Starting phenix.real_space_refine on Tue Aug 26 20:43:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sri_40732/08_2025/8sri_40732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sri_40732/08_2025/8sri_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/cci-nas-00/data/ceres_data/8sri_40732/08_2025/8sri_40732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sri_40732/08_2025/8sri_40732.map" model { file = "/net/cci-nas-00/data/ceres_data/8sri_40732/08_2025/8sri_40732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sri_40732/08_2025/8sri_40732.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.180 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40636 Number of models: 1 Model: "" Number of chains: 6 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: {'GLU:plan': 39, 'ASN:plan1': 12, 'ASP:plan': 39, 'GLN:plan1': 13, 'ARG:plan': 19, 'HIS:plan': 9, 'TYR:plan': 2, 'PHE:plan': 6} 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: {'GLU:plan': 39, 'ASN:plan1': 12, 'ASP:plan': 39, 'GLN:plan1': 13, 'ARG:plan': 19, 'HIS:plan': 9, 'TYR:plan': 2, 'PHE:plan': 6} 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: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'APR': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'APR': 1, 'CLR': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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} Restraints were copied for chains: B, C Time building chain proxies: 17.62, per 1000 atoms: 0.43 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=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 376 " distance=0.00 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 399 " distance=0.00 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 446 " distance=0.00 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 609 " distance=0.00 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 676 " distance=0.00 Simple disulfide: pdb=" SG CYS B 817 " - pdb=" SG CYS B 817 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B 997 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1006 " distance=0.00 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1060 " distance=0.00 Simple disulfide: pdb=" SG CYS B1291 " - pdb=" SG CYS B1291 " distance=0.00 Simple disulfide: pdb=" SG CYS B1424 " - pdb=" SG CYS B1424 " distance=0.00 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1439 " distance=0.00 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.79 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: 11.85 Time building geometry restraints manager: 4.77 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: 0.00 - 2.92: 52095 2.92 - 5.83: 4247 5.83 - 8.75: 498 8.75 - 11.66: 60 11.66 - 14.58: 12 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: 23056 17.95 - 35.91: 1749 35.91 - 53.86: 296 53.86 - 71.82: 80 71.82 - 89.77: 24 Dihedral angle restraints: 25205 sinusoidal: 9309 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 25202 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: 2.03 - 2.60: 345 2.60 - 3.18: 30199 3.18 - 3.75: 63189 3.75 - 4.33: 82710 4.33 - 4.90: 143836 Nonbonded interactions: 320279 Sorted by model distance: nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.029 3.760 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 ... (remaining 320274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.020 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: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 50.110 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.080 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:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.400 ------------------------------------------------------------------------------- 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 41611 Z= 0.667 Angle : 1.652 14.577 56930 Z= 1.049 Chirality : 0.081 0.417 6668 Planarity : 0.011 0.068 7196 Dihedral : 13.475 89.771 14876 Min Nonbonded Distance : 2.029 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (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 ARG 0.025 0.001 ARG D 112 TYR 0.046 0.005 TYR D 332 PHE 0.073 0.006 PHE D 572 TRP 0.042 0.003 TRP D 726 HIS 0.011 0.002 HIS C 903 Details of bonding type rmsd covalent geometry : bond 0.01146 (41608) covalent geometry : angle 1.65156 (56912) SS BOND : bond 0.00103 ( 3) SS BOND : angle 1.77694 ( 18) hydrogen bonds : bond 0.15277 ( 2348) hydrogen bonds : angle 7.22215 ( 6936) *********************** 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 to be fit. rotamer outliers: 12 poor density : 866 time to evaluate : 1.628 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: 0.7659 time to fit residues: 809.2241 Evaluate side-chains 540 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 532 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 394 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 307 GLN A 423 GLN A 598 GLN A 696 ASN A 702 ASN A 813 HIS A 923 ASN A 996 ASN A1038 ASN A1152 GLN A1167 GLN A1201 ASN A1292 HIS A1441 ASN B 173 GLN B 307 GLN B 423 GLN B 598 GLN B 696 ASN B 702 ASN B 813 HIS B 923 ASN B1038 ASN B1152 GLN B1167 GLN B1201 ASN B1292 HIS C 173 GLN C 307 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 598 GLN C 696 ASN C 702 ASN C 813 HIS C 923 ASN C 996 ASN C1038 ASN C1152 GLN C1167 GLN C1201 ASN C1292 HIS D 173 GLN D 307 GLN D 423 GLN D 598 GLN D 696 ASN D 702 ASN D 813 HIS D 923 ASN D 996 ASN D1038 