Starting phenix.real_space_refine on Sat Jul 27 23:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sri_40732/07_2024/8sri_40732_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sri_40732/07_2024/8sri_40732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sri_40732/07_2024/8sri_40732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sri_40732/07_2024/8sri_40732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sri_40732/07_2024/8sri_40732_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sri_40732/07_2024/8sri_40732_neut.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.180 sd= 1.657 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 16 5.21 5 S 216 5.16 5 C 26216 2.51 5 N 6968 2.21 5 O 7204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 40636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 9999 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 866 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 711 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 39, 'TYR:plan': 2, 'ASN:plan1': 12, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 551 Chain: "B" Number of atoms: 9999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 9999 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 866 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 711 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 39, 'TYR:plan': 2, 'ASN:plan1': 12, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 551 Chain: "C" Number of atoms: 9999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 9999 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 866 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 711 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 39, 'TYR:plan': 2, 'ASN:plan1': 12, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 551 Chain: "D" Number of atoms: 9999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 9999 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 866 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 711 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 39, 'TYR:plan': 2, 'ASN:plan1': 12, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 551 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 188 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 132 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 21.39, per 1000 atoms: 0.53 Number of scatterers: 40636 At special positions: 0 Unit cell: (142.898, 142.898, 185.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 216 16.00 P 16 15.00 Mg 16 11.99 O 7204 8.00 N 6968 7.00 C 26216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 14.81 Conformation dependent library (CDL) restraints added in 8.0 seconds 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10296 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 36 sheets defined 59.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.517A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.548A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.541A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.670A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.785A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.540A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.553A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.515A pdb=" N PHE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.527A pdb=" N GLU A 475 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 476' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.609A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.669A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.538A pdb=" N ARG A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.511A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.907A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.659A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 removed outlier: 3.545A pdb=" N GLY A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.652A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.704A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.615A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.513A pdb=" N ILE A 703 " --> pdb=" O ASN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.521A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 788 through 800 removed outlier: 3.868A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 removed outlier: 3.824A pdb=" N ARG A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 857 Processing helix chain 'A' and resid 859 through 866 removed outlier: 4.136A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 3.509A pdb=" N LYS A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.506A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.934A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 982 removed outlier: 3.697A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix removed outlier: 3.915A pdb=" N ILE A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.859A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.700A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 3.955A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1169 Processing helix chain 'A' and resid 1203 through 1208 Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1403 through 1413 Processing helix chain 'A' and resid 1478 through 1491 Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.517A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.548A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 287 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.542A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.670A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.785A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.540A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.552A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.516A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.528A pdb=" N GLU B 475 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.608A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.669A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.538A pdb=" N ARG B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.511A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.907A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.659A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 removed outlier: 3.545A pdb=" N GLY B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.652A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.704A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.615A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.512A pdb=" N ILE B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.521A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 788 through 800 removed outlier: 3.868A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.823A pdb=" N ARG B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 857 Processing helix chain 'B' and resid 859 through 866 removed outlier: 4.135A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 3.509A pdb=" N LYS B 896 " --> pdb=" O ASN B 892 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.507A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.934A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 982 removed outlier: 3.697A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix removed outlier: 3.915A pdb=" N ILE B 982 " --> pdb=" O PRO B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.859A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.701A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 3.955A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1169 Processing helix chain 'B' and resid 1203 through 1208 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1403 through 1413 Processing helix chain 'B' and resid 1478 through 1491 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.517A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.548A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 287 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.541A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.670A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.785A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 407 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.539A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.553A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.516A pdb=" N PHE C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.527A pdb=" N GLU C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.609A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.669A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 3.539A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.511A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.907A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.659A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 removed outlier: 3.545A pdb=" N GLY C 623 " --> pdb=" O PHE C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.652A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.704A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.615A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.513A pdb=" N ILE C 703 " --> pdb=" O ASN C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.521A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 788 through 800 removed outlier: 3.869A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 removed outlier: 3.824A pdb=" N ARG C 805 " --> pdb=" O ALA C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 857 Processing helix chain 'C' and resid 859 through 866 removed outlier: 4.135A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.662A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 3.509A pdb=" N LYS C 896 " --> pdb=" O ASN C 892 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 3.507A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.934A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 982 removed outlier: 3.697A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix removed outlier: 3.916A pdb=" N ILE C 982 " --> pdb=" O PRO C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1010 through 1012 No H-bonds generated for 'chain 'C' and resid 1010 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.858A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.700A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 3.955A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1169 Processing helix chain 'C' and resid 1203 through 1208 Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1378 through 1391 Processing helix chain 'C' and resid 1403 through 1413 Processing helix chain 'C' and resid 1478 through 1491 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.517A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 200 removed outlier: 3.548A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 287 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.541A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.670A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.785A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.540A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.553A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.515A pdb=" N PHE D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.527A pdb=" N GLU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 476' Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.609A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.669A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 removed outlier: 3.538A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.510A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.908A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.660A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 removed outlier: 3.545A pdb=" N GLY D 623 " --> pdb=" O PHE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.652A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.704A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.615A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.512A pdb=" N ILE D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.521A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 788 through 800 removed outlier: 3.869A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 removed outlier: 3.823A pdb=" N ARG D 805 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 857 Processing helix chain 'D' and resid 859 through 866 removed outlier: 4.136A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 3.509A pdb=" N LYS D 896 " --> pdb=" O ASN D 892 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 3.506A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.934A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 982 removed outlier: 3.697A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix removed outlier: 3.915A pdb=" N ILE D 982 " --> pdb=" O PRO D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.860A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.701A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D1066 " --> pdb=" O GLU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 3.955A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1169 Processing helix chain 'D' and resid 1203 through 1208 Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1403 through 1413 Processing helix chain 'D' and resid 1478 through 1491 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 236 removed outlier: 3.797A pdb=" N LYS A 232 