) REVERT: B 1371 MET cc_start: 0.8505 (mmt) cc_final: 0.8299 (tpp) REVERT: C 122 MET cc_start: 0.8136 (mpp) cc_final: 0.7759 (mpp) REVERT: C 215 MET cc_start: 0.8231 (mpp) cc_final: 0.7925 (ptp) REVERT: C 420 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7646 (mmt-90) REVERT: C 747 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9050 (pp) REVERT: C 1125 GLU cc_start: 0.9018 (tt0) cc_final: 0.8710 (tm-30) REVERT: D 122 MET cc_start: 0.8134 (mpp) cc_final: 0.7748 (mpp) REVERT: D 215 MET cc_start: 0.8137 (mpp) cc_final: 0.7850 (ptp) REVERT: D 420 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7643 (mmt-90) REVERT: D 747 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9051 (pp) REVERT: D 1125 GLU cc_start: 0.9014 (tt0) cc_final: 0.8705 (tm-30) REVERT: D 1371 MET cc_start: 0.8501 (mmt) cc_final: 0.8290 (tpp) outliers start: 74 outliers final: 47 residues processed: 276 average time/residue: 0.1886 time to fit residues: 92.2251 Evaluate side-chains 247 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 841 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 841 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain B residue 1059 THR Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 841 CYS Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1035 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 841 CYS Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 948 PHE Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain D residue 1059 THR Chi-restraints excluded: chain D residue 1270 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 486 optimal weight: 0.0270 chunk 410 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 287 optimal weight: 0.0170 chunk 383 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 387 optimal weight: 50.0000 chunk 137 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 393 optimal weight: 4.9990 overall best weight: 2.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 495 ASN C 495 ASN D 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.071663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049822 restraints weight = 172017.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051385 restraints weight = 86304.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052383 restraints weight = 57685.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053014 restraints weight = 45237.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053400 restraints weight = 39042.774| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39424 Z= 0.136 Angle : 0.572 11.766 53912 Z= 0.277 Chirality : 0.040 0.230 6284 Planarity : 0.004 0.039 6892 Dihedral : 4.934 77.332 5584 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 1.73 % Allowed : 19.19 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 5204 helix: 2.09 (0.10), residues: 2704 sheet: -0.99 (0.23), residues: 380 loop : -1.63 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 623 TYR 0.009 0.001 TYR D 682 PHE 0.014 0.001 PHE D1048 TRP 0.008 0.001 TRP B 743 HIS 0.004 0.001 HIS B1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (39424) covalent geometry : angle 0.57163 / 0.28 (53912) hydrogen bonds : bond 0.03961 / 2.79 ( 1973) hydrogen bonds : angle 3.62700 / 2.57 ( 5763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6419.61 seconds wall clock time: 111 minutes 22.01 seconds (6682.01 seconds total)