ASN D1152 GLN D1167 GLN D1201 ASN D1292 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099759 restraints weight = 71895.647| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.42 r_work: 0.3300 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41611 Z= 0.149 Angle : 0.592 10.680 56930 Z= 0.308 Chirality : 0.041 0.173 6668 Planarity : 0.005 0.060 7196 Dihedral : 8.507 89.058 7012 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.71 % Allowed : 10.98 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.11), residues: 5432 helix: 1.78 (0.09), residues: 3024 sheet: -0.72 (0.25), residues: 408 loop : -0.53 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 112 TYR 0.015 0.002 TYR B 466 PHE 0.026 0.002 PHE D 274 TRP 0.014 0.001 TRP C 96 HIS 0.004 0.001 HIS C1470 Details of bonding type rmsd covalent geometry : bond 0.00327 (41608) covalent geometry : angle 0.59180 (56912) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.34144 ( 18) hydrogen bonds : bond 0.04495 ( 2348) hydrogen bonds : angle 4.26844 ( 6936) *********************** 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 651 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 551 time to evaluate : 1.618 Fit side-chains REVERT: A 75 PHE cc_start: 0.6372 (t80) cc_final: 0.6147 (OUTLIER) REVERT: A 161 GLU cc_start: 0.5509 (tt0) cc_final: 0.5175 (tt0) REVERT: A 284 GLN cc_start: 0.6356 (mm-40) cc_final: 0.5746 (mt0) REVERT: A 326 ASP cc_start: 0.6907 (m-30) cc_final: 0.6621 (m-30) REVERT: A 352 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6803 (mt0) REVERT: A 455 MET cc_start: 0.6267 (mtm) cc_final: 0.6018 (mtt) REVERT: A 682 HIS cc_start: 0.6303 (t-90) cc_final: 0.5844 (m90) REVERT: A 683 MET cc_start: 0.7056 (tpt) cc_final: 0.6369 (mmm) REVERT: A 702 ASN cc_start: 0.7312 (m-40) cc_final: 0.7031 (m-40) REVERT: A 725 ASP cc_start: 0.7519 (m-30) cc_final: 0.7125 (m-30) REVERT: A 730 LEU cc_start: 0.6093 (mp) cc_final: 0.5861 (mt) REVERT: A 910 LEU cc_start: 0.8055 (pp) cc_final: 0.7807 (mt) REVERT: A 922 LYS cc_start: 0.6980 (pttm) cc_final: 0.6428 (ptmm) REVERT: A 930 MET cc_start: 0.7233 (mtt) cc_final: 0.6909 (mtp) REVERT: A 932 MET cc_start: 0.7409 (mmt) cc_final: 0.7201 (mpp) REVERT: A 936 LYS cc_start: 0.7031 (mttt) cc_final: 0.6453 (ptmt) REVERT: A 990 ASP cc_start: 0.7795 (m-30) cc_final: 0.7499 (m-30) REVERT: A 1050 ASP cc_start: 0.6620 (m-30) cc_final: 0.6234 (m-30) REVERT: A 1055 GLN cc_start: 0.6733 (mt0) cc_final: 0.6079 (tt0) REVERT: A 1084 MET cc_start: 0.5643 (mmt) cc_final: 0.5035 (mmp) REVERT: A 1122 ARG cc_start: 0.5713 (mtm-85) cc_final: 0.5493 (mtm110) REVERT: A 1126 ARG cc_start: 0.5647 (ttp-110) cc_final: 0.5141 (tmm160) REVERT: A 1128 ARG cc_start: 0.6108 (ttp80) cc_final: 0.5610 (ttm-80) REVERT: A 1145 GLN cc_start: 0.6963 (mt0) cc_final: 0.6739 (mt0) REVERT: A 1162 PHE cc_start: 0.7266 (t80) cc_final: 0.6990 (t80) REVERT: A 1166 GLN cc_start: 0.6705 (mm-40) cc_final: 0.5798 (tm-30) REVERT: A 1233 LEU cc_start: 0.7250 (tp) cc_final: 0.7000 (pp) REVERT: A 1234 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7023 (pp) REVERT: A 1365 MET cc_start: 0.7808 (ptm) cc_final: 0.7386 (ptm) REVERT: A 1408 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6824 (p) REVERT: A 1465 ARG cc_start: 0.8019 (ptt180) cc_final: 0.7508 (ptt180) REVERT: A 1467 MET cc_start: 0.8341 (mtp) cc_final: 0.8076 (mtp) REVERT: B 75 PHE cc_start: 0.6386 (t80) cc_final: 0.6160 (OUTLIER) REVERT: B 161 GLU cc_start: 0.5509 (tt0) cc_final: 0.5178 (tt0) REVERT: B 284 GLN cc_start: 0.6363 (mm-40) cc_final: 0.5746 (mt0) REVERT: B 326 ASP cc_start: 0.6901 (m-30) cc_final: 0.6621 (m-30) REVERT: B 455 MET cc_start: 0.6282 (mtm) cc_final: 0.6042 (mtt) REVERT: B 657 LYS cc_start: 0.4672 (tttm) cc_final: 0.4005 (tptt) REVERT: B 683 MET cc_start: 0.7056 (tpt) cc_final: 0.6402 (mmm) REVERT: B 702 ASN cc_start: 0.7310 (m-40) cc_final: 0.7026 (m-40) REVERT: B 725 ASP cc_start: 0.7511 (m-30) cc_final: 0.7115 (m-30) REVERT: B 730 LEU cc_start: 0.6073 (mp) cc_final: 0.5841 (mt) REVERT: B 910 LEU cc_start: 0.8064 (pp) cc_final: 0.7816 (mt) REVERT: B 922 LYS cc_start: 0.6971 (pttm) cc_final: 0.6418 (ptmm) REVERT: B 930 MET cc_start: 0.7231 (mtt) cc_final: 0.6922 (mtp) REVERT: B 932 MET cc_start: 0.7408 (mmt) cc_final: 0.7194 (mpp) REVERT: B 936 LYS cc_start: 0.7096 (mttt) cc_final: 0.6529 (ptmt) REVERT: B 990 ASP cc_start: 0.7786 (m-30) cc_final: 0.7489 (m-30) REVERT: B 1050 ASP cc_start: 0.6622 (m-30) cc_final: 0.6239 (m-30) REVERT: B 1055 GLN cc_start: 0.6630 (mt0) cc_final: 0.6082 (tt0) REVERT: B 1084 MET cc_start: 0.5677 (mmt) cc_final: 0.5075 (mmp) REVERT: B 1122 ARG cc_start: 0.5697 (mtm-85) cc_final: 0.5480 (mtm110) REVERT: B 1126 ARG cc_start: 0.5656 (ttp-110) cc_final: 0.5157 (tmm160) REVERT: B 1128 ARG cc_start: 0.6090 (ttp80) cc_final: 0.5592 (ttm-80) REVERT: B 1145 GLN cc_start: 0.6964 (mt0) cc_final: 0.6740 (mt0) REVERT: B 1162 PHE cc_start: 0.7261 (t80) cc_final: 0.6999 (t80) REVERT: B 1166 GLN cc_start: 0.6714 (mm-40) cc_final: 0.5776 (tm-30) REVERT: B 1233 LEU cc_start: 0.7247 (tp) cc_final: 0.7007 (pp) REVERT: B 1234 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6988 (pp) REVERT: B 1365 MET cc_start: 0.7824 (ptm) cc_final: 0.7391 (ptm) REVERT: B 1408 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6827 (p) REVERT: B 1465 ARG cc_start: 0.8023 (ptt180) cc_final: 0.7513 (ptt180) REVERT: B 1467 MET cc_start: 0.8350 (mtp) cc_final: 