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A 234 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG A 100 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU A 236 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 316 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A 292 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 318 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 294 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1200 removed outlier: 3.540A pdb=" N GLY B1416 " --> pdb=" O LEU A1200 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 17.797A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.941A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.647A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.941A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.797A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 5.886A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR A1253 " --> pdb=" O ARG A1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA8, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 4.437A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.647A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.597A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.798A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.798A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.597A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1353 through 1360 current: chain 'A' and resid 1416 through 1423 removed outlier: 3.536A pdb=" N GLY A1416 " --> pdb=" O LEU D1200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB3, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB5, first strand: chain 'B' and resid 231 through 236 removed outlier: 3.797A pdb=" N LYS B 232 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY B 234 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 100 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU B 236 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 316 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR B 292 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL B 318 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 294 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1199 through 1200 removed outlier: 3.531A pdb=" N GLY C1416 " --> pdb=" O LEU B1200 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 17.798A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.646A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.798A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 5.886A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG B1317 " --> pdb=" O VAL B1251 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR B1253 " --> pdb=" O ARG B1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AC1, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 4.437A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC3, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC4, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC5, first strand: chain 'C' and resid 231 through 236 removed outlier: 3.797A pdb=" N LYS C 232 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY C 234 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG C 100 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU C 236 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL C 316 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR C 292 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 318 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 294 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1199 through 1200 removed outlier: 3.537A pdb=" N GLY D1416 " --> pdb=" O LEU C1200 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 17.798A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.647A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.798A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 5.886A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG C1317 " --> pdb=" O VAL C1251 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR C1253 " --> pdb=" O ARG C1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AD1, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 4.436A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD3, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD5, first strand: chain 'D' and resid 231 through 236 removed outlier: 3.796A pdb=" N LYS D 232 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY D 234 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG D 100 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU D 236 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL D 316 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 292 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL D 318 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 294 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 5.886A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR D1253 " --> pdb=" O ARG D1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD8, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 4.437A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2360 hydrogen bonds defined for protein. 6936 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: 20.50 Time building geometry restraints manager: 16.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6444 1.31 - 1.44: 11300 1.44 - 1.57: 23428 1.57 - 1.69: 52 1.69 - 1.82: 384 Bond restraints: 41608 Sorted by residual: bond pdb=" C PRO B 245 " pdb=" O PRO B 245 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C PRO A 245 " pdb=" O PRO A 245 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C PRO D 245 " pdb=" O PRO D 245 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C PRO C 245 " pdb=" O PRO C 245 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C4 APR B1706 " pdb=" C5 APR B1706 " ideal model delta sigma weight residual 1.386 1.468 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 41603 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.86: 899 104.86 - 112.83: 20315 112.83 - 120.81: 21081 120.81 - 128.79: 14181 128.79 - 136.76: 436 Bond angle restraints: 56912 Sorted by residual: angle pdb=" N PRO D 244 " pdb=" CA PRO D 244 " pdb=" C PRO D 244 " ideal model delta sigma weight residual 110.70 124.21 -13.51 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N PRO A 244 " pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 110.70 124.21 -13.51 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N PRO C 244 " pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 110.70 124.21 -13.51 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N PRO B 244 " pdb=" CA PRO B 244 " pdb=" C PRO B 244 " ideal model delta sigma weight residual 110.70 124.21 -13.51 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N VAL C 844 " pdb=" CA VAL C 844 " pdb=" C VAL C 844 " ideal model delta sigma weight residual 110.53 103.29 7.24 9.40e-01 1.13e+00 5.93e+01 ... (remaining 56907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 23057 17.95 - 35.91: 1727 35.91 - 53.86: 296 53.86 - 71.82: 80 71.82 - 89.77: 24 Dihedral angle restraints: 25184 sinusoidal: 9288 harmonic: 15896 Sorted by residual: dihedral pdb=" C GLU B1096 " pdb=" N GLU B1096 " pdb=" CA GLU B1096 " pdb=" CB GLU B1096 " ideal model delta harmonic sigma weight residual -122.60 -135.14 12.54 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" C GLU C1096 " pdb=" N GLU C1096 " pdb=" CA GLU C1096 " pdb=" CB GLU C1096 " ideal model delta harmonic sigma weight residual -122.60 -135.14 12.54 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" C GLU D1096 " pdb=" N GLU D1096 " pdb=" CA GLU D1096 " pdb=" CB GLU D1096 " ideal model delta harmonic sigma weight residual -122.60 -135.14 12.54 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 25181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5123 0.083 - 0.167: 1174 0.167 - 0.250: 288 0.250 - 0.333: 59 0.333 - 0.417: 24 Chirality restraints: 6668 Sorted by residual: chirality pdb=" CA VAL C1239 " pdb=" N VAL C1239 " pdb=" C VAL C1239 " pdb=" CB VAL C1239 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA VAL A1239 " pdb=" N VAL A1239 " pdb=" C VAL A1239 " pdb=" CB VAL A1239 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA VAL D1239 " pdb=" N VAL D1239 " pdb=" C VAL D1239 " pdb=" CB VAL D1239 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 6665 not shown) Planarity restraints: 7196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 572 " -0.040 2.00e-02 2.50e+03 3.42e-02 2.05e+01 pdb=" CG PHE D 572 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE D 572 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 572 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 572 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 572 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE D 572 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 572 " 0.040 2.00e-02 2.50e+03 3.39e-02 2.01e+01 pdb=" CG PHE A 572 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE A 572 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 572 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 572 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 572 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 572 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 572 " 0.039 2.00e-02 2.50e+03 3.39e-02 2.01e+01 pdb=" CG PHE B 572 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE B 572 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 572 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 572 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 572 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE B 572 " -0.005 2.00e-02 2.50e+03 ... (remaining 7193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 424 2.63 - 3.20: 32188 3.20 - 3.77: 63200 3.77 - 4.33: 82164 4.33 - 4.90: 142300 Nonbonded interactions: 320276 Sorted by model distance: nonbonded pdb="MG MG A1703 " pdb=" O2B APR A1707 " model vdw 2.066 2.170 nonbonded pdb="MG MG B1703 " pdb=" O2B APR B1706 " model vdw 2.066 2.170 nonbonded pdb="MG MG D6005 " pdb=" O2B APR D6009 " model vdw 2.066 2.170 nonbonded pdb="MG MG C1703 " pdb=" O2B APR C1707 " model vdw 2.066 2.170 nonbonded pdb=" OE2 GLU C1390 " pdb="MG MG C1703 " model vdw 2.098 2.170 ... (remaining 320271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1494 or resid 1704 through 1705 or resid 1708)) \ selection = (chain 'B' and (resid 52 through 1494 or resid 1704 through 1705 or resid 1708)) \ selection = (chain 'C' and (resid 52 through 1494 or resid 1704 through 1705 or resid 1708)) \ selection = (chain 'D' and (resid 52 through 1494 or resid 6004 through 6005 or resid 6008)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 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: 0.040 Extract box with map and model: 1.750 Check model and map are aligned: 0.280 Set scattering table: 0.370 Process input model: 112.370 Find NCS groups from input model: 3.770 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 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 : 0.011 0.083 41608 Z= 0.758 Angle : 1.652 14.577 56912 Z= 1.049 Chirality : 0.081 0.417 6668 Planarity : 0.011 0.068 7196 Dihedral : 13.475 89.771 14876 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.33 % Allowed : 0.92 % Favored : 98.75 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.11), residues: 5432 helix: 1.14 (0.09), residues: 2960 sheet: -0.85 (0.23), residues: 408 loop : -0.44 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 726 HIS 0.011 0.002 HIS C 903 PHE 0.073 0.006 PHE D 572 TYR 0.046 0.005 TYR D 332 ARG 0.025 0.001 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 866 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.5600 (pt) cc_final: 0.5286 (mp) REVERT: A 138 TYR cc_start: 0.5274 (p90) cc_final: 0.5014 (p90) REVERT: A 240 HIS cc_start: 0.5638 (m-70) cc_final: 0.5378 (t70) REVERT: A 243 ASP cc_start: 0.5111 (m-30) cc_final: 0.4859 (t0) REVERT: A 456 MET cc_start: 0.4517 (mmm) cc_final: 0.4111 (tpp) REVERT: A 553 ARG cc_start: 0.5463 (mmm-85) cc_final: 0.5078 (mtt-85) REVERT: A 559 ARG cc_start: 0.4910 (ttt180) cc_final: 0.4684 (ttt90) REVERT: A 638 GLU cc_start: 0.5680 (mt-10) cc_final: 0.5290 (pt0) REVERT: A 658 MET cc_start: 0.6117 (mtm) cc_final: 0.5362 (mtm) REVERT: A 675 GLU cc_start: 0.6687 (tp30) cc_final: 0.6359 (tp30) REVERT: A 683 MET cc_start: 0.6964 (tpt) cc_final: 0.6174 (mmm) REVERT: A 690 SER cc_start: 0.6928 (p) cc_final: 0.6559 (m) REVERT: A 725 ASP cc_start: 0.7004 (m-30) cc_final: 0.6672 (m-30) REVERT: A 922 LYS cc_start: 0.6460 (pttm) cc_final: 0.6067 (mttm) REVERT: A 930 MET cc_start: 0.5568 (mtt) cc_final: 0.4897 (tpp) REVERT: A 932 MET cc_start: 0.6420 (mmt) cc_final: 0.6106 (mpp) REVERT: A 934 MET cc_start: 0.5819 (mmt) cc_final: 0.5122 (mmt) REVERT: A 936 LYS cc_start: 0.5245 (mttt) cc_final: 0.4664 (ptmt) REVERT: A 990 ASP cc_start: 0.6394 (m-30) cc_final: 0.5949 (m-30) REVERT: A 1050 ASP cc_start: 0.5975 (m-30) cc_final: 0.5660 (m-30) REVERT: A 1055 GLN cc_start: 0.6358 (mt0) cc_final: 0.5585 (tt0) REVERT: A 1084 MET cc_start: 0.5301 (mmt) cc_final: 0.4747 (mmp) REVERT: A 1126 ARG cc_start: 0.5059 (ttp-110) cc_final: 0.4641 (tmm160) REVERT: A 1128 ARG cc_start: 0.5536 (ttp80) cc_final: 0.5221 (ttm-80) REVERT: A 1162 PHE cc_start: 0.7300 (t80) cc_final: 0.6896 (t80) REVERT: A 1232 TYR cc_start: 0.6299 (t80) cc_final: 0.5906 (t80) REVERT: A 1365 MET cc_start: 0.7577 (ptm) cc_final: 0.6464 (ttm) REVERT: A 1465 ARG cc_start: 0.7610 (ptt180) cc_final: 0.7166 (ptt180) REVERT: B 59 ILE cc_start: 0.5622 (pt) cc_final: 0.5312 (mp) REVERT: B 138 TYR cc_start: 0.5278 (p90) cc_final: 0.5024 (p90) REVERT: B 240 HIS cc_start: 0.5608 (m-70) cc_final: 0.5371 (t70) REVERT: B 243 ASP cc_start: 0.5071 (m-30) cc_final: 0.4796 (t0) REVERT: B 456 MET cc_start: 0.4466 (mmm) cc_final: 0.4070 (tpp) REVERT: B 553 ARG cc_start: 0.5453 (mmm-85) cc_final: 0.5061 (mtt-85) REVERT: B 559 ARG cc_start: 0.4905 (ttt180) cc_final: 0.4678 (ttt90) REVERT: B 638 GLU cc_start: 0.5681 (mt-10) cc_final: 0.5289 (pt0) REVERT: B 658 MET cc_start: 0.6116 (mtm) cc_final: 0.5363 (mtm) REVERT: B 675 GLU cc_start: 0.6683 (tp30) cc_final: 0.6356 (tp30) REVERT: B 683 MET cc_start: 0.6964 (tpt) cc_final: 0.6175 (mmm) REVERT: B 690 SER cc_start: 0.6928 (p) cc_final: 0.6559 (m) REVERT: B 725 ASP cc_start: 0.7015 (m-30) cc_final: 0.6721 (m-30) REVERT: B 922 LYS cc_start: 0.6460 (pttm) cc_final: 0.6068 (mttm) REVERT: B 930 MET cc_start: 0.5561 (mtt) cc_final: 0.4887 (tpp) REVERT: B 932 MET cc_start: 0.6426 (mmt) cc_final: 0.6098 (mpp) REVERT: B 934 MET cc_start: 0.5831 (mmt) cc_final: 0.5169 (mmt) REVERT: B 936 LYS cc_start: 0.5252 (mttt) cc_final: 0.4671 (ptmt) REVERT: B 990 ASP cc_start: 0.6402 (m-30) cc_final: 0.5953 (m-30) REVERT: B 1050 ASP cc_start: 0.5973 (m-30) cc_final: 0.5659 (m-30) REVERT: B 1055 GLN cc_start: 0.6357 (mt0) cc_final: 0.5583 (tt0) REVERT: B 1084 MET cc_start: 0.5296 (mmt) cc_final: 0.4741 (mmp) REVERT: B 1126 ARG cc_start: 0.5059 (ttp-110) cc_final: 0.4641 (tmm160) REVERT: B 1128 ARG cc_start: 0.5560 (ttp80) cc_final: 0.5234 (ttm-80) REVERT: B 1162 PHE cc_start: 0.7290 (t80) cc_final: 0.6889 (t80) REVERT: B 1232 TYR cc_start: 0.6306 (t80) cc_final: 0.5917 (t80) REVERT: B 1365 MET cc_start: 0.7577 (ptm) cc_final: 0.6454 (ttm) REVERT: B 1465 ARG cc_start: 0.7603 (ptt180) cc_final: 0.7261 (ptt90) REVERT: C 59 ILE cc_start: 0.5586 (pt) cc_final: 0.5276 (mp) REVERT: C 240 HIS cc_start: 0.5640 (m-70) cc_final: 0.5384 (t70) REVERT: C 243 ASP cc_start: 0.5077 (m-30) cc_final: 0.4811 (t0) REVERT: C 456 MET cc_start: 0.4505 (mmm) cc_final: 0.4110 (tpp) REVERT: C 553 ARG cc_start: 0.5486 (mmm-85) cc_final: 0.5074 (mtt-85) REVERT: C 559 ARG cc_start: 0.4903 (ttt180) cc_final: 0.4677 (ttt90) REVERT: C 638 GLU cc_start: 0.5683 (mt-10) cc_final: 0.5290 (pt0) REVERT: C 658 MET cc_start: 0.6117 (mtm) cc_final: 0.5360 (mtm) REVERT: C 675 GLU cc_start: 0.6692 (tp30) cc_final: 0.6365 (tp30) REVERT: C 683 MET cc_start: 0.6966 (tpt) cc_final: 0.6177 (mmm) REVERT: C 690 SER cc_start: 0.6931 (p) cc_final: 0.6558 (m) REVERT: C 725 ASP cc_start: 0.7018 (m-30) cc_final: 0.6723 (m-30) REVERT: C 922 LYS cc_start: 0.6461 (pttm) cc_final: 0.6070 (mttm) REVERT: C 930 MET cc_start: 0.5562 (mtt) cc_final: 0.4887 (tpp) REVERT: C 932 MET cc_start: 0.6425 (mmt) cc_final: 0.6097 (mpp) REVERT: C 934 MET cc_start: 0.5826 (mmt) cc_final: 0.5162 (mmt) REVERT: C 936 LYS cc_start: 0.5251 (mttt) cc_final: 0.4670 (ptmt) REVERT: C 990 ASP cc_start: 0.6401 (m-30) cc_final: 0.5950 (m-30) REVERT: C 1050 ASP cc_start: 0.6069 (m-30) cc_final: 0.5747 (m-30) REVERT: C 1055 GLN cc_start: 0.6360 (mt0) cc_final: 0.5584 (tt0) REVERT: C 1084 MET cc_start: 0.5258 (mmt) cc_final: 0.4729 (mmp) REVERT: C 1126 ARG cc_start: 0.5040 (ttp-110) cc_final: 0.4687 (tmm160) REVERT: C 1128 ARG cc_start: 0.5561 (ttp80) cc_final: 0.5236 (ttm-80) REVERT: C 1162 PHE cc_start: 0.7297 (t80) cc_final: 0.6891 (t80) REVERT: C 1232 TYR cc_start: 0.6302 (t80) cc_final: 0.5907 (t80) REVERT: C 1365 MET cc_start: 0.7570 (ptm) cc_final: 0.6836 (ttp) REVERT: C 1465 ARG cc_start: 0.7618 (ptt180) cc_final: 0.7050 (ptt180) REVERT: D 59 ILE cc_start: 0.5621 (pt) cc_final: 0.5313 (mp) REVERT: D 138 TYR cc_start: 0.5280 (p90) cc_final: 0.5025 (p90) REVERT: D 240 HIS cc_start: 0.5636 (m-70) cc_final: 0.5374 (t70) REVERT: D 243 ASP cc_start: 0.5074 (m-30) cc_final: 0.4798 (t0) REVERT: D 456 MET cc_start: 0.4517 (mmm) cc_final: 0.4127 (tpp) REVERT: D 553 ARG cc_start: 0.5436 (mmm-85) cc_final: 0.4985 (mtt180) REVERT: D 559 ARG cc_start: 0.4909 (ttt180) cc_final: 0.4682 (ttt90) REVERT: D 638 GLU cc_start: 0.5680 (mt-10) cc_final: 0.5290 (pt0) REVERT: D 658 MET cc_start: 0.6117 (mtm) cc_final: 0.5365 (mtm) REVERT: D 675 GLU cc_start: 0.6691 (tp30) cc_final: 0.6365 (tp30) REVERT: D 683 MET cc_start: 0.6964 (tpt) cc_final: 0.6178 (mmm) REVERT: D 690 SER cc_start: 0.6928 (p) cc_final: 0.6559 (m) REVERT: D 725 ASP cc_start: 0.7014 (m-30) cc_final: 0.6719 (m-30) REVERT: D 922 LYS cc_start: 0.6462 (pttm) cc_final: 0.6068 (mttm) REVERT: D 930 MET cc_start: 0.5563 (mtt) cc_final: 0.4886 (tpp) REVERT: D 932 MET cc_start: 0.6423 (mmt) cc_final: 0.6107 (mpp) REVERT: D 934 MET cc_start: 0.5830 (mmt) cc_final: 0.5172 (mmt) REVERT: D 936 LYS cc_start: 0.5249 (mttt) cc_final: 0.4668 (ptmt) REVERT: D 990 ASP cc_start: 0.6400 (m-30) cc_final: 0.5950 (m-30) REVERT: D 1050 ASP cc_start: 0.5974 (m-30) cc_final: 0.5660 (m-30) REVERT: D 1055 GLN cc_start: 0.6358 (mt0) cc_final: 0.5584 (tt0) REVERT: D 1084 MET cc_start: 0.5303 (mmt) cc_final: 0.4747 (mmp) REVERT: D 1126 ARG cc_start: 0.5035 (ttp-110) cc_final: 0.4682 (tmm160) REVERT: D 1128 ARG cc_start: 0.5559 (ttp80) cc_final: 0.5233 (ttm-80) REVERT: D 1162 PHE cc_start: 0.7288 (t80) cc_final: 0.6887 (t80) REVERT: D 1232 TYR cc_start: 0.6304 (t80) cc_final: 0.5914 (t80) REVERT: D 1365 MET cc_start: 0.7578 (ptm) cc_final: 0.6457 (ttm) REVERT: D 1465 ARG cc_start: 0.7606 (ptt180) cc_final: 0.7263 (ptt90) outliers start: 12 outliers final: 8 residues processed: 866 average time/residue: 1.3938 time to fit residues: 1484.2813 Evaluate side-chains 540 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 532 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 910 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 459 optimal weight: 0.9980 chunk 412 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 426 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 259 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 494 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 356 GLN A 423 GLN A 598 GLN A 696 ASN ** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 HIS A 923 ASN A 996 ASN A1038 ASN A1152 GLN A1167 GLN A1201 ASN A1441 ASN B 173 GLN B 356 GLN B 423 GLN B 598 GLN B 696 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 813 HIS B 923 ASN B 996 ASN B1038 ASN B1152 GLN B1167 GLN B1201 ASN B1441 ASN C 173 GLN C 356 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 598 GLN C 696 ASN ** C 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 HIS C 923 ASN C 996 ASN C1038 ASN C1152 GLN C1167 GLN C1201 ASN C1441 ASN D 173 GLN D 356 GLN D 423 GLN D 598 GLN D 696 ASN ** D 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 HIS D 923 ASN D 996 ASN D1038 ASN D1152 GLN D1167 GLN D1201 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 41608 Z= 0.161 Angle : 0.530 8.640 56912 Z= 0.279 Chirality : 0.039 0.172 6668 Planarity : 0.004 0.057 7196 Dihedral : 8.320 88.275 7012 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.49 % Allowed : 10.74 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.11), residues: 5432 helix: 1.96 (0.09), residues: 3016 sheet: -0.66 (0.24), residues: 396 loop : -0.49 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 96 HIS 0.003 0.001 HIS D 813 PHE 0.023 0.001 PHE D 274 TYR 0.015 0.001 TYR C 466 ARG 0.006 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 554 time to evaluate : 4.469 Fit side-chains REVERT: A 129 MET cc_start: 0.6055 (mmm) cc_final: 0.5399 (tmt) REVERT: A 161 GLU cc_start: 0.5280 (tt0) cc_final: 0.4972 (tt0) REVERT: A 240 HIS cc_start: 0.5740 (m-70) cc_final: 0.5522 (t70) REVERT: A 243 ASP cc_start: 0.5454 (m-30) cc_final: 0.5131 (t70) REVERT: A 250 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.6005 (tp) REVERT: A 284 GLN cc_start: 0.6249 (mm-40) cc_final: 0.5715 (mt0) REVERT: A 326 ASP cc_start: 0.6502 (m-30) cc_final: 0.6024 (m-30) REVERT: A 352 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6435 (mt0) REVERT: A 368 ASN cc_start: 0.6751 (OUTLIER) cc_final: 0.6180 (t0) REVERT: A 413 ASN cc_start: 0.3285 (OUTLIER) cc_final: 0.3021 (t160) REVERT: A 420 TYR cc_start: 0.5806 (m-80) cc_final: 0.5268 (m-80) REVERT: A 455 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5503 (mtt) REVERT: A 683 MET cc_start: 0.6755 (tpt) cc_final: 0.6047 (mmm) REVERT: A 690 SER cc_start: 0.6773 (p) cc_final: 0.6525 (m) REVERT: A 710 LEU cc_start: 0.6650 (mt) cc_final: 0.6428 (tp) REVERT: A 725 ASP cc_start: 0.7057 (m-30) cc_final: 0.6819 (m-30) REVERT: A 856 PHE cc_start: 0.6049 (m-80) cc_final: 0.5622 (m-10) REVERT: A 870 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6178 (mtt180) REVERT: A 910 LEU cc_start: 0.7182 (pp) cc_final: 0.6919 (mt) REVERT: A 922 LYS cc_start: 0.6465 (pttm) cc_final: 0.5782 (ptmm) REVERT: A 930 MET cc_start: 0.5810 (mtt) cc_final: 0.5406 (mtp) REVERT: A 932 MET cc_start: 0.6340 (mmt) cc_final: 0.6041 (mpp) REVERT: A 936 LYS cc_start: 0.5644 (mttt) cc_final: 0.4976 (ptmt) REVERT: A 990 ASP cc_start: 0.6743 (m-30) cc_final: 0.6350 (m-30) REVERT: A 1050 ASP cc_start: 0.5693 (m-30) cc_final: 0.5426 (m-30) REVERT: A 1055 GLN cc_start: 0.6384 (mt0) cc_final: 0.5642 (tt0) REVERT: A 1084 MET cc_start: 0.5485 (mmt) cc_final: 0.4881 (mmp) REVERT: A 1122 ARG cc_start: 0.5342 (mtm-85) cc_final: 0.5034 (mtm110) REVERT: A 1126 ARG cc_start: 0.5111 (ttp-110) cc_final: 0.4650 (tmm160) REVERT: A 1128 ARG cc_start: 0.5580 (ttp80) cc_final: 0.5250 (ttm-80) REVERT: A 1145 GLN cc_start: 0.6576 (mt0) cc_final: 0.6348 (mt0) REVERT: A 1162 PHE cc_start: 0.6987 (t80) cc_final: 0.6755 (t80) REVERT: A 1166 GLN cc_start: 0.6538 (mm-40) cc_final: 0.5675 (tm-30) REVERT: A 1233 LEU cc_start: 0.6937 (tp) cc_final: 0.6388 (pp) REVERT: A 1365 MET cc_start: 0.7303 (ptm) cc_final: 0.6934 (ptm) REVERT: A 1465 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7191 (ptt90) REVERT: A 1467 MET cc_start: 0.8176 (mtp) cc_final: 0.7725 (mtp) REVERT: B 129 MET cc_start: 0.6070 (mmm) cc_final: 0.5415 (tmt) REVERT: B 161 GLU cc_start: 0.5246 (tt0) cc_final: 0.4942 (tt0) REVERT: B 240 HIS cc_start: 0.5720 (m-70) cc_final: 0.5503 (t70) REVERT: B 243 ASP cc_start: 0.5441 (m-30) cc_final: 0.5165 (t0) REVERT: B 284 GLN cc_start: 0.6242 (mm-40) cc_final: 0.5706 (mt0) REVERT: B 326 ASP cc_start: 0.6420 (m-30) cc_final: 0.5942 (m-30) REVERT: B 352 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6465 (mt0) REVERT: B 368 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6178 (t0) REVERT: B 413 ASN cc_start: 0.3209 (OUTLIER) cc_final: 0.2951 (t160) REVERT: B 420 TYR cc_start: 0.5786 (m-80) cc_final: 0.5251 (m-80) REVERT: B 455 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5545 (mtt) REVERT: B 683 MET cc_start: 0.6754 (tpt) cc_final: 0.6050 (mmm) REVERT: B 690 SER cc_start: 0.6811 (p) cc_final: 0.6558 (m) REVERT: B 710 LEU cc_start: 0.6664 (mt) cc_final: 0.6437 (tp) REVERT: B 725 ASP cc_start: 0.7059 (m-30) cc_final: 0.6821 (m-30) REVERT: B 856 PHE cc_start: 0.6048 (m-80) cc_final: 0.5621 (m-10) REVERT: B 870 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6181 (mtt180) REVERT: B 910 LEU cc_start: 0.7183 (pp) cc_final: 0.6923 (mt) REVERT: B 922 LYS cc_start: 0.6466 (pttm) cc_final: 0.5783 (ptmm) REVERT: B 930 MET cc_start: 0.5812 (mtt) cc_final: 0.5407 (mtp) REVERT: B 932 MET cc_start: 0.6392 (mmt) cc_final: 0.6091 (mpp) REVERT: B 936 LYS cc_start: 0.5647 (mttt) cc_final: 0.4980 (ptmt) REVERT: B 990 ASP cc_start: 0.6748 (m-30) cc_final: 0.6355 (m-30) REVERT: B 1050 ASP cc_start: 0.5691 (m-30) cc_final: 0.5424 (m-30) REVERT: B 1055 GLN cc_start: 0.6382 (mt0) cc_final: 0.5639 (tt0) REVERT: B 1084 MET cc_start: 0.5484 (mmt) cc_final: 0.4879 (mmp) REVERT: B 1122 ARG cc_start: 0.5342 (mtm-85) cc_final: 0.5034 (mtm110) REVERT: B 1126 ARG cc_start: 0.5142 (ttp-110) cc_final: 0.4688 (tmm160) REVERT: B 1128 ARG cc_start: 0.5554 (ttp80) cc_final: 0.5227 (ttm-80) REVERT: B 1145 GLN cc_start: 0.6584 (mt0) cc_final: 0.6366 (mt0) REVERT: B 1162 PHE cc_start: 0.6986 (t80) cc_final: 0.6752 (t80) REVERT: B 1166 GLN cc_start: 0.6563 (mm-40) cc_final: 0.5695 (tm-30) REVERT: B 1233 LEU cc_start: 0.6931 (tp) cc_final: 0.6382 (pp) REVERT: B 1365 MET cc_start: 0.7304 (ptm) cc_final: 0.6934 (ptm) REVERT: B 1465 ARG cc_start: 0.7729 (ptt180) cc_final: 0.7194 (ptt90) REVERT: B 1467 MET cc_start: 0.8193 (mtp) cc_final: 0.7749 (mtp) REVERT: C 113 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6231 (pp) REVERT: C 129 MET cc_start: 0.6064 (mmm) cc_final: 0.5399 (tmt) REVERT: C 161 GLU cc_start: 0.5282 (tt0) cc_final: 0.4974 (tt0) REVERT: C 240 HIS cc_start: 0.5744 (m-70) cc_final: 0.5528 (t70) REVERT: C 243 ASP cc_start: 0.5463 (m-30) cc_final: 0.5189 (t0) REVERT: C 284 GLN cc_start: 0.6237 (mm-40) cc_final: 0.5702 (mt0) REVERT: C 326 ASP cc_start: 0.6505 (m-30) cc_final: 0.6029 (m-30) REVERT: C 352 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6438 (mt0) REVERT: C 368 ASN cc_start: 0.6780 (OUTLIER) cc_final: 0.6205 (t0) REVERT: C 413 ASN cc_start: 0.3217 (OUTLIER) cc_final: 0.2953 (t160) REVERT: C 420 TYR cc_start: 0.5811 (m-80) cc_final: 0.5277 (m-80) REVERT: C 455 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5533 (mtt) REVERT: C 683 MET cc_start: 0.6758 (tpt) cc_final: 0.6053 (mmm) REVERT: C 690 SER cc_start: 0.6784 (p) cc_final: 0.6529 (m) REVERT: C 710 LEU cc_start: 0.6654 (mt) cc_final: 0.6431 (tp) REVERT: C 725 ASP cc_start: 0.7061 (m-30) cc_final: 0.6823 (m-30) REVERT: C 856 PHE cc_start: 