0.8071 (mtp) REVERT: C 75 PHE cc_start: 0.6446 (t80) cc_final: 0.6201 (OUTLIER) REVERT: C 76 MET cc_start: 0.6263 (tpp) cc_final: 0.5941 (ttp) REVERT: C 113 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7482 (pt) REVERT: C 161 GLU cc_start: 0.5501 (tt0) cc_final: 0.5190 (tt0) REVERT: C 284 GLN cc_start: 0.6366 (mm-40) cc_final: 0.5754 (mt0) REVERT: C 326 ASP cc_start: 0.6896 (m-30) cc_final: 0.6586 (m-30) REVERT: C 455 MET cc_start: 0.6270 (mtm) cc_final: 0.6020 (mtt) REVERT: C 657 LYS cc_start: 0.4659 (tttm) cc_final: 0.4002 (tptt) REVERT: C 683 MET cc_start: 0.7058 (tpt) cc_final: 0.6415 (mmm) REVERT: C 702 ASN cc_start: 0.7362 (m-40) cc_final: 0.7077 (m-40) REVERT: C 725 ASP cc_start: 0.7521 (m-30) cc_final: 0.7128 (m-30) REVERT: C 910 LEU cc_start: 0.8054 (pp) cc_final: 0.7816 (mt) REVERT: C 922 LYS cc_start: 0.6959 (pttm) cc_final: 0.6457 (ptmm) REVERT: C 930 MET cc_start: 0.7246 (mtt) cc_final: 0.6923 (mtp) REVERT: C 932 MET cc_start: 0.7430 (mmt) cc_final: 0.7211 (mpp) REVERT: C 936 LYS cc_start: 0.7079 (mttt) cc_final: 0.6508 (ptmt) REVERT: C 990 ASP cc_start: 0.7806 (m-30) cc_final: 0.7510 (m-30) REVERT: C 1050 ASP cc_start: 0.6616 (m-30) cc_final: 0.6233 (m-30) REVERT: C 1055 GLN cc_start: 0.6630 (mt0) cc_final: 0.6083 (tt0) REVERT: C 1084 MET cc_start: 0.5681 (mmt) cc_final: 0.5072 (mmp) REVERT: C 1122 ARG cc_start: 0.5686 (mtm-85) cc_final: 0.5472 (mtm110) REVERT: C 1126 ARG cc_start: 0.5656 (ttp-110) cc_final: 0.5144 (tmm160) REVERT: C 1128 ARG cc_start: 0.6096 (ttp80) cc_final: 0.5598 (ttm-80) REVERT: C 1145 GLN cc_start: 0.7017 (mt0) cc_final: 0.6798 (mt0) REVERT: C 1162 PHE cc_start: 0.7241 (t80) cc_final: 0.6952 (t80) REVERT: C 1166 GLN cc_start: 0.6673 (mm-40) cc_final: 0.5739 (tm-30) REVERT: C 1233 LEU cc_start: 0.7261 (tp) cc_final: 0.7014 (pp) REVERT: C 1234 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7000 (pp) REVERT: C 1365 MET cc_start: 0.7818 (ptm) cc_final: 0.7401 (ptm) REVERT: C 1408 SER cc_start: 0.7166 (OUTLIER) cc_final: 0.6856 (p) REVERT: C 1465 ARG cc_start: 0.7889 (ptt180) cc_final: 0.7506 (ptt90) REVERT: C 1467 MET cc_start: 0.8139 (mtp) cc_final: 0.7863 (mtp) REVERT: D 75 PHE cc_start: 0.6386 (t80) cc_final: 0.6159 (OUTLIER) REVERT: D 161 GLU cc_start: 0.5504 (tt0) cc_final: 0.5177 (tt0) REVERT: D 284 GLN cc_start: 0.6370 (mm-40) cc_final: 0.5753 (mt0) REVERT: D 326 ASP cc_start: 0.6885 (m-30) cc_final: 0.6603 (m-30) REVERT: D 352 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6807 (mt0) REVERT: D 455 MET cc_start: 0.6277 (mtm) cc_final: 0.6036 (mtt) REVERT: D 683 MET cc_start: 0.7060 (tpt) cc_final: 0.6410 (mmm) REVERT: D 702 ASN cc_start: 0.7315 (m-40) cc_final: 0.7035 (m-40) REVERT: D 725 ASP cc_start: 0.7513 (m-30) cc_final: 0.7117 (m-30) REVERT: D 730 LEU cc_start: 0.6065 (mp) cc_final: 0.5838 (mt) REVERT: D 910 LEU cc_start: 0.8067 (pp) cc_final: 0.7818 (mt) REVERT: D 922 LYS cc_start: 0.6981 (pttm) cc_final: 0.6430 (ptmm) REVERT: D 930 MET cc_start: 0.7237 (mtt) cc_final: 0.6911 (mtp) REVERT: D 932 MET cc_start: 0.7419 (mmt) cc_final: 0.7201 (mpp) REVERT: D 936 LYS cc_start: 0.7081 (mttt) cc_final: 0.6510 (ptmt) REVERT: D 990 ASP cc_start: 0.7724 (m-30) cc_final: 0.7419 (m-30) REVERT: D 1050 ASP cc_start: 0.6597 (m-30) cc_final: 0.6210 (m-30) REVERT: D 1055 GLN cc_start: 0.6698 (mt0) cc_final: 0.6079 (tt0) REVERT: D 1084 MET cc_start: 0.5672 (mmt) cc_final: 0.5073 (mmp) REVERT: D 1122 ARG cc_start: 0.5695 (mtm-85) cc_final: 0.5477 (mtm110) REVERT: D 1126 ARG cc_start: 0.5644 (ttp-110) cc_final: 0.5147 (tmm160) REVERT: D 1128 ARG cc_start: 0.6083 (ttp80) cc_final: 0.5585 (ttm-80) REVERT: D 1145 GLN cc_start: 0.6968 (mt0) cc_final: 0.6756 (mt0) REVERT: D 1162 PHE cc_start: 0.7265 (t80) cc_final: 0.7000 (t80) REVERT: D 1166 GLN cc_start: 0.6736 (mm-40) cc_final: 0.5795 (tm-30) REVERT: D 1233 LEU cc_start: 0.7247 (tp) cc_final: 0.7001 (pp) REVERT: D 1234 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7020 (pp) REVERT: D 1365 MET cc_start: 0.7822 (ptm) cc_final: 0.7402 (ptm) REVERT: D 1408 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6828 (p) REVERT: D 1465 ARG cc_start: 0.8018 (ptt180) cc_final: 0.7506 (ptt180) REVERT: D 1467 MET cc_start: 0.8340 (mtp) cc_final: 0.8072 (mtp) outliers start: 100 outliers final: 33 residues processed: 639 average time/residue: 0.7902 time to fit residues: 613.3261 Evaluate side-chains 468 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR 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 352 GLN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1408 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1408 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1408 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1312 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 298 optimal weight: 0.6980 chunk 472 optimal weight: 0.8980 chunk 349 optimal weight: 6.9990 chunk 499 optimal weight: 0.0370 chunk 396 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 chunk 247 optimal weight: 0.7980 chunk 528 optimal weight: 0.0970 chunk 266 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 368 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 ASN A1201 ASN B 364 GLN B 368 ASN ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 ASN B1140 ASN B1201 ASN B1441 ASN C 364 GLN C 368 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 ASN C1201 ASN C1441 ASN D 368 ASN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 