0.6053 (m-80) cc_final: 0.5621 (m-10) REVERT: C 870 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6162 (mtt180) REVERT: C 910 LEU cc_start: 0.7181 (pp) cc_final: 0.6926 (mt) REVERT: C 922 LYS cc_start: 0.6466 (pttm) cc_final: 0.5786 (ptmm) REVERT: C 930 MET cc_start: 0.5813 (mtt) cc_final: 0.5409 (mtp) REVERT: C 932 MET cc_start: 0.6333 (mmt) cc_final: 0.6034 (mpp) REVERT: C 936 LYS cc_start: 0.5647 (mttt) cc_final: 0.4979 (ptmt) REVERT: C 990 ASP cc_start: 0.6752 (m-30) cc_final: 0.6356 (m-30) REVERT: C 1050 ASP cc_start: 0.5693 (m-30) cc_final: 0.5425 (m-30) REVERT: C 1055 GLN cc_start: 0.6385 (mt0) cc_final: 0.5642 (tt0) REVERT: C 1084 MET cc_start: 0.5520 (mmt) cc_final: 0.4910 (mmp) REVERT: C 1122 ARG cc_start: 0.5342 (mtm-85) cc_final: 0.5035 (mtm110) REVERT: C 1126 ARG cc_start: 0.5113 (ttp-110) cc_final: 0.4653 (tmm160) REVERT: C 1128 ARG cc_start: 0.5551 (ttp80) cc_final: 0.5227 (ttm-80) REVERT: C 1145 GLN cc_start: 0.6557 (mt0) cc_final: 0.6340 (mt0) REVERT: C 1162 PHE cc_start: 0.6982 (t80) cc_final: 0.6741 (t80) REVERT: C 1166 GLN cc_start: 0.6562 (mm-40) cc_final: 0.5688 (tm-30) REVERT: C 1233 LEU cc_start: 0.6964 (tp) cc_final: 0.6421 (pp) REVERT: C 1365 MET cc_start: 0.7303 (ptm) cc_final: 0.6932 (ptm) REVERT: C 1465 ARG cc_start: 0.7691 (ptt180) cc_final: 0.7088 (ptt180) REVERT: C 1467 MET cc_start: 0.7984 (mtp) cc_final: 0.7630 (mtp) REVERT: D 129 MET cc_start: 0.6072 (mmm) cc_final: 0.5417 (tmt) REVERT: D 161 GLU cc_start: 0.5247 (tt0) cc_final: 0.4943 (tt0) REVERT: D 240 HIS cc_start: 0.5724 (m-70) cc_final: 0.5507 (t70) REVERT: D 243 ASP cc_start: 0.5446 (m-30) cc_final: 0.5169 (t0) REVERT: D 284 GLN cc_start: 0.6251 (mm-40) cc_final: 0.5715 (mt0) REVERT: D 326 ASP cc_start: 0.6501 (m-30) cc_final: 0.6023 (m-30) REVERT: D 352 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6440 (mt0) REVERT: D 368 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.6179 (t0) REVERT: D 413 ASN cc_start: 0.3212 (OUTLIER) cc_final: 0.2952 (t160) REVERT: D 420 TYR cc_start: 0.5808 (m-80) cc_final: 0.5270 (m-80) REVERT: D 455 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.5536 (mtt) REVERT: D 683 MET cc_start: 0.6748 (tpt) cc_final: 0.6059 (mmm) REVERT: D 690 SER cc_start: 0.6813 (p) cc_final: 0.6560 (m) REVERT: D 710 LEU cc_start: 0.6650 (mt) cc_final: 0.6427 (tp) REVERT: D 725 ASP cc_start: 0.7058 (m-30) cc_final: 0.6821 (m-30) REVERT: D 856 PHE cc_start: 0.6049 (m-80) cc_final: 0.5622 (m-10) REVERT: D 870 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6179 (mtt180) REVERT: D 910 LEU cc_start: 0.7181 (pp) cc_final: 0.6921 (mt) REVERT: D 922 LYS cc_start: 0.6469 (pttm) cc_final: 0.5786 (ptmm) REVERT: D 930 MET cc_start: 0.5812 (mtt) cc_final: 0.5409 (mtp) REVERT: D 932 MET cc_start: 0.6391 (mmt) cc_final: 0.6091 (mpp) REVERT: D 936 LYS cc_start: 0.5647 (mttt) cc_final: 0.4980 (ptmt) REVERT: D 990 ASP cc_start: 0.6747 (m-30) cc_final: 0.6354 (m-30) REVERT: D 1046 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5621 (mm-30) REVERT: D 1050 ASP cc_start: 0.5693 (m-30) cc_final: 0.5425 (m-30) REVERT: D 1055 GLN cc_start: 0.6384 (mt0) cc_final: 0.5641 (tt0) REVERT: D 1084 MET cc_start: 0.5485 (mmt) cc_final: 0.4881 (mmp) REVERT: D 1122 ARG cc_start: 0.5340 (mtm-85) cc_final: 0.5032 (mtm110) REVERT: D 1126 ARG cc_start: 0.5111 (ttp-110) cc_final: 0.4651 (tmm160) REVERT: D 1128 ARG cc_start: 0.5550 (ttp80) cc_final: 0.5224 (ttm-80) REVERT: D 1145 GLN cc_start: 0.6585 (mt0) cc_final: 0.6371 (mt0) REVERT: D 1162 PHE cc_start: 0.6982 (t80) cc_final: 0.6749 (t80) REVERT: D 1166 GLN cc_start: 0.6560 (mm-40) cc_final: 0.5689 (tm-30) REVERT: D 1233 LEU cc_start: 0.6938 (tp) cc_final: 0.6390 (pp) REVERT: D 1365 MET cc_start: 0.7302 (ptm) cc_final: 0.6934 (ptm) REVERT: D 1465 ARG cc_start: 0.7731 (ptt180) cc_final: 0.7195 (ptt90) REVERT: D 1467 MET cc_start: 0.8195 (mtp) cc_final: 0.7749 (mtp) outliers start: 92 outliers final: 28 residues processed: 631 average time/residue: 1.3934 time to fit residues: 1088.0019 Evaluate side-chains 514 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 464 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1408 SER Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1110 THR Chi-restraints excluded: chain B residue 1408 SER Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1408 SER Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1110 THR Chi-restraints excluded: chain D residue 1408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 274 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 chunk 336 optimal weight: 0.5980 chunk 136 optimal weight: 9.9990 chunk 494 optimal weight: 0.8980 chunk 534 optimal weight: 5.9990 chunk 440 optimal weight: 2.9990 chunk 490 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 397 optimal weight: 0.0370 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN A1201 ASN A1292 HIS ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B1201 ASN B1292 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 ASN C1201 ASN C1292 HIS ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 ASN D1201 ASN D1292 HIS D1441 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41608 Z= 0.173 Angle : 0.516 10.318 56912 Z= 0.268 Chirality : 0.038 0.152 6668 Planarity : 0.004 0.054 7196 Dihedral : 8.336 89.761 7004 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.68 % Allowed : 14.34 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.11), residues: 5432 helix: 2.07 (0.09), residues: 3020 sheet: -0.76 (0.24), residues: 408 loop : -0.50 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 726 HIS 0.003 0.001 HIS C 715 PHE 0.021 0.002 PHE B 274 TYR 0.015 0.002 TYR D 466 ARG 0.005 0.001 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 473 time to evaluate : 4.487 Fit side-chains REVERT: A 129 MET cc_start: 0.6244 (mmm) cc_final: 0.5594 (tmt) REVERT: A 161 GLU cc_start: 0.5276 (tt0) cc_final: 0.4912 (OUTLIER) REVERT: A 173 GLN cc_start: 0.5782 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: A 243 ASP cc_start: 0.5605 (m-30) cc_final: 0.5273 (t0) REVERT: A 284 GLN cc_start: 0.6213 (mm-40) cc_final: 0.5579 (mt0) REVERT: A 368 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.6418 (m-40) REVERT: A 413 ASN cc_start: 0.3276 (OUTLIER) cc_final: 0.2968 (t160) REVERT: A 621 LEU cc_start: 0.6705 (tt) cc_final: 0.6421 (mt) REVERT: A 683 MET cc_start: 0.6959 (tpt) cc_final: 0.6298 (mmm) REVERT: A 702 ASN cc_start: 0.6916 (m-40) cc_final: 0.6420 (m-40) REVERT: A 725 ASP cc_start: 0.7002 (m-30) cc_final: 0.6542 (m-30) REVERT: A 870 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6053 (mtt180) REVERT: A 922 LYS cc_start: 0.6407 (pttm) cc_final: 0.5725 (ptmm) REVERT: A 932 MET cc_start: 0.6002 (mmt) cc_final: 0.5188 (mtt) REVERT: A 936 LYS cc_start: 0.5414 (mttt) cc_final: 0.4891 (tttm) REVERT: A 963 ASP cc_start: 0.6336 (t70) cc_final: 0.5796 (t70) REVERT: A 990 ASP cc_start: 0.6729 (m-30) cc_final: 0.6384 (m-30) REVERT: A 1042 MET cc_start: 0.6601 (mtp) cc_final: 0.5997 (mmp) REVERT: A 1046 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5408 (mm-30) REVERT: A 1050 ASP cc_start: 0.5785 (m-30) cc_final: 0.5435 (m-30) REVERT: A 1055 GLN cc_start: 0.6407 (mt0) cc_final: 0.5581 (pt0) REVERT: A 1084 MET cc_start: 0.5408 (mmt) cc_final: 0.4920 (mmp) REVERT: A 1126 ARG cc_start: 0.5093 (ttp-110) cc_final: 0.4662 (tmm160) REVERT: A 1128 ARG cc_start: 0.5493 (ttp80) cc_final: 0.4988 (ttm-80) REVERT: A 1145 GLN cc_start: 0.6846 (mt0) cc_final: 0.6470 (mt0) REVERT: A 1162 PHE cc_start: 0.6966 (t80) cc_final: 0.6694 (t80) REVERT: A 1166 GLN cc_start: 0.6364 (mm-40) cc_final: 0.5807 (tm-30) REVERT: A 1354 GLU cc_start: 0.7627 (tt0) cc_final: 0.6996 (tt0) REVERT: A 1365 MET cc_start: 0.7049 (ptm) cc_final: 0.6637 (ttm) REVERT: A 1465 ARG cc_start: 0.7750 (ptt180) cc_final: 0.7065 (ptt180) REVERT: A 1467 MET cc_start: 0.8326 (mtp) cc_final: 0.8015 (mtp) REVERT: B 112 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.6052 (ttp-170) REVERT: B 129 MET cc_start: 0.6213 (mmm) cc_final: 0.5592 (tmt) REVERT: B 161 GLU cc_start: 0.5257 (tt0) cc_final: 0.4891 (OUTLIER) REVERT: B 173 GLN cc_start: 0.5776 (OUTLIER) cc_final: 0.5498 (tm-30) REVERT: B 243 ASP cc_start: 0.5548 (m-30) cc_final: 0.5220 (t0) REVERT: B 284 GLN cc_start: 0.6198 (mm-40) cc_final: 0.5543 (mt0) REVERT: B 368 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6417 (m-40) REVERT: B 413 ASN cc_start: 0.3274 (OUTLIER) cc_final: 0.2966 (t160) REVERT: B 621 LEU cc_start: 0.6704 (tt) cc_final: 0.6421 (mt) REVERT: B 683 MET cc_start: 0.6959 (tpt) cc_final: 0.6302 (mmm) REVERT: B 702 ASN cc_start: 0.6914 (m-40) cc_final: 0.6420 (m-40) REVERT: B 725 ASP cc_start: 0.7006 (m-30) cc_final: 0.6544 (m-30) REVERT: B 870 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6054 (mtt180) REVERT: B 922 LYS cc_start: 0.6397 (pttm) cc_final: 0.5713 (ptmm) REVERT: B 932 MET cc_start: 0.6002 (mmt) cc_final: 0.5189 (mtt) REVERT: B 936 LYS cc_start: 0.5442 (mttt) cc_final: 0.4916 (tttm) REVERT: B 963 ASP cc_start: 0.6340 (t70) cc_final: 0.5798 (t70) REVERT: B 990 ASP cc_start: 0.6712 (m-30) cc_final: 0.6366 (m-30) REVERT: B 1042 MET cc_start: 0.6622 (mtp) cc_final: 0.6007 (mmp) REVERT: B 1046 GLU cc_start: 0.5743 (mm-30) cc_final: 0.5409 (mm-30) REVERT: B 1050 ASP cc_start: 0.5784 (m-30) cc_final: 0.5434 (m-30) REVERT: B 1055 GLN cc_start: 0.6406 (mt0) cc_final: 0.5579 (pt0) REVERT: B 1084 MET cc_start: 0.5409 (mmt) cc_final: 0.4921 (mmp) REVERT: B 1126 ARG cc_start: 0.5072 (ttp-110) cc_final: 0.4645 (tmm160) REVERT: B 1128 ARG cc_start: 0.5497 (ttp80) cc_final: 0.4989 (ttm-80) REVERT: B 1145 GLN cc_start: 0.6896 (mt0) cc_final: 0.6575 (tt0) REVERT: B 1162 PHE cc_start: 0.6969 (t80) cc_final: 0.6704 (t80) REVERT: B 1166 GLN cc_start: 0.6366 (mm-40) cc_final: 0.5825 (tm-30) REVERT: B 1365 MET cc_start: 0.7112 (ptm) cc_final: 0.6697 (ttm) REVERT: B 1465 ARG cc_start: 0.7746 (ptt180) cc_final: 0.7055 (ptt180) REVERT: B 1467 MET cc_start: 0.8360 (mtp) cc_final: 0.8066 (mtp) REVERT: C 129 MET cc_start: 0.6254 (mmm) cc_final: 0.5588 (tmt) REVERT: C 161 GLU cc_start: 0.5269 (tt0) cc_final: 0.4905 (OUTLIER) REVERT: C 243 ASP cc_start: 0.5612 (m-30) cc_final: 0.5279 (t0) REVERT: C 284 GLN cc_start: 0.6214 (mm-40) cc_final: 0.5581 (mt0) REVERT: C 368 ASN cc_start: 0.6747 (OUTLIER) cc_final: 0.6423 (m-40) REVERT: C 413 ASN cc_start: 0.3273 (OUTLIER) cc_final: 0.2966 (t160) REVERT: C 621 LEU cc_start: 0.6710 (tt) cc_final: 0.6426 (mt) REVERT: C 683 MET cc_start: 0.6963 (tpt) cc_final: 0.6277 (mmm) REVERT: C 702 ASN cc_start: 0.6918 (m-40) cc_final: 0.6424 (m-40) REVERT: C 725 ASP cc_start: 0.7010 (m-30) cc_final: 0.6547 (m-30) REVERT: C 870 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6056 (mtt180) REVERT: C 922 LYS cc_start: 0.6411 (pttm) cc_final: 0.5726 (ptmm) REVERT: C 932 MET cc_start: 0.6003 (mmt) cc_final: 0.5192 (mtt) REVERT: C 936 LYS cc_start: 0.5444 (mttt) cc_final: 0.4918 (tttm) REVERT: C 963 ASP cc_start: 0.6339 (t70) cc_final: 0.5799 (t70) REVERT: C 990 ASP cc_start: 0.6711 (m-30) cc_final: 0.6366 (m-30) REVERT: C 1042 MET cc_start: 0.6624 (mtp) cc_final: 0.6006 (mmp) REVERT: C 1046 GLU cc_start: 0.5746 (mm-30) cc_final: 0.5411 (mm-30) REVERT: C 1050 ASP cc_start: 0.5786 (m-30) cc_final: 0.5436 (m-30) REVERT: C 1055 GLN cc_start: 0.6409 (mt0) cc_final: 0.5582 (pt0) REVERT: C 1084 MET cc_start: 0.5470 (mmt) cc_final: 0.4963 (mmp) REVERT: C 1126 ARG cc_start: 0.5095 (ttp-110) cc_final: 0.4665 (tmm160) REVERT: C 1128 ARG cc_start: 0.5496 (ttp80) cc_final: 0.4991 (ttm-80) REVERT: C 1145 GLN cc_start: 0.6843 (mt0) cc_final: 0.6519 (tt0) REVERT: C 1162 PHE cc_start: 0.6920 (t80) cc_final: 0.6638 (t80) REVERT: C 1166 GLN cc_start: 0.6401 (mm-40) cc_final: 0.5655 (tm-30) REVERT: C 1365 MET cc_start: 0.7102 (ptm) cc_final: 0.6714 (ttm) REVERT: D 112 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.6052 (ttp-170) REVERT: D 129 MET cc_start: 0.6196 (mmm) cc_final: 0.5593 (tmt) REVERT: D 161 GLU cc_start: 0.5257 (tt0) cc_final: 0.4892 (OUTLIER) REVERT: D 173 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.5501 (tm-30) REVERT: D 243 ASP cc_start: 0.5554 (m-30) cc_final: 0.5194 (t0) REVERT: D 284 GLN cc_start: 0.6198 (mm-40) cc_final: 0.5545 (mt0) REVERT: D 368 ASN cc_start: 0.6739 (OUTLIER) cc_final: 0.6418 (m-40) REVERT: D 413 ASN cc_start: 0.3274 (OUTLIER) cc_final: 0.2967 (t160) REVERT: D 621 LEU cc_start: 0.6706 (tt) cc_final: 0.6422 (mt) REVERT: D 683 MET cc_start: 0.6990 (tpt) cc_final: 0.6330 (mmm) REVERT: D 702 ASN cc_start: 0.6914 (m-40) cc_final: 0.6420 (m-40) REVERT: D 725 ASP cc_start: 0.7005 (m-30) cc_final: 0.6544 (m-30) REVERT: D 870 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.6053 (mtt180) REVERT: D 922 LYS cc_start: 0.6410 (pttm) cc_final: 0.5727 (ptmm) REVERT: D 932 MET cc_start: 0.6003 (mmt) cc_final: 0.5191 (mtt) REVERT: D 936 LYS cc_start: 0.5416 (mttt) cc_final: 0.4894 (tttm) REVERT: D 963 ASP cc_start: 0.6339 (t70) cc_final: 0.5798 (t70) REVERT: D 990 ASP cc_start: 0.6713 (m-30) cc_final: 0.6366 (m-30) REVERT: D 1042 MET cc_start: 0.6622 (mtp) cc_final: 0.6007 (mmp) REVERT: D 1050 ASP cc_start: 0.5786 (m-30) cc_final: 0.5432 (m-30) REVERT: D 1055 GLN cc_start: 0.6407 (mt0) cc_final: 0.5581 (pt0) REVERT: D 1084 MET cc_start: 0.5409 (mmt) cc_final: 0.4922 (mmp) REVERT: D 1126 ARG cc_start: 0.5091 (ttp-110) cc_final: 0.4660 (tmm160) REVERT: D 1128 ARG cc_start: 0.5495 (ttp80) cc_final: 0.4988 (ttm-80) REVERT: D 1145 GLN cc_start: 0.6900 (mt0) cc_final: 0.6535 (mt0) REVERT: D 1162 PHE cc_start: 0.6941 (t80) cc_final: 0.6673 (t80) REVERT: D 1166 GLN cc_start: 0.6363 (mm-40) cc_final: 0.5806 (tm-30) REVERT: D 1365 MET cc_start: 0.7112 (ptm) cc_final: 0.6698 (ttm) REVERT: D 1465 ARG cc_start: 0.7764 (ptt180) cc_final: 0.7114 (ptt180) REVERT: D 1467 MET cc_start: 0.8361 (mtp) cc_final: 0.8133 (mtp) outliers start: 99 outliers final: 49 residues processed: 553 average time/residue: 1.3714 time to fit residues: 943.3621 Evaluate side-chains 457 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 395 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1110 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1382 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1382 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1110 THR Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1382 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 488 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 496 optimal weight: 0.9980 chunk 525 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 470 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 378 GLN A 598 GLN A 643 HIS ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN B 378 GLN B 598 GLN B 643 HIS ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 253 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN C 643 HIS ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 378 GLN D 598 GLN D 643 HIS ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1201 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41608 Z= 0.289 Angle : 0.621 10.003 56912 Z= 0.324 Chirality : 0.042 0.167 6668 Planarity : 0.005 0.055 7196 Dihedral : 8.951 89.498 7002 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.34 % Allowed : 15.24 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5432 helix: 1.50 (0.09), residues: 3020 sheet: -1.09 (0.24), residues: 388 loop : -0.66 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1309 HIS 0.005 0.002 HIS A 813 PHE 0.020 0.002 PHE C 274 TYR 0.035 0.003 TYR C 420 ARG 0.007 0.001 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 419 time to evaluate : 4.484 Fit side-chains REVERT: A 129 MET cc_start: 0.6650 (mmm) cc_final: 0.5834 (tmt) REVERT: A 161 GLU cc_start: 0.5471 (tt0) cc_final: 0.4973 (OUTLIER) REVERT: A 243 ASP cc_start: 0.5864 (m-30) cc_final: 0.5226 (t0) REVERT: A 253 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6486 (m110) REVERT: A 284 GLN cc_start: 0.6208 (mm-40) cc_final: 0.5537 (mt0) REVERT: A 368 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6460 (m-40) REVERT: A 413 ASN cc_start: 0.3427 (OUTLIER) cc_final: 0.3198 (t160) REVERT: A 420 TYR cc_start: 0.5345 (m-80) cc_final: 0.4891 (m-80) REVERT: A 621 LEU cc_start: 0.6829 (tt) cc_final: 0.6583 (tm) REVERT: A 683 MET cc_start: 0.7020 (tpt) cc_final: 0.6403 (mmm) REVERT: A 696 ASN cc_start: 0.6180 (OUTLIER) cc_final: 0.5919 (m-40) REVERT: A 702 ASN cc_start: 0.6920 (m-40) cc_final: 0.6469 (m-40) REVERT: A 725 ASP cc_start: 0.7133 (m-30) cc_final: 0.6625 (m-30) REVERT: A 870 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6137 (mtt180) REVERT: A 922 LYS cc_start: 0.6311 (pttm) cc_final: 0.5719 (ptmm) REVERT: A 932 MET cc_start: 0.6214 (mmt) cc_final: 0.5405 (mtt) REVERT: A 963 ASP cc_start: 0.6356 (t70) cc_final: 0.5671 (t0) REVERT: A 990 ASP cc_start: 0.6688 (m-30) cc_final: 0.6354 (m-30) REVERT: A 994 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5944 (mt-10) REVERT: A 1042 MET cc_start: 0.6645 (mtp) cc_final: 0.6057 (mmp) REVERT: A 1050 ASP cc_start: 0.5700 (m-30) cc_final: 0.5351 (m-30) REVERT: A 1084 MET cc_start: 0.5251 (mmt) cc_final: 0.4813 (mmp) REVERT: A 1126 ARG cc_start: 0.5184 (ttp-110) cc_final: 0.4932 (ttp80) REVERT: A 1128 ARG cc_start: 0.5547 (ttp80) cc_final: 0.5026 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5705 (mt0) cc_final: 0.5224 (mm110) REVERT: A 1166 GLN cc_start: 0.6332 (mm-40) cc_final: 0.5908 (tm-30) REVERT: A 1233 LEU cc_start: 0.7009 (tp) cc_final: 0.6557 (pp) REVERT: A 1365 MET cc_start: 0.7082 (ptm) cc_final: 0.6802 (ttm) REVERT: B 129 MET cc_start: 0.6652 (mmm) cc_final: 0.5819 (tmt) REVERT: B 161 GLU cc_start: 0.5471 (tt0) cc_final: 0.4974 (OUTLIER) REVERT: B 173 GLN cc_start: 0.5966 (OUTLIER) cc_final: 0.5739 (pp30) REVERT: B 253 ASN cc_start: 0.6774 (OUTLIER) cc_final: 0.6522 (m110) REVERT: B 284 GLN cc_start: 0.6208 (mm-40) cc_final: 0.5523 (mt0) REVERT: B 368 ASN cc_start: 0.6708 (OUTLIER) cc_final: 0.6459 (m-40) REVERT: B 413 ASN cc_start: 0.3427 (OUTLIER) cc_final: 0.3214 (t160) REVERT: B 621 LEU cc_start: 0.6828 (tt) cc_final: 0.6582 (tm) REVERT: B 683 MET cc_start: 0.7019 (tpt) cc_final: 0.6404 (mmm) REVERT: B 696 ASN cc_start: 0.6179 (OUTLIER) cc_final: 0.5917 (m-40) REVERT: B 702 ASN cc_start: 0.6920 (m-40) cc_final: 0.6468 (m-40) REVERT: B 725 ASP cc_start: 0.7136 (m-30) cc_final: 0.6632 (m-30) REVERT: B 870 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6133 (mtt180) REVERT: B 922 LYS cc_start: 0.6311 (pttm) cc_final: 0.5719 (ptmm) REVERT: B 932 MET cc_start: 0.6083 (mmt) cc_final: 0.5267 (mtt) REVERT: B 963 ASP cc_start: 0.6354 (t70) cc_final: 0.5667 (t0) REVERT: B 990 ASP cc_start: 0.6694 (m-30) cc_final: 0.6348 (m-30) REVERT: B 994 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5954 (mt-10) REVERT: B 1042 MET cc_start: 0.6652 (mtp) cc_final: 0.6058 (mmp) REVERT: B 1050 ASP cc_start: 0.5708 (m-30) cc_final: 0.5351 (m-30) REVERT: B 1084 MET cc_start: 0.5293 (mmt) cc_final: 0.4862 (mmp) REVERT: B 1126 ARG cc_start: 0.5198 (ttp-110) cc_final: 0.4906 (ttp80) REVERT: B 1128 ARG cc_start: 0.5520 (ttp80) cc_final: 0.4997 (mpt180) REVERT: B 1166 GLN cc_start: 0.6334 (mm-40) cc_final: 0.5909 (tm-30) REVERT: B 1233 LEU cc_start: 0.7010 (tp) cc_final: 0.6563 (pp) REVERT: B 1365 MET cc_start: 0.7064 (ptm) cc_final: 0.6797 (ttm) REVERT: C 129 MET cc_start: 0.6654 (mmm) cc_final: 0.5821 (tmt) REVERT: C 161 GLU cc_start: 0.5472 (tt0) cc_final: 0.4975 (OUTLIER) REVERT: C 243 ASP cc_start: 0.5873 (m-30) cc_final: 0.5235 (t0) REVERT: C 253 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6491 (m110) REVERT: C 284 GLN cc_start: 0.6215 (mm-40) cc_final: 0.5539 (mt0) REVERT: C 368 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.6465 (m-40) REVERT: C 413 ASN cc_start: 0.3446 (OUTLIER) cc_final: 0.3184 (t160) REVERT: C 420 TYR cc_start: 0.5326 (m-80) cc_final: 0.4848 (m-80) REVERT: C 621 LEU cc_start: 0.6832 (tt) cc_final: 0.6583 (tm) REVERT: C 683 MET cc_start: 0.7021 (tpt) cc_final: 0.6409 (mmm) REVERT: C 696 ASN cc_start: 0.6183 (OUTLIER) cc_final: 0.5922 (m-40) REVERT: C 702 ASN cc_start: 0.6921 (m-40) cc_final: 0.6469 (m-40) REVERT: C 725 ASP cc_start: 0.7139 (m-30) cc_final: 0.6633 (m-30) REVERT: C 870 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6140 (mtt180) REVERT: C 922 LYS cc_start: 0.6285 (pttm) cc_final: 0.5695 (ptmm) REVERT: C 932 MET cc_start: 0.6113 (mmt) cc_final: 0.5295 (mtt) REVERT: C 963 ASP cc_start: 0.6356 (t70) cc_final: 0.5659 (t0) REVERT: C 990 ASP cc_start: 0.6695 (m-30) cc_final: 0.6385 (m-30) REVERT: C 1042 MET cc_start: 0.6646 (mtp) cc_final: 0.6059 (mmp) REVERT: C 1050 ASP cc_start: 0.5710 (m-30) cc_final: 0.5357 (m-30) REVERT: C 1084 MET cc_start: 0.5295 (mmt) cc_final: 0.4864 (mmp) REVERT: C 1122 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.5241 (mtm110) REVERT: C 1128 ARG cc_start: 0.5564 (ttp80) cc_final: 0.5040 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5682 (mt0) cc_final: 0.5213 (mm110) REVERT: C 1166 GLN cc_start: 0.6325 (mm-40) cc_final: 0.5888 (tm-30) REVERT: C 1233 LEU cc_start: 0.7015 (tp) cc_final: 0.6569 (pp) REVERT: C 1365 MET cc_start: 0.7078 (ptm) cc_final: 0.6797 (ttm) REVERT: D 129 MET cc_start: 0.6652 (mmm) cc_final: 0.5831 (tmt) REVERT: D 161 GLU cc_start: 0.5470 (tt0) cc_final: 0.4973 (OUTLIER) REVERT: D 173 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5716 (pp30) REVERT: D 243 ASP cc_start: 0.5850 (m-30) cc_final: 0.5225 (t70) REVERT: D 253 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6515 (m110) REVERT: D 284 GLN cc_start: 0.6210 (mm-40) cc_final: 0.5525 (mt0) REVERT: D 368 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6460 (m-40) REVERT: D 413 ASN cc_start: 0.3421 (OUTLIER) cc_final: 0.3203 (t160) REVERT: D 420 TYR cc_start: 0.5345 (m-80) cc_final: 0.4888 (m-80) REVERT: D 621 LEU cc_start: 0.6830 (tt) cc_final: 0.6583 (tm) REVERT: D 683 MET cc_start: 0.7020 (tpt) cc_final: 0.6405 (mmm) REVERT: D 696 ASN cc_start: 0.6180 (OUTLIER) cc_final: 0.5918 (m-40) REVERT: D 702 ASN cc_start: 0.6920 (m-40) cc_final: 0.6471 (m-40) REVERT: D 725 ASP cc_start: 0.7137 (m-30) cc_final: 0.6633 (m-30) REVERT: D 870 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6135 (mtt180) REVERT: D 922 LYS cc_start: 0.6279 (pttm) cc_final: 0.5691 (ptmm) REVERT: D 932 MET cc_start: 0.6085 (mmt) cc_final: 0.5271 (mtt) REVERT: D 963 ASP cc_start: 0.6355 (t70) cc_final: 0.5657 (t0) REVERT: D 990 ASP cc_start: 0.6695 (m-30) cc_final: 0.6384 (m-30) REVERT: D 1042 MET cc_start: 0.6650 (mtp) cc_final: 0.6056 (mmp) REVERT: D 1050 ASP cc_start: 0.5695 (m-30) cc_final: 0.5350 (m-30) REVERT: D 1084 MET cc_start: 0.5292 (mmt) cc_final: 0.4862 (mmp) REVERT: D 1122 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.5235 (mtm110) REVERT: D 1128 ARG cc_start: 0.5515 (ttp80) cc_final: 0.4994 (mpt180) REVERT: D 1166 GLN cc_start: 0.6331 (mm-40) cc_final: 0.5907 (tm-30) REVERT: D 1233 LEU cc_start: 0.6981 (tp) cc_final: 0.6523 (pp) REVERT: D 1365 MET cc_start: 0.7092 (ptm) cc_final: 0.6813 (ttm) outliers start: 123 outliers final: 55 residues processed: 509 average time/residue: 1.3768 time to fit residues: 871.1144 Evaluate side-chains 441 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 364 time to evaluate : 4.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1330 ASP Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1382 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 ARG Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1382 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1382 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 437 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 391 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 448 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 471 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 307 GLN A 417 GLN A 702 ASN A 813 HIS A1055 GLN ** A1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 ASN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN B 417 GLN B 702 ASN B 813 HIS ** B1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 307 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 GLN C 702 ASN C 813 HIS ** C1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 417 GLN D 702 ASN D 813 HIS ** D1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1201 ASN ** D1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 41608 Z= 0.387 Angle : 0.722 12.428 56912 Z= 0.376 Chirality : 0.046 0.185 6668 Planarity : 0.006 0.056 7196 Dihedral : 9.114 88.106 6996 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.96 % Allowed : 16.05 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5432 helix: 0.84 (0.09), residues: 3032 sheet: -1.43 (0.23), residues: 412 loop : -1.15 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C1366 HIS 0.008 0.002 HIS B 514 PHE 0.018 0.003 PHE C 274 TYR 0.023 0.003 TYR A 420 ARG 0.008 0.001 ARG A 916 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 361 time to evaluate : 4.485 Fit side-chains REVERT: A 129 MET cc_start: 0.6667 (mmm) cc_final: 0.5839 (tmt) REVERT: A 161 GLU cc_start: 0.5575 (tt0) cc_final: 0.5064 (tt0) REVERT: A 284 GLN cc_start: 0.6258 (mm-40) cc_final: 0.5635 (mt0) REVERT: A 368 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6536 (m-40) REVERT: A 449 ASP cc_start: 0.5150 (OUTLIER) cc_final: 0.4753 (m-30) REVERT: A 591 ILE cc_start: 0.3786 (tp) cc_final: 0.3518 (mm) REVERT: A 621 LEU cc_start: 0.6674 (tt) cc_final: 0.6441 (tm) REVERT: A 683 MET cc_start: 0.6855 (tpt) cc_final: 0.6245 (mmm) REVERT: A 696 ASN cc_start: 0.5898 (OUTLIER) cc_final: 0.5642 (m-40) REVERT: A 870 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6201 (mtt180) REVERT: A 932 MET cc_start: 0.6176 (mmt) cc_final: 0.5341 (mtt) REVERT: A 963 ASP cc_start: 0.6512 (t70) cc_final: 0.5780 (t0) REVERT: A 990 ASP cc_start: 0.6599 (m-30) cc_final: 0.6281 (m-30) REVERT: A 994 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6002 (mt-10) REVERT: A 1042 MET cc_start: 0.6626 (mtp) cc_final: 0.6037 (mmp) REVERT: A 1084 MET cc_start: 0.5244 (mmt) cc_final: 0.4843 (mmp) REVERT: A 1128 ARG cc_start: 0.5764 (ttp80) cc_final: 0.5144 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5688 (mt0) cc_final: 0.5244 (mm110) REVERT: A 1233 LEU cc_start: 0.7043 (tp) cc_final: 0.6695 (pp) REVERT: B 129 MET cc_start: 0.6675 (mmm) cc_final: 0.5840 (tmt) REVERT: B 161 GLU cc_start: 0.5579 (tt0) cc_final: 0.5066 (tt0) REVERT: B 173 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: B 284 GLN cc_start: 0.6288 (mm-40) cc_final: 0.5681 (mt0) REVERT: B 368 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6573 (m-40) REVERT: B 449 ASP cc_start: 0.5185 (OUTLIER) cc_final: 0.4766 (m-30) REVERT: B 591 ILE cc_start: 0.3782 (tp) cc_final: 0.3515 (mm) REVERT: B 621 LEU cc_start: 0.6672 (tt) cc_final: 0.6441 (tm) REVERT: B 683 MET cc_start: 0.6852 (tpt) cc_final: 0.6246 (mmm) REVERT: B 696 ASN cc_start: 0.5908 (OUTLIER) cc_final: 0.5651 (m-40) REVERT: B 870 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6216 (mtt180) REVERT: B 932 MET cc_start: 0.6168 (mmt) cc_final: 0.5332 (mtt) REVERT: B 963 ASP cc_start: 0.6536 (t70) cc_final: 0.5802 (t0) REVERT: B 990 ASP cc_start: 0.6603 (m-30) cc_final: 0.6285 (m-30) REVERT: B 994 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5847 (mt-10) REVERT: B 1042 MET cc_start: 0.6626 (mtp) cc_final: 0.6038 (mmp) REVERT: B 1084 MET cc_start: 0.5298 (mmt) cc_final: 0.4887 (mmp) REVERT: B 1128 ARG cc_start: 0.5730 (ttp80) cc_final: 0.5112 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5619 (mt0) cc_final: 0.5167 (mm110) REVERT: B 1233 LEU cc_start: 0.7042 (tp) cc_final: 0.6691 (pp) REVERT: C 129 MET cc_start: 0.6621 (mmm) cc_final: 0.5852 (tmt) REVERT: C 161 GLU cc_start: 0.5624 (tt0) cc_final: 0.5094 (tt0) REVERT: C 284 GLN cc_start: 0.6290 (mm-40) cc_final: 0.5690 (mt0) REVERT: C 368 ASN cc_start: 0.6765 (OUTLIER) cc_final: 0.6538 (m-40) REVERT: C 413 ASN cc_start: 0.4193 (OUTLIER) cc_final: 0.3880 (t160) REVERT: C 449 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4743 (m-30) REVERT: C 591 ILE cc_start: 0.3781 (tp) cc_final: 0.3514 (mm) REVERT: C 621 LEU cc_start: 0.6679 (tt) cc_final: 0.6448 (tm) REVERT: C 683 MET cc_start: 0.6856 (tpt) cc_final: 0.6248 (mmm) REVERT: C 696 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.5655 (m-40) REVERT: C 870 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.6225 (mtt180) REVERT: C 932 MET cc_start: 0.6168 (mmt) cc_final: 0.5334 (mtt) REVERT: C 963 ASP cc_start: 0.6515 (t70) cc_final: 0.5789 (t0) REVERT: C 990 ASP cc_start: 0.6610 (m-30) cc_final: 0.6315 (m-30) REVERT: C 1042 MET cc_start: 0.6640 (mtp) cc_final: 0.6050 (mmp) REVERT: C 1084 MET cc_start: 0.5301 (mmt) cc_final: 0.4893 (mmp) REVERT: C 1128 ARG cc_start: 0.5825 (ttp80) cc_final: 0.5187 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5692 (mt0) cc_final: 0.5249 (mm110) REVERT: C 1233 LEU cc_start: 0.7099 (tp) cc_final: 0.6750 (pp) REVERT: D 112 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6172 (tmm-80) REVERT: D 129 MET cc_start: 0.6683 (mmm) cc_final: 0.5844 (tmt) REVERT: D 161 GLU cc_start: 0.5579 (tt0) cc_final: 0.5067 (tt0) REVERT: D 173 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5899 (tm-30) REVERT: D 284 GLN cc_start: 0.6303 (mm-40) cc_final: 0.5689 (mt0) REVERT: D 368 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6534 (m-40) REVERT: D 449 ASP cc_start: 0.5091 (OUTLIER) cc_final: 0.4709 (m-30) REVERT: D 591 ILE cc_start: 0.3780 (tp) cc_final: 0.3517 (mm) REVERT: D 621 LEU cc_start: 0.6679 (tt) cc_final: 0.6447 (tm) REVERT: D 683 MET cc_start: 0.6853 (tpt) cc_final: 0.6251 (mmm) REVERT: D 696 ASN cc_start: 0.5910 (OUTLIER) cc_final: 0.5652 (m-40) REVERT: D 870 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.6234 (mtt180) REVERT: D 932 MET cc_start: 0.6176 (mmt) cc_final: 0.5344 (mtt) REVERT: D 963 ASP cc_start: 0.6496 (t70) cc_final: 0.5767 (t0) REVERT: D 990 ASP cc_start: 0.6614 (m-30) cc_final: 0.6320 (m-30) REVERT: D 1042 MET cc_start: 0.6627 (mtp) cc_final: 0.6040 (mmp) REVERT: D 1084 MET cc_start: 0.5299 (mmt) cc_final: 0.4887 (mmp) REVERT: D 1128 ARG cc_start: 0.5729 (ttp80) cc_final: 0.5092 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5588 (mt0) cc_final: 0.5133 (mm110) REVERT: D 1233 LEU cc_start: 0.7043 (tp) cc_final: 0.6690 (pp) outliers start: 146 outliers final: 66 residues processed: 482 average time/residue: 1.3727 time to fit residues: 822.5156 Evaluate side-chains 428 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 340 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1330 ASP Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1382 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1382 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 510 LYS Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1382 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 176 optimal weight: 4.9990 chunk 473 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 526 optimal weight: 0.9980 chunk 436 optimal weight: 0.4980 chunk 243 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A1140 ASN A1201 ASN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 413 ASN B 598 GLN B1140 ASN B1201 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 ASN C1201 ASN C1261 GLN ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 413 ASN D1140 ASN D1201 ASN ** D1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41608 Z= 0.189 Angle : 0.531 9.822 56912 Z= 0.276 Chirality : 0.039 0.153 6668 Planarity : 0.004 0.055 7196 Dihedral : 8.726 88.134 6996 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.39 % Allowed : 17.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.11), residues: 5432 helix: 1.51 (0.09), residues: 3028 sheet: -1.19 (0.22), residues: 460 loop : -0.99 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1366 HIS 0.004 0.001 HIS B 886 PHE 0.013 0.001 PHE A 274 TYR 0.016 0.002 TYR B 466 ARG 0.005 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 391 time to evaluate : 4.385 Fit side-chains REVERT: A 129 MET cc_start: 0.6749 (mmm) cc_final: 0.5870 (tmt) REVERT: A 161 GLU cc_start: 0.5609 (tt0) cc_final: 0.5080 (tt0) REVERT: A 284 GLN cc_start: 0.6212 (mm-40) cc_final: 0.5630 (mt0) REVERT: A 368 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6509 (m-40) REVERT: A 591 ILE cc_start: 0.4061 (tp) cc_final: 0.3795 (mm) REVERT: A 621 LEU cc_start: 0.6876 (tt) cc_final: 0.6591 (tm) REVERT: A 683 MET cc_start: 0.6887 (tpt) cc_final: 0.6251 (mmm) REVERT: A 696 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5561 (t0) REVERT: A 725 ASP cc_start: 0.7249 (m-30) cc_final: 0.6740 (m-30) REVERT: A 870 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6097 (mtt180) REVERT: A 922 LYS cc_start: 0.6371 (pttm) cc_final: 0.5764 (ptmm) REVERT: A 932 MET cc_start: 0.6180 (mmt) cc_final: 0.5361 (mtt) REVERT: A 963 ASP cc_start: 0.6491 (t70) cc_final: 0.5710 (t0) REVERT: A 990 ASP cc_start: 0.6611 (m-30) cc_final: 0.6329 (m-30) REVERT: A 994 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6119 (mt-10) REVERT: A 1042 MET cc_start: 0.6643 (mtp) cc_final: 0.6049 (mmp) REVERT: A 1084 MET cc_start: 0.5443 (mmt) cc_final: 0.5006 (mmp) REVERT: A 1128 ARG cc_start: 0.5689 (ttp80) cc_final: 0.5098 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5556 (mt0) cc_final: 0.5134 (mm110) REVERT: A 1144 VAL cc_start: 0.7261 (t) cc_final: 0.6971 (t) REVERT: A 1233 LEU cc_start: 0.6926 (tp) cc_final: 0.6580 (pp) REVERT: A 1365 MET cc_start: 0.6821 (ttm) cc_final: 0.6587 (ttp) REVERT: B 112 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6295 (ttp-170) REVERT: B 129 MET cc_start: 0.6744 (mmm) cc_final: 0.5863 (tmt) REVERT: B 161 GLU cc_start: 0.5620 (tt0) cc_final: 0.5078 (tt0) REVERT: B 173 GLN cc_start: 0.6188 (OUTLIER) cc_final: 0.5863 (tm-30) REVERT: B 284 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5628 (mt0) REVERT: B 368 ASN cc_start: 0.6806 (OUTLIER) cc_final: 0.6507 (m-40) REVERT: B 591 ILE cc_start: 0.4109 (tp) cc_final: 0.3848 (mm) REVERT: B 621 LEU cc_start: 0.6866 (tt) cc_final: 0.6585 (tm) REVERT: B 683 MET cc_start: 0.6889 (tpt) cc_final: 0.6260 (mmm) REVERT: B 696 ASN cc_start: 0.5958 (OUTLIER) cc_final: 0.5557 (t0) REVERT: B 725 ASP cc_start: 0.7248 (m-30) cc_final: 0.6739 (m-30) REVERT: B 870 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6046 (mtt180) REVERT: B 922 LYS cc_start: 0.6298 (pttm) cc_final: 0.5690 (ptmm) REVERT: B 932 MET cc_start: 0.6119 (mmt) cc_final: 0.5299 (mtt) REVERT: B 963 ASP cc_start: 0.6500 (t70) cc_final: 0.5703 (t0) REVERT: B 990 ASP cc_start: 0.6622 (m-30) cc_final: 0.6298 (m-30) REVERT: B 994 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6102 (mt-10) REVERT: B 1042 MET cc_start: 0.6644 (mtp) cc_final: 0.6050 (mmp) REVERT: B 1084 MET cc_start: 0.5419 (mmt) cc_final: 0.4990 (mmp) REVERT: B 1085 ARG cc_start: 0.4210 (tpt170) cc_final: 0.3918 (tpp80) REVERT: B 1128 ARG cc_start: 0.5710 (ttp80) cc_final: 0.5119 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5510 (mt0) cc_final: 0.5067 (mm110) REVERT: B 1144 VAL cc_start: 0.7271 (t) cc_final: 0.6981 (t) REVERT: B 1233 LEU cc_start: 0.6914 (tp) cc_final: 0.6587 (pp) REVERT: B 1365 MET cc_start: 0.6804 (ttm) cc_final: 0.6557 (ttp) REVERT: B 1467 MET cc_start: 0.8224 (mtp) cc_final: 0.7735 (ttm) REVERT: C 129 MET cc_start: 0.6671 (mmm) cc_final: 0.5779 (tmt) REVERT: C 161 GLU cc_start: 0.5631 (tt0) cc_final: 0.5085 (tt0) REVERT: C 284 GLN cc_start: 0.6222 (mm-40) cc_final: 0.5633 (mt0) REVERT: C 368 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6504 (m-40) REVERT: C 413 ASN cc_start: 0.4168 (OUTLIER) cc_final: 0.3693 (t160) REVERT: C 591 ILE cc_start: 0.4061 (tp) cc_final: 0.3807 (mm) REVERT: C 621 LEU cc_start: 0.6868 (tt) cc_final: 0.6585 (tm) REVERT: C 683 MET cc_start: 0.6912 (tpt) cc_final: 0.6286 (mmm) REVERT: C 696 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.5563 (t0) REVERT: C 725 ASP cc_start: 0.7250 (m-30) cc_final: 0.6741 (m-30) REVERT: C 870 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6099 (mtt180) REVERT: C 922 LYS cc_start: 0.6371 (pttm) cc_final: 0.5768 (ptmm) REVERT: C 932 MET cc_start: 0.6203 (mmt) cc_final: 0.5364 (mtt) REVERT: C 963 ASP cc_start: 0.6495 (t70) cc_final: 0.5698 (t0) REVERT: C 990 ASP cc_start: 0.6595 (m-30) cc_final: 0.6293 (m-30) REVERT: C 1042 MET cc_start: 0.6652 (mtp) cc_final: 0.6049 (mmp) REVERT: C 1084 MET cc_start: 0.5376 (mmt) cc_final: 0.4973 (mmp) REVERT: C 1085 ARG cc_start: 0.4214 (tpt170) cc_final: 0.3921 (tpp80) REVERT: C 1128 ARG cc_start: 0.5722 (ttp80) cc_final: 0.5129 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5563 (mt0) cc_final: 0.5140 (mm110) REVERT: C 1144 VAL cc_start: 0.7274 (t) cc_final: 0.6986 (t) REVERT: C 1233 LEU cc_start: 0.6922 (tp) cc_final: 0.6588 (pp) REVERT: D 112 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6273 (ttp-170) REVERT: D 129 MET cc_start: 0.6748 (mmm) cc_final: 0.5871 (tmt) REVERT: D 161 GLU cc_start: 0.5613 (tt0) cc_final: 0.5082 (tt0) REVERT: D 173 GLN cc_start: 0.6188 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: D 284 GLN cc_start: 0.6219 (mm-40) cc_final: 0.5632 (mt0) REVERT: D 368 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6507 (m-40) REVERT: D 591 ILE cc_start: 0.3945 (tp) cc_final: 0.3668 (mm) REVERT: D 621 LEU cc_start: 0.6867 (tt) cc_final: 0.6584 (tm) REVERT: D 683 MET cc_start: 0.6902 (tpt) cc_final: 0.6271 (mmm) REVERT: D 696 ASN cc_start: 0.5959 (OUTLIER) cc_final: 0.5559 (t0) REVERT: D 725 ASP cc_start: 0.7249 (m-30) cc_final: 0.6741 (m-30) REVERT: D 870 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6044 (mtt180) REVERT: D 922 LYS cc_start: 0.6297 (pttm) cc_final: 0.5689 (ptmm) REVERT: D 932 MET cc_start: 0.6163 (mmt) cc_final: 0.5345 (mtt) REVERT: D 963 ASP cc_start: 0.6499 (t70) cc_final: 0.5707 (t0) REVERT: D 990 ASP cc_start: 0.6595 (m-30) cc_final: 0.6294 (m-30) REVERT: D 1042 MET cc_start: 0.6643 (mtp) cc_final: 0.6049 (mmp) REVERT: D 1084 MET cc_start: 0.5419 (mmt) cc_final: 0.4981 (mmp) REVERT: D 1085 ARG cc_start: 0.4174 (tpt170) cc_final: 0.3896 (tpp80) REVERT: D 1128 ARG cc_start: 0.5731 (ttp80) cc_final: 0.5141 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5520 (mt0) cc_final: 0.5059 (mm110) REVERT: D 1144 VAL cc_start: 0.7274 (t) cc_final: 0.6985 (t) REVERT: D 1233 LEU cc_start: 0.6925 (tp) cc_final: 0.6579 (pp) REVERT: D 1365 MET cc_start: 0.6807 (ttm) cc_final: 0.6562 (ttp) REVERT: D 1467 MET cc_start: 0.8225 (mtp) cc_final: 0.7734 (ttm) outliers start: 125 outliers final: 66 residues processed: 498 average time/residue: 1.3179 time to fit residues: 823.4911 Evaluate side-chains 447 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 362 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1382 THR Chi-restraints excluded: chain B residue 1430 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1382 THR Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1430 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 507 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 chunk 384 optimal weight: 0.7980 chunk 297 optimal weight: 0.6980 chunk 443 optimal weight: 0.0770 chunk 293 optimal weight: 8.9990 chunk 524 optimal weight: 7.9990 chunk 328 optimal weight: 0.0980 chunk 319 optimal weight: 10.0000 chunk 242 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A1201 ASN A1261 GLN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN B1201 ASN B1261 GLN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 GLN C 598 GLN C1201 ASN ** C1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN D1201 ASN D1261 GLN ** D1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 41608 Z= 0.135 Angle : 0.476 7.591 56912 Z= 0.243 Chirality : 0.037 0.157 6668 Planarity : 0.004 0.054 7196 Dihedral : 8.396 89.072 6996 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.74 % Allowed : 18.17 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 5432 helix: 2.05 (0.09), residues: 3016 sheet: -0.94 (0.23), residues: 432 loop : -0.84 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1366 HIS 0.003 0.001 HIS A 886 PHE 0.010 0.001 PHE A 941 TYR 0.017 0.001 TYR D 466 ARG 0.004 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 382 time to evaluate : 4.648 Fit side-chains REVERT: A 129 MET cc_start: 0.6471 (mmm) cc_final: 0.5875 (tmt) REVERT: A 161 GLU cc_start: 0.5657 (tt0) cc_final: 0.5140 (tt0) REVERT: A 248 THR cc_start: 0.6737 (m) cc_final: 0.5927 (p) REVERT: A 284 GLN cc_start: 0.6213 (mm-40) cc_final: 0.5660 (mt0) REVERT: A 368 ASN