ASN D1201 ASN D1441 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100803 restraints weight = 72116.965| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.41 r_work: 0.3308 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 41611 Z= 0.101 Angle : 0.485 9.289 56930 Z= 0.251 Chirality : 0.037 0.174 6668 Planarity : 0.004 0.056 7196 Dihedral : 8.229 89.114 6996 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.11 % Allowed : 14.61 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.12), residues: 5432 helix: 2.15 (0.09), residues: 3020 sheet: -0.73 (0.24), residues: 424 loop : -0.46 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 100 TYR 0.046 0.002 TYR D 420 PHE 0.018 0.001 PHE D 274 TRP 0.009 0.001 TRP D 726 HIS 0.002 0.000 HIS B 886 Details of bonding type rmsd covalent geometry : bond 0.00203 (41608) covalent geometry : angle 0.48471 (56912) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.18852 ( 18) hydrogen bonds : bond 0.03649 ( 2348) hydrogen bonds : angle 3.89183 ( 6936) *********************** 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 523 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 445 time to evaluate : 1.631 Fit side-chains REVERT: A 81 MET cc_start: 0.5299 (ttp) cc_final: 0.5071 (ttm) REVERT: A 129 MET cc_start: 0.6578 (mmm) cc_final: 0.5911 (tmt) REVERT: A 161 GLU cc_start: 0.5431 (tt0) cc_final: 0.5077 (tt0) REVERT: A 284 GLN cc_start: 0.6222 (mm-40) cc_final: 0.5649 (mt0) REVERT: A 326 ASP cc_start: 0.6889 (m-30) cc_final: 0.6593 (m-30) REVERT: A 368 ASN cc_start: 0.6711 (m110) cc_final: 0.6261 (t0) REVERT: A 396 PHE cc_start: 0.6848 (t80) cc_final: 0.6140 (t80) REVERT: A 621 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6872 (mt) REVERT: A 666 GLU cc_start: 0.6313 (tt0) cc_final: 0.5788 (mt-10) REVERT: A 683 MET cc_start: 0.7120 (tpt) cc_final: 0.6547 (mmm) REVERT: A 702 ASN cc_start: 0.7207 (m-40) cc_final: 0.6797 (m-40) REVERT: A 725 ASP cc_start: 0.7480 (m-30) cc_final: 0.7051 (m-30) REVERT: A 870 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6507 (mtt180) REVERT: A 922 LYS cc_start: 0.6921 (pttm) cc_final: 0.6327 (ptmm) REVERT: A 930 MET cc_start: 0.7088 (mtt) cc_final: 0.6808 (mtp) REVERT: A 932 MET cc_start: 0.7250 (mmt) cc_final: 0.6568 (mtt) REVERT: A 936 LYS cc_start: 0.7021 (mttt) cc_final: 0.6472 (tttm) REVERT: A 990 ASP cc_start: 0.7706 (m-30) cc_final: 0.7417 (m-30) REVERT: A 1042 MET cc_start: 0.7647 (mtp) cc_final: 0.7267 (mmt) REVERT: A 1050 ASP cc_start: 0.6606 (m-30) cc_final: 0.6182 (m-30) REVERT: A 1084 MET cc_start: 0.5524 (mmt) cc_final: 0.5033 (mmp) REVERT: A 1122 ARG cc_start: 0.5576 (mtm-85) cc_final: 0.5357 (mtm110) REVERT: A 1126 ARG cc_start: 0.5633 (ttp-110) cc_final: 0.5365 (ttp80) REVERT: A 1128 ARG cc_start: 0.6041 (ttp80) cc_final: 0.5498 (ttm-80) REVERT: A 1145 GLN cc_start: 0.6995 (mt0) cc_final: 0.6691 (mt0) REVERT: A 1162 PHE cc_start: 0.7194 (t80) cc_final: 0.6901 (t80) REVERT: A 1166 GLN cc_start: 0.6584 (mm-40) cc_final: 0.5862 (tm-30) REVERT: A 1233 LEU cc_start: 0.7303 (tp) cc_final: 0.7030 (pp) REVERT: A 1234 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6983 (pp) REVERT: A 1354 GLU cc_start: 0.7795 (tt0) cc_final: 0.7360 (tt0) REVERT: A 1365 MET cc_start: 0.7688 (ptm) cc_final: 0.6911 (ttm) REVERT: A 1408 SER cc_start: 0.7257 (OUTLIER) cc_final: 0.6983 (p) REVERT: A 1465 ARG cc_start: 0.8024 (ptt180) cc_final: 0.7531 (ptt180) REVERT: B 129 MET cc_start: 0.6598 (mmm) cc_final: 0.5912 (tmt) REVERT: B 161 GLU cc_start: 0.5520 (tt0) cc_final: 0.5149 (tt0) REVERT: B 284 GLN cc_start: 0.6231 (mm-40) cc_final: 0.5667 (mt0) REVERT: B 326 ASP cc_start: 0.6873 (m-30) cc_final: 0.6574 (m-30) REVERT: B 368 ASN cc_start: 0.6712 (m110) cc_final: 0.6257 (t0) REVERT: B 396 PHE cc_start: 0.6849 (t80) cc_final: 0.6239 (t80) REVERT: B 621 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6873 (mt) REVERT: B 657 LYS cc_start: 0.4794 (tttm) cc_final: 0.4235 (tptt) REVERT: B 666 GLU cc_start: 0.6295 (tt0) cc_final: 0.5766 (mt-10) REVERT: B 683 MET cc_start: 0.7124 (tpt) cc_final: 0.6490 (mmm) REVERT: B 702 ASN cc_start: 0.7196 (m-40) cc_final: 0.6800 (m-40) REVERT: B 725 ASP cc_start: 0.7475 (m-30) cc_final: 0.7044 (m-30) REVERT: B 870 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6510 (mtt180) REVERT: B 922 LYS cc_start: 0.6919 (pttm) cc_final: 0.6323 (ptmm) REVERT: B 930 MET cc_start: 0.7078 (mtt) cc_final: 0.6803 (mtp) REVERT: B 932 MET cc_start: 0.7193 (mmt) cc_final: 0.6522 (mtt) REVERT: B 936 LYS cc_start: 0.7012 (mttt) cc_final: 0.6476 (tttm) REVERT: B 963 ASP cc_start: 0.6712 (t70) cc_final: 0.6090 (t0) REVERT: B 990 ASP cc_start: 0.7707 (m-30) cc_final: 0.7418 (m-30) REVERT: B 1042 MET cc_start: 0.7673 (mtp) cc_final: 0.7291 (mmt) REVERT: B 1050 ASP cc_start: 0.6617 (m-30) cc_final: 0.6205 (m-30) REVERT: B 1084 MET cc_start: 0.5542 (mmt) cc_final: 0.5050 (mmp) REVERT: B 1122 ARG cc_start: 0.5574 (mtm-85) cc_final: 0.5347 (mtm110) REVERT: B 1126 ARG cc_start: 0.5617 (ttp-110) cc_final: 0.5351 (ttp80) REVERT: B 1128 ARG cc_start: 0.6039 (ttp80) cc_final: 0.5479 (ttm-80) REVERT: B 1145 GLN cc_start: 0.6987 (mt0) cc_final: 0.6642 (mt0) REVERT: B 1162 PHE cc_start: 0.7200 (t80) cc_final: 0.6932 (t80) REVERT: B 1166 GLN cc_start: 0.6564 (mm-40) cc_final: 0.5851 (tm-30) REVERT: B 1233 LEU cc_start: 0.7298 (tp) cc_final: 0.7029 (pp) REVERT: B 1234 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6965 (pp) REVERT: B 1354 GLU cc_start: 0.7795 (tt0) cc_final: 0.7307 (tt0) REVERT: B 1365 MET cc_start: 0.7694 (ptm) cc_final: 0.6907 (ttm) REVERT: B 1408 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6989 (p) REVERT: B 1465 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7521 (ptt180) REVERT: B 1467 MET cc_start: 0.8435 (mtp) cc_final: 0.8234 (mtp) REVERT: C 75 PHE cc_start: 0.6432 (t80) cc_final: 0.6215 (OUTLIER) REVERT: C 76 MET cc_start: 0.6303 (tpp) cc_final: 0.5978 (ttp) REVERT: C 81 MET cc_start: 0.5138 (ttp) cc_final: 0.4935 (ttm) REVERT: C 129 MET cc_start: 0.6653 (mmm) cc_final: 0.5960 (tmt) REVERT: C 161 GLU cc_start: 0.5429 (tt0) cc_final: 0.5097 (tt0) REVERT: C 189 MET cc_start: 0.6842 (mtt) cc_final: 0.6611 (mtp) REVERT: C 284 GLN cc_start: 0.6240 (mm-40) cc_final: 0.5658 (mt0) REVERT: C 326 ASP cc_start: 0.6864 (m-30) cc_final: 0.6569 (m-30) REVERT: C 368 ASN cc_start: 0.6746 (m110) cc_final: 0.6300 (t0) REVERT: C 621 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6863 (mt) REVERT: C 657 LYS cc_start: 0.4796 (tttm) cc_final: 0.4242 (tptt) REVERT: C 666 GLU cc_start: 0.6311 (tt0) cc_final: 0.5783 (mt-10) REVERT: C 683 MET cc_start: 0.7163 (tpt) cc_final: 0.6592 (mmm) REVERT: C 691 LYS cc_start: 0.6941 (mttp) cc_final: 0.6701 (mttt) REVERT: C 702 ASN cc_start: 0.7201 (m-40) cc_final: 0.6803 (m-40) REVERT: C 725 ASP cc_start: 0.7499 (m-30) cc_final: 0.7067 (m-30) REVERT: C 870 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6510 (mtt180) REVERT: C 922 LYS cc_start: 0.6923 (pttm) cc_final: 0.6327 (ptmm) REVERT: C 930 MET cc_start: 0.7087 (mtt) cc_final: 0.6809 (mtp) REVERT: C 932 MET cc_start: 0.7215 (mmt) cc_final: 0.6546 (mtt) REVERT: C 936 LYS cc_start: 0.7010 (mttt) cc_final: 0.6475 (tttm) REVERT: C 990 ASP cc_start: 0.7701 (m-30) cc_final: 0.7410 (m-30) REVERT: C 1042 MET cc_start: 0.7645 (mtp) cc_final: 0.7267 (mmt) REVERT: C 1050 ASP cc_start: 0.6601 (m-30) cc_final: 0.6182 (m-30) REVERT: C 1084 MET cc_start: 0.5555 (mmt) cc_final: 0.5066 (mmp) REVERT: C 1122 ARG cc_start: 0.5555 (mtm-85) cc_final: 0.5335 (mtm110) REVERT: C 1126 ARG cc_start: 0.5656 (ttp-110) cc_final: 0.5392 (ttp80) REVERT: C 1128 ARG cc_start: 0.6045 (ttp80) cc_final: 0.5485 (ttm-80) REVERT: C 1145 GLN cc_start: 0.7031 (mt0) cc_final: 0.6693 (mt0) REVERT: C 1162 PHE cc_start: 0.7172 (t80) cc_final: 0.6872 (t80) REVERT: C 1166 GLN cc_start: 0.6559 (mm-40) cc_final: 0.5848 (tm-30) REVERT: C 1233 LEU cc_start: 0.7316 (tp) cc_final: 0.7031 (pp) REVERT: C 1234 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7049 (pp) REVERT: C 1354 GLU cc_start: 0.7768 (tt0) cc_final: 0.7281 (tt0) REVERT: C 1365 MET cc_start: 0.7698 (ptm) cc_final: 0.6931 (ttm) REVERT: C 1408 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6987 (p) REVERT: C 1465 ARG cc_start: 0.7934 (ptt180) cc_final: 0.7538 (ptt180) REVERT: D 75 PHE cc_start: 0.6435 (t80) cc_final: 0.6232 (OUTLIER) REVERT: D 129 MET cc_start: 0.6594 (mmm) cc_final: 0.5906 (tmt) REVERT: D 161 GLU cc_start: 0.5480 (tt0) cc_final: 0.5102 (tt0) REVERT: D 189 MET cc_start: 0.6827 (mtt) cc_final: 0.6591 (mtp) REVERT: D 284 GLN cc_start: 0.6228 (mm-40) cc_final: 0.5652 (mt0) REVERT: D 326 ASP cc_start: 0.6866 (m-30) cc_final: 0.6566 (m-30) REVERT: D 368 ASN cc_start: 0.6714 (m110) cc_final: 0.6491 (m-40) REVERT: D 396 PHE cc_start: 0.6850 (t80) cc_final: 0.6244 (t80) REVERT: D 621 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6878 (mt) REVERT: D 666 GLU cc_start: 0.6326 (tt0) cc_final: 0.5801 (mt-10) REVERT: D 683 MET cc_start: 0.7160 (tpt) cc_final: 0.6593 (mmm) REVERT: D 702 ASN cc_start: 0.7206 (m-40) cc_final: 0.6825 (m-40) REVERT: D 725 ASP cc_start: 0.7482 (m-30) cc_final: 0.7054 (m-30) REVERT: D 870 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6505 (mtt180) REVERT: D 922 LYS cc_start: 0.6962 (pttm) cc_final: 0.6365 (ptmm) REVERT: D 930 MET cc_start: 0.7089 (mtt) cc_final: 0.6812 (mtp) REVERT: D 932 MET cc_start: 0.7209 (mmt) cc_final: 0.6543 (mtt) REVERT: D 936 LYS cc_start: 0.7014 (mttt) cc_final: 0.6473 (tttm) REVERT: D 963 ASP cc_start: 0.6717 (t70) cc_final: 0.6091 (t0) REVERT: D 990 ASP cc_start: 0.7741 (m-30) cc_final: 0.7458 (m-30) REVERT: D 1042 MET cc_start: 0.7652 (mtp) cc_final: 0.7275 (mmt) REVERT: D 1050 ASP cc_start: 0.6576 (m-30) cc_final: 0.6151 (m-30) REVERT: D 1084 MET cc_start: 0.5527 (mmt) cc_final: 0.5037 (mmp) REVERT: D 1122 ARG cc_start: 0.5572 (mtm-85) cc_final: 0.5351 (mtm110) REVERT: D 1126 ARG cc_start: 0.5615 (ttp-110) cc_final: 0.5350 (ttp80) REVERT: D 1128 ARG cc_start: 0.6037 (ttp80) cc_final: 0.5482 (ttm-80) REVERT: D 1145 GLN cc_start: 0.6993 (mt0) cc_final: 0.6734 (mt0) REVERT: D 1162 PHE cc_start: 0.7202 (t80) cc_final: 0.6932 (t80) REVERT: D 1166 GLN cc_start: 0.6575 (mm-40) cc_final: 0.5858 (tm-30) REVERT: D 1233 LEU cc_start: 0.7314 (tp) cc_final: 0.7034 (pp) REVERT: D 1234 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6954 (pp) REVERT: D 1354 GLU cc_start: 0.7796 (tt0) cc_final: 0.7307 (tt0) REVERT: D 1365 MET cc_start: 0.7693 (ptm) cc_final: 0.6915 (ttm) REVERT: D 1408 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6985 (p) REVERT: D 1465 ARG cc_start: 0.8027 (ptt180) cc_final: 0.7532 (ptt180) REVERT: D 1467 MET cc_start: 0.8447 (mtp) cc_final: 0.8246 (mtp) outliers start: 78 outliers final: 34 residues processed: 515 average time/residue: 0.7698 time to fit residues: 482.4677 Evaluate side-chains 460 