cc_start: 0.6674 (OUTLIER) cc_final: 0.6349 (m-40) REVERT: A 591 ILE cc_start: 0.4201 (tp) cc_final: 0.3947 (mm) REVERT: A 621 LEU cc_start: 0.6843 (tt) cc_final: 0.6565 (tm) REVERT: A 683 MET cc_start: 0.6820 (tpt) cc_final: 0.6202 (mmm) REVERT: A 696 ASN cc_start: 0.5924 (OUTLIER) cc_final: 0.5579 (t0) REVERT: A 725 ASP cc_start: 0.7143 (m-30) cc_final: 0.6656 (m-30) REVERT: A 870 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6032 (mtt180) REVERT: A 922 LYS cc_start: 0.6261 (pttm) cc_final: 0.5667 (ptmm) REVERT: A 932 MET cc_start: 0.6129 (mmt) cc_final: 0.5331 (mtt) REVERT: A 990 ASP cc_start: 0.6592 (m-30) cc_final: 0.6263 (m-30) REVERT: A 1042 MET cc_start: 0.6622 (mtp) cc_final: 0.6027 (mmp) REVERT: A 1084 MET cc_start: 0.5339 (mmt) cc_final: 0.4864 (mmp) REVERT: A 1128 ARG cc_start: 0.5671 (ttp80) cc_final: 0.5104 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5593 (mt0) cc_final: 0.5116 (mm110) REVERT: A 1144 VAL cc_start: 0.7227 (t) cc_final: 0.6957 (t) REVERT: A 1233 LEU cc_start: 0.6962 (tp) cc_final: 0.6491 (mm) REVERT: A 1467 MET cc_start: 0.8200 (mtp) cc_final: 0.7641 (ttm) REVERT: B 129 MET cc_start: 0.6468 (mmm) cc_final: 0.5785 (tmt) REVERT: B 161 GLU cc_start: 0.5663 (tt0) cc_final: 0.5104 (tt0) REVERT: B 284 GLN cc_start: 0.6209 (mm-40) cc_final: 0.5658 (mt0) REVERT: B 368 ASN cc_start: 0.6674 (OUTLIER) cc_final: 0.6350 (m-40) REVERT: B 591 ILE cc_start: 0.4131 (tp) cc_final: 0.3759 (mp) REVERT: B 621 LEU cc_start: 0.6839 (tt) cc_final: 0.6558 (tm) REVERT: B 683 MET cc_start: 0.6814 (tpt) cc_final: 0.6210 (mmm) REVERT: B 696 ASN cc_start: 0.5923 (OUTLIER) cc_final: 0.5581 (t0) REVERT: B 725 ASP cc_start: 0.7186 (m-30) cc_final: 0.6683 (m-30) REVERT: B 870 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6031 (mtt180) REVERT: B 922 LYS cc_start: 0.6252 (pttm) cc_final: 0.5652 (ptmm) REVERT: B 932 MET cc_start: 0.6108 (mmt) cc_final: 0.5305 (mtt) REVERT: B 990 ASP cc_start: 0.6548 (m-30) cc_final: 0.6227 (m-30) REVERT: B 1042 MET cc_start: 0.6625 (mtp) cc_final: 0.6033 (mmp) REVERT: B 1084 MET cc_start: 0.5475 (mmt) cc_final: 0.5032 (mmp) REVERT: B 1085 ARG cc_start: 0.4253 (tpt170) cc_final: 0.3931 (tpp80) REVERT: B 1128 ARG cc_start: 0.5668 (ttp80) cc_final: 0.5092 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5572 (mt0) cc_final: 0.5077 (mm110) REVERT: B 1144 VAL cc_start: 0.7224 (t) cc_final: 0.6956 (t) REVERT: B 1233 LEU cc_start: 0.6956 (tp) cc_final: 0.6576 (pp) REVERT: B 1365 MET cc_start: 0.6897 (ttm) cc_final: 0.6675 (ttp) REVERT: B 1467 MET cc_start: 0.8218 (mtp) cc_final: 0.7685 (ttm) REVERT: C 76 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4773 (tpp) REVERT: C 129 MET cc_start: 0.6427 (mmm) cc_final: 0.5844 (tmt) REVERT: C 161 GLU cc_start: 0.5666 (tt0) cc_final: 0.5159 (tt0) REVERT: C 248 THR cc_start: 0.6756 (m) cc_final: 0.5952 (p) REVERT: C 284 GLN cc_start: 0.6238 (mm-40) cc_final: 0.5691 (mt0) REVERT: C 368 ASN cc_start: 0.6676 (OUTLIER) cc_final: 0.6348 (m-40) REVERT: C 413 ASN cc_start: 0.3736 (OUTLIER) cc_final: 0.3492 (t160) REVERT: C 591 ILE cc_start: 0.4142 (tp) cc_final: 0.3750 (mp) REVERT: C 621 LEU cc_start: 0.6827 (tt) cc_final: 0.6550 (tm) REVERT: C 683 MET cc_start: 0.6788 (tpt) cc_final: 0.6194 (mmm) REVERT: C 696 ASN cc_start: 0.5953 (OUTLIER) cc_final: 0.5577 (t0) REVERT: C 725 ASP cc_start: 0.7145 (m-30) cc_final: 0.6658 (m-30) REVERT: C 870 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6035 (mtt180) REVERT: C 922 LYS cc_start: 0.6252 (pttm) cc_final: 0.5668 (ptmm) REVERT: C 932 MET cc_start: 0.6100 (mmt) cc_final: 0.5285 (mtt) REVERT: C 990 ASP cc_start: 0.6568 (m-30) cc_final: 0.6289 (m-30) REVERT: C 1042 MET cc_start: 0.6623 (mtp) cc_final: 0.6027 (mmp) REVERT: C 1084 MET cc_start: 0.5447 (mmt) cc_final: 0.5016 (mmp) REVERT: C 1085 ARG cc_start: 0.4263 (tpt170) cc_final: 0.3940 (tpp80) REVERT: C 1128 ARG cc_start: 0.5682 (ttp80) cc_final: 0.5103 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5607 (mt0) cc_final: 0.5131 (mm110) REVERT: C 1144 VAL cc_start: 0.7246 (t) cc_final: 0.6980 (t) REVERT: C 1233 LEU cc_start: 0.6990 (tp) cc_final: 0.6494 (mm) REVERT: C 1365 MET cc_start: 0.6961 (ttm) cc_final: 0.6706 (ttp) REVERT: C 1467 MET cc_start: 0.8280 (mtp) cc_final: 0.7705 (ttm) REVERT: D 129 MET cc_start: 0.6464 (mmm) cc_final: 0.5874 (tmt) REVERT: D 161 GLU cc_start: 0.5663 (tt0) cc_final: 0.5105 (tt0) REVERT: D 284 GLN cc_start: 0.6219 (mm-40) cc_final: 0.5662 (mt0) REVERT: D 368 ASN cc_start: 0.6674 (OUTLIER) cc_final: 0.6349 (m-40) REVERT: D 591 ILE cc_start: 0.4256 (tp) cc_final: 0.3932 (mm) REVERT: D 621 LEU cc_start: 0.6829 (tt) cc_final: 0.6554 (tm) REVERT: D 683 MET cc_start: 0.6790 (tpt) cc_final: 0.6194 (mmm) REVERT: D 696 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.5584 (t0) REVERT: D 725 ASP cc_start: 0.7144 (m-30) cc_final: 0.6656 (m-30) REVERT: D 870 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6036 (mtt180) REVERT: D 922 LYS cc_start: 0.6288 (pttm) cc_final: 0.5679 (ptmm) REVERT: D 932 MET cc_start: 0.6155 (mmt) cc_final: 0.5311 (mtt) REVERT: D 990 ASP cc_start: 0.6604 (m-30) cc_final: 0.6325 (m-30) REVERT: D 1042 MET cc_start: 0.6624 (mtp) cc_final: 0.6033 (mmp) REVERT: D 1084 MET cc_start: 0.5474 (mmt) cc_final: 0.5032 (mmp) REVERT: D 1085 ARG cc_start: 0.4254 (tpt170) cc_final: 0.3931 (tpp80) REVERT: D 1128 ARG cc_start: 0.5688 (ttp80) cc_final: 0.5087 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5576 (mt0) cc_final: 0.5105 (mm110) REVERT: D 1144 VAL cc_start: 0.7241 (t) cc_final: 0.6972 (t) REVERT: D 1233 LEU cc_start: 0.7005 (tp) cc_final: 0.6519 (mm) REVERT: D 1467 MET cc_start: 0.8225 (mtp) cc_final: 0.7680 (ttm) outliers start: 101 outliers final: 38 residues processed: 463 average time/residue: 1.3520 time to fit residues: 783.3998 Evaluate side-chains 414 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 362 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 324 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 357 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 412 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A1201 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1276 ASN B 598 GLN B1201 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1276 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 GLN C 598 GLN C1201 ASN ** C1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN D1201 ASN ** D1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1276 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 41608 Z= 0.406 Angle : 0.735 12.084 56912 Z= 0.378 Chirality : 0.046 0.173 6668 Planarity : 0.006 0.053 7196 Dihedral : 9.016 88.070 6996 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.39 % Allowed : 18.11 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5432 helix: 1.04 (0.09), residues: 3016 sheet: -1.53 (0.21), residues: 468 loop : -1.27 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 842 HIS 0.007 0.002 HIS A 677 PHE 0.018 0.003 PHE B 268 TYR 0.023 0.003 TYR B 420 ARG 0.008 0.001 ARG C1465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 366 time to evaluate : 4.551 Fit side-chains REVERT: A 129 MET cc_start: 0.6347 (mmm) cc_final: 0.5663 (tmt) REVERT: A 284 GLN cc_start: 0.6343 (mm-40) cc_final: 0.5749 (mt0) REVERT: A 368 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6550 (m-40) REVERT: A 449 ASP cc_start: 0.5139 (OUTLIER) cc_final: 0.4837 (m-30) REVERT: A 621 LEU cc_start: 0.6723 (tt) cc_final: 0.6504 (tm) REVERT: A 683 MET cc_start: 0.6825 (tpt) cc_final: 0.6153 (mmm) REVERT: A 696 ASN cc_start: 0.5981 (OUTLIER) cc_final: 0.5617 (t0) REVERT: A 870 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6242 (mtt180) REVERT: A 932 MET cc_start: 0.6234 (mmt) cc_final: 0.5433 (mtt) REVERT: A 963 ASP cc_start: 0.6515 (t70) cc_final: 0.5799 (t0) REVERT: A 994 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5965 (mt-10) REVERT: A 1042 MET cc_start: 0.6627 (mtp) cc_final: 0.6030 (mmp) REVERT: A 1122 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.5207 (mtm110) REVERT: A 1128 ARG cc_start: 0.5930 (ttp80) cc_final: 0.5215 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5610 (mt0) cc_final: 0.5140 (mm110) REVERT: A 1166 GLN cc_start: 0.6372 (mm-40) cc_final: 0.5997 (tm-30) REVERT: A 1233 LEU cc_start: 0.6996 (tp) cc_final: 0.6690 (pp) REVERT: A 1467 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7601 (ttm) REVERT: B 129 MET cc_start: 0.6592 (mmm) cc_final: 0.5812 (tmt) REVERT: B 284 GLN cc_start: 0.6350 (mm-40) cc_final: 0.5744 (mt0) REVERT: B 368 ASN cc_start: 0.6765 (OUTLIER) cc_final: 0.6551 (m-40) REVERT: B 449 ASP cc_start: 0.5145 (OUTLIER) cc_final: 0.4810 (m-30) REVERT: B 621 LEU cc_start: 0.6723 (tt) cc_final: 0.6506 (tm) REVERT: B 683 MET cc_start: 0.6823 (tpt) cc_final: 0.6158 (mmm) REVERT: B 696 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5624 (t0) REVERT: B 870 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6243 (mtt180) REVERT: B 932 MET cc_start: 0.6265 (mmt) cc_final: 0.5456 (mtt) REVERT: B 963 ASP cc_start: 0.6521 (t70) cc_final: 0.5809 (t0) REVERT: B 994 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6022 (mt-10) REVERT: B 1042 MET cc_start: 0.6627 (mtp) cc_final: 0.6029 (mmp) REVERT: B 1085 ARG cc_start: 0.4293 (tpt170) cc_final: 0.4028 (tpp80) REVERT: B 1122 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.5207 (mtm110) REVERT: B 1128 ARG cc_start: 0.5879 (ttp80) cc_final: 0.5098 (ttm-80) REVERT: B 1166 GLN cc_start: 0.6379 (mm-40) cc_final: 0.6001 (tm-30) REVERT: B 1233 LEU cc_start: 0.6959 (tp) cc_final: 0.6675 (pp) REVERT: B 1365 MET cc_start: 0.7010 (ttm) cc_final: 0.6696 (ttp) REVERT: C 76 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4860 (tpp) REVERT: C 129 MET cc_start: 0.6388 (mmm) cc_final: 0.5699 (tmt) REVERT: C 284 GLN cc_start: 0.6329 (mm-40) cc_final: 0.5728 (mt0) REVERT: C 368 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6617 (m-40) REVERT: C 413 ASN cc_start: 0.4429 (OUTLIER) cc_final: 0.4087 (t0) REVERT: C 449 ASP cc_start: 0.5081 (OUTLIER) cc_final: 0.4743 (m-30) REVERT: C 621 LEU cc_start: 0.6725 (tt) cc_final: 0.6506 (tm) REVERT: C 683 MET cc_start: 0.6822 (tpt) cc_final: 0.6165 (mmm) REVERT: C 696 ASN cc_start: 0.5958 (OUTLIER) cc_final: 0.5586 (t0) REVERT: C 870 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.6243 (mtt180) REVERT: C 932 MET cc_start: 0.6260 (mmt) cc_final: 0.5452 (mtt) REVERT: C 963 ASP cc_start: 0.6515 (t70) cc_final: 0.5783 (t0) REVERT: C 990 ASP cc_start: 0.6598 (m-30) cc_final: 0.6394 (m-30) REVERT: C 1042 MET cc_start: 0.6631 (mtp) cc_final: 0.6032 (mmp) REVERT: C 1128 ARG cc_start: 0.5923 (ttp80) cc_final: 0.5264 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5582 (mt0) cc_final: 0.5114 (mm110) REVERT: C 1166 GLN cc_start: 0.6375 (mm-40) cc_final: 0.5993 (tm-30) REVERT: C 1233 LEU cc_start: 0.7009 (tp) cc_final: 0.6694 (pp) REVERT: C 1365 MET cc_start: 0.7036 (ttm) cc_final: 0.6731 (ttp) REVERT: C 1467 MET cc_start: 0.8161 (mtp) cc_final: 0.7617 (ttm) REVERT: D 129 MET cc_start: 0.6344 (mmm) cc_final: 0.5664 (tmt) REVERT: D 284 GLN cc_start: 0.6341 (mm-40) cc_final: 0.5741 (mt0) REVERT: D 368 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6551 (m-40) REVERT: D 621 LEU cc_start: 0.6725 (tt) cc_final: 0.6505 (tm) REVERT: D 683 MET cc_start: 0.6830 (tpt) cc_final: 0.6167 (mmm) REVERT: D 696 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5625 (t0) REVERT: D 870 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6241 (mtt180) REVERT: D 932 MET cc_start: 0.6265 (mmt) cc_final: 0.5456 (mtt) REVERT: D 963 ASP cc_start: 0.6540 (t70) cc_final: 0.5810 (t0) REVERT: D 990 ASP cc_start: 0.6595 (m-30) cc_final: 0.6374 (m-30) REVERT: D 1042 MET cc_start: 0.6629 (mtp) cc_final: 0.6032 (mmp) REVERT: D 1085 ARG cc_start: 0.4271 (tpt170) cc_final: 0.4016 (tpp80) REVERT: D 1128 ARG cc_start: 0.5896 (ttp80) cc_final: 0.5238 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5358 (mt0) cc_final: 0.4849 (mm110) REVERT: D 1166 GLN cc_start: 0.6373 (mm-40) cc_final: 0.5994 (tm-30) REVERT: D 1233 LEU cc_start: 0.7006 (tp) cc_final: 0.6689 (pp) outliers start: 125 outliers final: 69 residues processed: 474 average time/residue: 1.3373 time to fit residues: 794.0458 Evaluate side-chains 430 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 339 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 ARG Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1467 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1382 THR Chi-restraints excluded: chain B residue 1430 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1382 THR Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1382 THR Chi-restraints excluded: chain D residue 1430 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 476 optimal weight: 0.0010 chunk 502 optimal weight: 0.8980 chunk 458 optimal weight: 5.9990 chunk 488 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 383 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 441 optimal weight: 4.9990 chunk 462 optimal weight: 0.0040 chunk 486 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A1201 ASN A1261 GLN A1276 ASN B 598 GLN B1201 ASN B1261 GLN B1276 ASN C 417 GLN C 598 GLN C1201 ASN ** C1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN D1201 ASN D1261 GLN D1276 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41608 Z= 0.143 Angle : 0.499 8.514 56912 Z= 0.255 Chirality : 0.038 0.156 6668 Planarity : 0.004 0.055 7196 Dihedral : 8.512 89.087 6996 