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 412 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 346 THR 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 621 LEU Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1408 SER Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR 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 621 LEU Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1408 SER 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 463 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1408 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR 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 621 LEU Chi-restraints excluded: chain D residue 833 SER Chi-restraints excluded: chain D residue 870 ARG Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1408 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 145 optimal weight: 2.9990 chunk 381 optimal weight: 0.1980 chunk 319 optimal weight: 6.9990 chunk 539 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 440 optimal weight: 4.9990 chunk 443 optimal weight: 0.9990 chunk 427 optimal weight: 8.9990 chunk 479 optimal weight: 3.9990 chunk 402 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 364 GLN A 378 GLN A 598 GLN A 702 ASN B 364 GLN B 378 GLN B 598 GLN B 702 ASN C 253 ASN C 364 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN C 702 ASN D 253 ASN D 364 GLN D 378 GLN D 598 GLN D 702 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094527 restraints weight = 71922.551| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.41 r_work: 0.3209 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41611 Z= 0.186 Angle : 0.628 9.766 56930 Z= 0.329 Chirality : 0.042 0.174 6668 Planarity : 0.005 0.057 7196 Dihedral : 8.895 89.001 6996 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.87 % Allowed : 14.34 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.11), residues: 5432 helix: 1.42 (0.09), residues: 3040 sheet: -0.84 (0.25), residues: 376 loop : -0.67 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 100 TYR 0.030 0.002 TYR B 420 PHE 0.020 0.002 PHE C 274 TRP 0.010 0.002 TRP D1309 HIS 0.006 0.002 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00426 (41608) covalent geometry : angle 0.62833 (56912) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.75539 ( 18) hydrogen bonds : bond 0.05142 ( 2348) hydrogen bonds : angle 4.36917 ( 6936) *********************** 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 522 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 416 time to evaluate : 1.683 Fit side-chains REVERT: A 129 MET cc_start: 0.6775 (mmm) cc_final: 0.6035 (tmt) REVERT: A 161 GLU cc_start: 0.5684 (tt0) cc_final: 0.5257 (OUTLIER) REVERT: A 162 THR cc_start: 0.5499 (m) cc_final: 0.5288 (p) REVERT: A 284 GLN cc_start: 0.6387 (mm-40) cc_final: 0.5644 (mt0) REVERT: A 368 ASN cc_start: 0.6820 (m110) cc_final: 0.6587 (m-40) REVERT: A 419 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6566 (tmm) REVERT: A 420 TYR cc_start: 0.5561 (m-80) cc_final: 0.5304 (m-80) REVERT: A 683 MET cc_start: 0.7132 (tpt) cc_final: 0.6552 (mmm) REVERT: A 696 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.6054 (m-40) REVERT: A 725 ASP cc_start: 0.7412 (m-30) cc_final: 0.6929 (m-30) REVERT: A 870 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6543 (mtt180) REVERT: A 922 LYS cc_start: 0.6870 (pttm) cc_final: 0.6403 (ptmm) REVERT: A 930 MET cc_start: 0.7319 (mtt) cc_final: 0.6967 (mtp) REVERT: A 932 MET cc_start: 0.7349 (mmt) cc_final: 0.6710 (mtt) REVERT: A 963 ASP cc_start: 0.7043 (t70) cc_final: 0.6293 (t0) REVERT: A 990 ASP cc_start: 0.7746 (m-30) cc_final: 0.7395 (m-30) REVERT: A 1042 MET cc_start: 0.7742 (mtp) cc_final: 0.7361 (mmp) REVERT: A 1046 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6437 (mm-30) REVERT: A 1050 ASP cc_start: 0.6591 (m-30) cc_final: 0.6137 (m-30) REVERT: A 1084 MET cc_start: 0.5369 (mmt) cc_final: 0.4910 (mmp) REVERT: A 1122 ARG cc_start: 0.5762 (mtm-85) cc_final: 0.5513 (mtm110) REVERT: A 1128 ARG cc_start: 0.6010 (ttp80) cc_final: 0.5411 (mpt180) REVERT: A 1129 GLN cc_start: 0.6028 (mt0) cc_final: 0.5593 (mm110) REVERT: A 1166 GLN cc_start: 0.6503 (mm-40) cc_final: 0.6025 (tm-30) REVERT: A 1234 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7005 (pp) REVERT: A 1365 MET cc_start: 0.7715 (ptm) cc_final: 0.7026 (ttm) REVERT: B 129 MET cc_start: 0.6787 (mmm) cc_final: 0.6040 (tmt) REVERT: B 161 GLU cc_start: 0.5689 (tt0) cc_final: 0.5266 (OUTLIER) REVERT: B 162 THR cc_start: 0.5461 (m) cc_final: 0.5254 (p) REVERT: B 284 GLN cc_start: 0.6374 (mm-40) cc_final: 0.5655 (mt0) REVERT: B 368 ASN cc_start: 0.6770 (m110) cc_final: 0.6521 (m-40) REVERT: B 419 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6553 (tmm) REVERT: B 657 LYS cc_start: 0.4862 (tttm) cc_final: 0.4251 (tptt) REVERT: B 683 MET cc_start: 0.7177 (tpt) cc_final: 0.6568 (mmm) REVERT: B 696 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.6048 (m-40) REVERT: B 725 ASP cc_start: 0.7426 (m-30) cc_final: 0.6946 (m-30) REVERT: B 870 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6557 (mtt180) REVERT: B 922 LYS cc_start: 0.6844 (pttm) cc_final: 0.6372 (ptmm) REVERT: B 930 MET cc_start: 0.7326 (mtt) cc_final: 0.6966 (mtp) REVERT: B 932 MET cc_start: 0.7343 (mmt) cc_final: 0.6710 (mtt) REVERT: B 963 ASP cc_start: 0.7055 (t70) cc_final: 0.6312 (t0) REVERT: B 990 ASP cc_start: 0.7748 (m-30) cc_final: 0.7403 (m-30) REVERT: B 1042 MET cc_start: 0.7760 (mtp) cc_final: 0.7373 (mmp) REVERT: B 1046 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6417 (mm-30) REVERT: B 1050 ASP cc_start: 0.6590 (m-30) cc_final: 0.6139 (m-30) REVERT: B 1084 MET cc_start: 0.5391 (mmt) cc_final: 0.4926 (mmp) REVERT: B 1122 ARG cc_start: 0.5753 (mtm-85) cc_final: 0.5506 (mtm110) REVERT: B 1128 ARG cc_start: 0.6009 (ttp80) cc_final: 0.5376 (mpt180) REVERT: B 1166 GLN cc_start: 0.6518 (mm-40) cc_final: 0.6038 (tm-30) REVERT: B 1229 VAL cc_start: 0.6434 (t) cc_final: 0.6228 (t) REVERT: B 1234 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6998 (pp) REVERT: B 1365 MET cc_start: 0.7692 (ptm) cc_final: 0.6997 (ttm) REVERT: C 76 MET cc_start: 0.6467 (tpp) cc_final: 0.6229 (tpt) REVERT: C 129 MET cc_start: 0.6797 (mmm) cc_final: 0.6053 (tmt) REVERT: C 161 GLU cc_start: 0.5685 (tt0) cc_final: 0.5256 (OUTLIER) REVERT: C 162 THR cc_start: 0.5455 (m) cc_final: 0.5248 (p) REVERT: C 189 MET cc_start: 0.7093 (mtt) cc_final: 0.6881 (mtp) REVERT: C 284 GLN cc_start: 0.6381 (mm-40) cc_final: 0.5655 (mt0) REVERT: C 368 ASN cc_start: 0.6833 (m110) cc_final: 0.6599 (m-40) REVERT: C 657 LYS cc_start: 0.4875 (tttm) cc_final: 0.4272 (tptt) REVERT: C 683 MET cc_start: 0.7181 (tpt) cc_final: 0.6562 (mmm) REVERT: C 696 ASN cc_start: 0.6283 (OUTLIER) cc_final: 0.6059 (m-40) REVERT: C 725 ASP cc_start: 0.7451 (m-30) cc_final: 0.6985 (m-30) REVERT: C 870 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6550 (mtt180) REVERT: C 922 LYS cc_start: 0.6922 (pttm) cc_final: 0.6402 (ptmm) REVERT: C 930 MET cc_start: 0.7341 (mtt) cc_final: 0.6988 (mtp) REVERT: C 932 MET cc_start: 0.7349 (mmt) cc_final: 0.6716 (mtt) REVERT: C 963 ASP cc_start: 0.7057 (t70) cc_final: 0.6316 (t0) REVERT: C 990 ASP cc_start: 0.7750 (m-30) cc_final: 0.7391 (m-30) REVERT: C 1042 MET cc_start: 0.7731 (mtp) cc_final: 0.7360 (mmp) REVERT: C 1046 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6403 (mm-30) REVERT: C 1050 ASP cc_start: 0.6585 (m-30) cc_final: 0.6126 (m-30) REVERT: C 1084 MET cc_start: 0.5377 (mmt) cc_final: 0.4918 (mmp) REVERT: C 1122 ARG cc_start: 0.5749 (mtm-85) cc_final: 0.5499 (mtm110) REVERT: C 1128 ARG cc_start: 0.6009 (ttp80) cc_final: 0.5373 (mpt180) REVERT: C 1166 GLN cc_start: 0.6520 (mm-40) cc_final: 0.6016 (tm-30) REVERT: C 1234 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7004 (pp) REVERT: C 1365 MET cc_start: 0.7682 (ptm) cc_final: 0.7005 (ttm) REVERT: D 129 MET cc_start: 0.6805 (mmm) cc_final: 0.5982 (tmt) REVERT: D 161 GLU cc_start: 0.5681 (tt0) cc_final: 0.5253 (OUTLIER) REVERT: D 162 THR cc_start: 0.5469 (m) cc_final: 0.5258 (p) REVERT: D 189 MET cc_start: 0.7083 (mtt) cc_final: 0.6876 (mtp) REVERT: D 284 GLN cc_start: 0.6378 (mm-40) cc_final: 0.5655 (mt0) REVERT: D 368 ASN cc_start: 0.6701 (m110) cc_final: 0.6500 (m-40) REVERT: D 419 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6547 (tmm) REVERT: D 683 MET cc_start: 0.7164 (tpt) cc_final: 0.6558 (mmm) REVERT: D 696 ASN cc_start: 0.6274 (OUTLIER) cc_final: 0.6058 (m-40) REVERT: D 725 ASP cc_start: 0.7415 (m-30) cc_final: 0.6931 (m-30) REVERT: D 870 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6540 (mtt180) REVERT: D 922 LYS cc_start: 0.6847 (pttm) cc_final: 0.6375 (ptmm) REVERT: D 930 MET cc_start: 0.7321 (mtt) cc_final: 0.6959 (mtp) REVERT: D 932 MET cc_start: 0.7360 (mmt) cc_final: 0.6736 (mtt) REVERT: D 963 ASP cc_start: 0.7044 (t70) cc_final: 0.6296 (t0) REVERT: D 990 ASP cc_start: 0.7808 (m-30) cc_final: 0.7464 (m-30) REVERT: D 1042 MET cc_start: 0.7752 (mtp) cc_final: 0.7373 (mmp) REVERT: D 1046 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6424 (mm-30) REVERT: D 1050 ASP cc_start: 0.6581 (m-30) cc_final: 0.6117 (m-30) REVERT: D 1084 MET cc_start: 0.5399 (mmt) cc_final: 0.4939 (mmp) REVERT: D 1122 ARG cc_start: 0.5757 (mtm-85) cc_final: 0.5527 (mtm110) REVERT: D 1128 ARG cc_start: 0.6014 (ttp80) cc_final: 0.5379 (mpt180) REVERT: D 1166 GLN cc_start: 0.6518 (mm-40) cc_final: 0.6031 (tm-30) REVERT: D 1229 VAL cc_start: 0.6433 (t) cc_final: 0.6227 (t) REVERT: D 1234 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6999 (pp) REVERT: D 1365 MET cc_start: 0.7694 (ptm) cc_final: 0.7012 (ttm) outliers start: 106 outliers final: 56 residues processed: 495 average time/residue: 0.7301 time to fit residues: 446.1571 Evaluate side-chains 429 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 362 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL 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 346 THR Chi-restraints excluded: chain A residue 419 MET 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 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 419 MET 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 1105 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain C residue 115 VAL 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 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 1144 VAL Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 419 MET 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 1144 VAL Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 528 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 242 optimal weight: 0.8980 chunk 188 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 429 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 HIS A1201 ASN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 HIS