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 19.90 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.11), residues: 5432 helix: 1.90 (0.09), residues: 2992 sheet: -1.13 (0.23), residues: 432 loop : -0.93 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1366 HIS 0.003 0.001 HIS C 886 PHE 0.016 0.001 PHE B 268 TYR 0.032 0.002 TYR C 110 ARG 0.005 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 351 time to evaluate : 5.066 Fit side-chains REVERT: A 76 MET cc_start: 0.5096 (ttp) cc_final: 0.4866 (tpp) REVERT: A 129 MET cc_start: 0.6266 (mmm) cc_final: 0.5637 (tmt) REVERT: A 284 GLN cc_start: 0.6384 (mm-40) cc_final: 0.5703 (mt0) REVERT: A 368 ASN cc_start: 0.6706 (OUTLIER) cc_final: 0.6388 (m-40) REVERT: A 621 LEU cc_start: 0.6845 (tt) cc_final: 0.6557 (tm) REVERT: A 683 MET cc_start: 0.6893 (tpt) cc_final: 0.6301 (mmm) REVERT: A 696 ASN cc_start: 0.5929 (t0) cc_final: 0.5577 (t0) REVERT: A 725 ASP cc_start: 0.7148 (m-30) cc_final: 0.6663 (m-30) REVERT: A 870 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.6023 (mtt180) REVERT: A 922 LYS cc_start: 0.6272 (pttm) cc_final: 0.5700 (ptmm) REVERT: A 932 MET cc_start: 0.6160 (mmt) cc_final: 0.5368 (mtt) REVERT: A 963 ASP cc_start: 0.6428 (t70) cc_final: 0.5643 (t0) REVERT: A 1042 MET cc_start: 0.6618 (mtp) cc_final: 0.6019 (mmp) REVERT: A 1084 MET cc_start: 0.5233 (mpt) cc_final: 0.4863 (mmp) REVERT: A 1128 ARG cc_start: 0.5752 (ttp80) cc_final: 0.5191 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5470 (mt0) cc_final: 0.5033 (mm110) REVERT: A 1144 VAL cc_start: 0.7292 (t) cc_final: 0.7038 (t) REVERT: A 1233 LEU cc_start: 0.7075 (tp) cc_final: 0.6674 (pp) REVERT: A 1467 MET cc_start: 0.8195 (mtp) cc_final: 0.7611 (ttm) REVERT: B 76 MET cc_start: 0.5171 (ttp) cc_final: 0.4936 (tpp) REVERT: B 129 MET cc_start: 0.6485 (mmm) cc_final: 0.5721 (tmt) REVERT: B 284 GLN cc_start: 0.6438 (mm-40) cc_final: 0.5737 (mt0) REVERT: B 368 ASN cc_start: 0.6704 (OUTLIER) cc_final: 0.6387 (m-40) REVERT: B 621 LEU cc_start: 0.6844 (tt) cc_final: 0.6557 (tm) REVERT: B 683 MET cc_start: 0.6911 (tpt) cc_final: 0.6322 (mmm) REVERT: B 696 ASN cc_start: 0.5925 (t0) cc_final: 0.5572 (t0) REVERT: B 725 ASP cc_start: 0.7147 (m-30) cc_final: 0.6662 (m-30) REVERT: B 870 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.6023 (mtt180) REVERT: B 922 LYS cc_start: 0.6258 (pttm) cc_final: 0.5686 (ptmm) REVERT: B 932 MET cc_start: 0.6131 (mmt) cc_final: 0.5318 (mtt) REVERT: B 963 ASP cc_start: 0.6416 (t70) cc_final: 0.5608 (t0) REVERT: B 1042 MET cc_start: 0.6615 (mtp) cc_final: 0.6014 (mmp) REVERT: B 1085 ARG cc_start: 0.4107 (tpt170) cc_final: 0.3796 (tpp80) REVERT: B 1128 ARG cc_start: 0.5794 (ttp80) cc_final: 0.5123 (ttm-80) REVERT: B 1144 VAL cc_start: 0.7287 (t) cc_final: 0.7025 (t) REVERT: B 1233 LEU cc_start: 0.7072 (tp) cc_final: 0.6669 (pp) REVERT: B 1467 MET cc_start: 0.8203 (mtp) cc_final: 0.7658 (ttm) REVERT: C 76 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.5022 (tpp) REVERT: C 129 MET cc_start: 0.6271 (mmm) cc_final: 0.5635 (tmt) REVERT: C 284 GLN cc_start: 0.6387 (mm-40) cc_final: 0.5709 (mt0) REVERT: C 368 ASN cc_start: 0.6721 (OUTLIER) cc_final: 0.6390 (m-40) REVERT: C 413 ASN cc_start: 0.4212 (OUTLIER) cc_final: 0.3631 (t0) REVERT: C 621 LEU cc_start: 0.6843 (tt) cc_final: 0.6556 (tm) REVERT: C 683 MET cc_start: 0.6897 (tpt) cc_final: 0.6313 (mmm) REVERT: C 696 ASN cc_start: 0.5930 (t0) cc_final: 0.5580 (t0) REVERT: C 725 ASP cc_start: 0.7150 (m-30) cc_final: 0.6663 (m-30) REVERT: C 870 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6026 (mtt180) REVERT: C 922 LYS cc_start: 0.6266 (pttm) cc_final: 0.5677 (ptmm) REVERT: C 932 MET cc_start: 0.6131 (mmt) cc_final: 0.5319 (mtt) REVERT: C 963 ASP cc_start: 0.6431 (t70) cc_final: 0.5644 (t0) REVERT: C 1042 MET cc_start: 0.6618 (mtp) cc_final: 0.6020 (mmp) REVERT: C 1085 ARG cc_start: 0.4100 (tpt170) cc_final: 0.3798 (tpp80) REVERT: C 1128 ARG cc_start: 0.5758 (ttp80) cc_final: 0.5178 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5448 (mt0) cc_final: 0.5005 (mm110) REVERT: C 1144 VAL cc_start: 0.7294 (t) cc_final: 0.7041 (t) REVERT: C 1233 LEU cc_start: 0.7090 (tp) cc_final: 0.6694 (pp) REVERT: C 1467 MET cc_start: 0.8184 (mtp) cc_final: 0.7651 (ttm) REVERT: D 76 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4703 (tpp) REVERT: D 129 MET cc_start: 0.6248 (mmm) cc_final: 0.5629 (tmt) REVERT: D 284 GLN cc_start: 0.6397 (mm-40) cc_final: 0.5715 (mt0) REVERT: D 368 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6390 (m-40) REVERT: D 621 LEU cc_start: 0.6843 (tt) cc_final: 0.6556 (tm) REVERT: D 683 MET cc_start: 0.6894 (tpt) cc_final: 0.6305 (mmm) REVERT: D 696 ASN cc_start: 0.5866 (t0) cc_final: 0.5537 (t0) REVERT: D 725 ASP cc_start: 0.7147 (m-30) cc_final: 0.6661 (m-30) REVERT: D 870 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.6023 (mtt180) REVERT: D 922 LYS cc_start: 0.6276 (pttm) cc_final: 0.5706 (ptmm) REVERT: D 932 MET cc_start: 0.6131 (mmt) cc_final: 0.5317 (mtt) REVERT: D 963 ASP cc_start: 0.6371 (t70) cc_final: 0.5566 (t0) REVERT: D 1042 MET cc_start: 0.6616 (mtp) cc_final: 0.6020 (mmp) REVERT: D 1085 ARG cc_start: 0.4098 (tpt170) cc_final: 0.3796 (tpp80) REVERT: D 1128 ARG cc_start: 0.5721 (ttp80) cc_final: 0.5177 (mpt180) REVERT: D 1129 GLN cc_start: 0.5346 (mt0) cc_final: 0.4835 (mm110) REVERT: D 1144 VAL cc_start: 0.7296 (t) cc_final: 0.7044 (t) REVERT: D 1233 LEU cc_start: 0.7079 (tp) cc_final: 0.6681 (pp) REVERT: D 1361 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6354 (tp40) REVERT: D 1467 MET cc_start: 0.8206 (mtp) cc_final: 0.7663 (ttm) outliers start: 70 outliers final: 36 residues processed: 408 average time/residue: 1.3903 time to fit residues: 706.3691 Evaluate side-chains 385 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 337 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1430 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 320 optimal weight: 7.9990 chunk 516 optimal weight: 0.4980 chunk 315 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 359 optimal weight: 0.0970 chunk 541 optimal weight: 0.0970 chunk 498 optimal weight: 0.6980 chunk 431 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 overall best weight: 0.8778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 598 GLN C 598 GLN ** C1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN D 660 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41608 Z= 0.171 Angle : 0.520 9.757 56912 Z= 0.264 Chirality : 0.038 0.148 6668 Planarity : 0.004 0.057 7196 Dihedral : 8.467 88.315 6996 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.55 % Allowed : 19.88 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.11), residues: 5432 helix: 1.95 (0.09), residues: 3000 sheet: -1.21 (0.22), residues: 452 loop : -0.92 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1366 HIS 0.004 0.001 HIS C 886 PHE 0.017 0.001 PHE A 268 TYR 0.030 0.002 TYR A 110 ARG 0.004 0.000 ARG B 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 351 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.5079 (ttp) cc_final: 0.4863 (tpp) REVERT: A 129 MET cc_start: 0.6293 (mmm) cc_final: 0.5722 (tmt) REVERT: A 284 GLN cc_start: 0.6447 (mm-40) cc_final: 0.5767 (mt0) REVERT: A 368 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.6407 (m-40) REVERT: A 621 LEU cc_start: 0.6836 (tt) cc_final: 0.6554 (tm) REVERT: A 683 MET cc_start: 0.6841 (tpt) cc_final: 0.6240 (mmm) REVERT: A 696 ASN cc_start: 0.5953 (t0) cc_final: 0.5603 (t0) REVERT: A 725 ASP cc_start: 0.7166 (m-30) cc_final: 0.6662 (m-30) REVERT: A 870 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6011 (mtt180) REVERT: A 922 LYS cc_start: 0.6265 (pttm) cc_final: 0.5693 (ptmm) REVERT: A 932 MET cc_start: 0.6177 (mmt) cc_final: 0.5375 (mtt) REVERT: A 963 ASP cc_start: 0.6516 (t70) cc_final: 0.5729 (t0) REVERT: A 1042 MET cc_start: 0.6626 (mtp) cc_final: 0.6021 (mmp) REVERT: A 1128 ARG cc_start: 0.5727 (ttp80) cc_final: 0.5152 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5468 (mt0) cc_final: 0.4983 (mm110) REVERT: A 1233 LEU cc_start: 0.7018 (tp) cc_final: 0.6602 (pp) REVERT: B 129 MET cc_start: 0.6476 (mmm) cc_final: 0.5728 (tmt) REVERT: B 284 GLN cc_start: 0.6454 (mm-40) cc_final: 0.5746 (mt0) REVERT: B 368 ASN cc_start: 0.6724 (OUTLIER) cc_final: 0.6405 (m-40) REVERT: B 608 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6788 (mp) REVERT: B 621 LEU cc_start: 0.6835 (tt) cc_final: 0.6555 (tm) REVERT: B 683 MET cc_start: 0.6836 (tpt) cc_final: 0.6253 (mmm) REVERT: B 725 ASP cc_start: 0.7162 (m-30) cc_final: 0.6658 (m-30) REVERT: B 870 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6048 (mtt180) REVERT: B 922 LYS cc_start: 0.6264 (pttm) cc_final: 0.5692 (ptmm) REVERT: B 932 MET cc_start: 0.6172 (mmt) cc_final: 0.5364 (mtt) REVERT: B 1042 MET cc_start: 0.6625 (mtp) cc_final: 0.6021 (mmp) REVERT: B 1084 MET cc_start: 0.5222 (mpt) cc_final: 0.4912 (mmp) REVERT: B 1085 ARG cc_start: 0.4177 (tpt170) cc_final: 0.3875 (tpp80) REVERT: B 1128 ARG cc_start: 0.5783 (ttp80) cc_final: 0.5100 (ttm-80) REVERT: B 1233 LEU cc_start: 0.7066 (tp) cc_final: 0.6664 (pp) REVERT: B 1361 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6442 (tp40) REVERT: C 76 MET cc_start: 0.5292 (OUTLIER) cc_final: 0.4958 (tpp) REVERT: C 129 MET cc_start: 0.6291 (mmm) cc_final: 0.5713 (tmt) REVERT: C 284 GLN cc_start: 0.6465 (mm-40) cc_final: 0.5767 (mt0) REVERT: C 368 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6406 (m-40) REVERT: C 413 ASN cc_start: 0.4314 (OUTLIER) cc_final: 0.3647 (t0) REVERT: C 608 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6802 (mp) REVERT: C 621 LEU cc_start: 0.6832 (tt) cc_final: 0.6561 (tm) REVERT: C 683 MET cc_start: 0.6842 (tpt) cc_final: 0.6259 (mmm) REVERT: C 696 ASN cc_start: 0.5971 (t0) cc_final: 0.5601 (t0) REVERT: C 725 ASP cc_start: 0.7166 (m-30) cc_final: 0.6662 (m-30) REVERT: C 870 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6053 (mtt180) REVERT: C 922 LYS cc_start: 0.6261 (pttm) cc_final: 0.5679 (ptmm) REVERT: C 932 MET cc_start: 0.6196 (mmt) cc_final: 0.5384 (mtt) REVERT: C 963 ASP cc_start: 0.6517 (t70) cc_final: 0.5730 (t0) REVERT: C 1042 MET cc_start: 0.6626 (mtp) cc_final: 0.6017 (mmp) REVERT: C 1084 MET cc_start: 0.5227 (mpt) cc_final: 0.4917 (mmp) REVERT: C 1085 ARG cc_start: 0.4181 (tpt170) cc_final: 0.3877 (tpp80) REVERT: C 1128 ARG cc_start: 0.5724 (ttp80) cc_final: 0.5152 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5424 (mt0) cc_final: 0.4964 (mm110) REVERT: C 1233 LEU cc_start: 0.7074 (tp) cc_final: 0.6672 (pp) REVERT: C 1467 MET cc_start: 0.8195 (mtp) cc_final: 0.7612 (ttm) REVERT: D 76 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.4692 (tpp) REVERT: D 129 MET cc_start: 0.6299 (mmm) cc_final: 0.5722 (tmt) REVERT: D 284 GLN cc_start: 0.6462 (mm-40) cc_final: 0.5763 (mt0) REVERT: D 368 ASN cc_start: 0.6726 (OUTLIER) cc_final: 0.6406 (m-40) REVERT: D 608 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6791 (mp) REVERT: D 621 LEU cc_start: 0.6835 (tt) cc_final: 0.6554 (tm) REVERT: D 683 MET cc_start: 0.6807 (tpt) cc_final: 0.6239 (mmm) REVERT: D 725 ASP cc_start: 0.7165 (m-30) cc_final: 0.6661 (m-30) REVERT: D 870 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6012 (mtt180) REVERT: D 922 LYS cc_start: 0.6267 (pttm) cc_final: 0.5694 (ptmm) REVERT: D 932 MET cc_start: 0.6172 (mmt) cc_final: 0.5366 (mtt) REVERT: D 1042 MET cc_start: 0.6623 (mtp) cc_final: 0.6016 (mmp) REVERT: D 1084 MET cc_start: 0.5226 (mpt) cc_final: 0.4916 (mmp) REVERT: D 1085 ARG cc_start: 0.4182 (tpt170) cc_final: 0.3878 (tpp80) REVERT: D 1128 ARG cc_start: 0.5737 (ttp80) cc_final: 0.5099 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5405 (mt0) cc_final: 0.4901 (mm110) REVERT: D 1233 LEU cc_start: 0.7049 (tp) cc_final: 0.6649 (pp) REVERT: D 1361 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6453 (tp40) outliers start: 57 outliers final: 32 residues processed: 397 average time/residue: 1.4117 time to fit residues: 699.5843 Evaluate side-chains 397 residues out of total 4664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 349 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1361 GLN Chi-restraints excluded: chain B residue 1430 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1430 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 342 optimal weight: 0.7980 chunk 459 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 397 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 432 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 443 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 598 GLN C 598 GLN ** C1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095452 restraints weight = 71528.180| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.39 r_work: 0.3214 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41608 Z= 0.225 Angle : 0.570 10.488 56912 Z= 0.291 Chirality : 0.040 0.146 6668 Planarity : 0.005 0.057 7196 Dihedral : 8.634 88.051 6996 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 2.14 % Allowed : 19.39 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.11), residues: 5432 helix: 1.73 (0.09), residues: 3000 sheet: -1.23 (0.22), residues: 468 loop : -1.07 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1366 HIS 0.004 0.001 HIS B1470 PHE 0.018 0.002 PHE A 268 TYR 0.030 0.002 TYR B 110 ARG 0.004 0.001 ARG C1465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15612.01 seconds wall clock time: 272 minutes 55.32 seconds (16375.32 seconds total)