B1201 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS C1201 ASN C1261 GLN ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 643 HIS D1201 ASN ** D1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.095806 restraints weight = 72158.674| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.40 r_work: 0.3227 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41611 Z= 0.118 Angle : 0.513 9.211 56930 Z= 0.265 Chirality : 0.038 0.161 6668 Planarity : 0.004 0.057 7196 Dihedral : 8.690 89.856 6996 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.79 % Allowed : 15.75 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.11), residues: 5432 helix: 1.75 (0.09), residues: 3024 sheet: -0.98 (0.24), residues: 408 loop : -0.60 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1126 TYR 0.037 0.002 TYR C 420 PHE 0.013 0.001 PHE D 274 TRP 0.009 0.001 TRP B1124 HIS 0.004 0.001 HIS B 886 Details of bonding type rmsd covalent geometry : bond 0.00255 (41608) covalent geometry : angle 0.51343 (56912) SS BOND : bond 0.00172 ( 3) SS BOND : angle 0.33013 ( 18) hydrogen bonds : bond 0.04104 ( 2348) hydrogen bonds : angle 4.00907 ( 6936) *********************** 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 487 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 384 time to evaluate : 1.682 Fit side-chains REVERT: A 129 MET cc_start: 0.6894 (mmm) cc_final: 0.6139 (tmt) REVERT: A 284 GLN cc_start: 0.6349 (mm-40) cc_final: 0.5806 (mt0) REVERT: A 368 ASN cc_start: 0.6775 (m110) cc_final: 0.6500 (m-40) REVERT: A 396 PHE cc_start: 0.7225 (t80) cc_final: 0.6670 (t80) REVERT: A 683 MET cc_start: 0.7081 (tpt) cc_final: 0.6515 (mmm) REVERT: A 696 ASN cc_start: 0.6119 (OUTLIER) cc_final: 0.5912 (m-40) REVERT: A 725 ASP cc_start: 0.7440 (m-30) cc_final: 0.6987 (m-30) REVERT: A 870 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6484 (mtt180) REVERT: A 922 LYS cc_start: 0.6809 (pttm) cc_final: 0.6295 (ptmm) REVERT: A 930 MET cc_start: 0.7299 (mtt) cc_final: 0.6902 (mtp) REVERT: A 932 MET cc_start: 0.7414 (mmt) cc_final: 0.6735 (mtt) REVERT: A 963 ASP cc_start: 0.6996 (t70) cc_final: 0.6221 (t0) REVERT: A 990 ASP cc_start: 0.7650 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1042 MET cc_start: 0.7702 (mtp) cc_final: 0.7354 (mmp) REVERT: A 1046 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6615 (mm-30) REVERT: A 1050 ASP cc_start: 0.6680 (m-30) cc_final: 0.6296 (m-30) REVERT: A 1084 MET cc_start: 0.5492 (mmt) cc_final: 0.4955 (mmp) REVERT: A 1122 ARG cc_start: 0.5759 (mtm-85) cc_final: 0.5470 (mtm110) REVERT: A 1128 ARG cc_start: 0.6153 (ttp80) cc_final: 0.5503 (ttm-80) REVERT: A 1129 GLN cc_start: 0.6023 (mt0) cc_final: 0.5544 (mm110) REVERT: A 1166 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6116 (tm-30) REVERT: A 1234 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6932 (pp) REVERT: A 1314 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.5032 (tpt) REVERT: A 1365 MET cc_start: 0.7625 (ptm) cc_final: 0.7118 (ttm) REVERT: B 129 MET cc_start: 0.6913 (mmm) cc_final: 0.6127 (tmt) REVERT: B 284 GLN cc_start: 0.6340 (mm-40) cc_final: 0.5780 (mt0) REVERT: B 368 ASN cc_start: 0.6775 (m110) cc_final: 0.6493 (m-40) REVERT: B 396 PHE cc_start: 0.7214 (t80) cc_final: 0.6659 (t80) REVERT: B 657 LYS cc_start: 0.4793 (tttm) cc_final: 0.4225 (tptt) REVERT: B 683 MET cc_start: 0.7085 (tpt) cc_final: 0.6527 (mmm) REVERT: B 696 ASN cc_start: 0.6113 (OUTLIER) cc_final: 0.5906 (m-40) REVERT: B 725 ASP cc_start: 0.7400 (m-30) cc_final: 0.6960 (m-30) REVERT: B 870 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6494 (mtt180) REVERT: B 922 LYS cc_start: 0.6784 (pttm) cc_final: 0.6290 (ptmm) REVERT: B 930 MET cc_start: 0.7252 (mtt) cc_final: 0.6872 (mtp) REVERT: B 932 MET cc_start: 0.7406 (mmt) cc_final: 0.6732 (mtt) REVERT: B 963 ASP cc_start: 0.7013 (t70) cc_final: 0.6245 (t0) REVERT: B 990 ASP cc_start: 0.7641 (m-30) cc_final: 0.7356 (m-30) REVERT: B 1042 MET cc_start: 0.7715 (mtp) cc_final: 0.7362 (mmp) REVERT: B 1046 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6594 (mm-30) REVERT: B 1050 ASP cc_start: 0.6679 (m-30) cc_final: 0.6298 (m-30) REVERT: B 1084 MET cc_start: 0.5529 (mmt) cc_final: 0.4984 (mmp) REVERT: B 1122 ARG cc_start: 0.5775 (mtm-85) cc_final: 0.5479 (mtm110) REVERT: B 1128 ARG cc_start: 0.6157 (ttp80) cc_final: 0.5509 (ttm-80) REVERT: B 1129 GLN cc_start: 0.6055 (mt0) cc_final: 0.5609 (mm110) REVERT: B 1166 GLN cc_start: 0.6620 (mm-40) cc_final: 0.6120 (tm-30) REVERT: B 1233 LEU cc_start: 0.7557 (pp) cc_final: 0.7353 (mm) REVERT: B 1234 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6900 (pp) REVERT: B 1314 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.5037 (tpt) REVERT: B 1365 MET cc_start: 0.7616 (ptm) cc_final: 0.7137 (ttm) REVERT: C 129 MET cc_start: 0.6940 (mmm) cc_final: 0.6164 (tmt) REVERT: C 284 GLN cc_start: 0.6361 (mm-40) cc_final: 0.5822 (mt0) REVERT: C 368 ASN cc_start: 0.6797 (m110) cc_final: 0.6520 (m-40) REVERT: C 396 PHE cc_start: 0.7056 (t80) cc_final: 0.6564 (t80) REVERT: C 657 LYS cc_start: 0.4786 (tttm) cc_final: 0.4222 (tptt) REVERT: C 683 MET cc_start: 0.7104 (tpt) cc_final: 0.6544 (mmm) REVERT: C 696 ASN cc_start: 0.6124 (OUTLIER) cc_final: 0.5917 (m-40) REVERT: C 725 ASP cc_start: 0.7447 (m-30) cc_final: 0.7000 (m-30) REVERT: C 870 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6496 (mtt180) REVERT: C 922 LYS cc_start: 0.6795 (pttm) cc_final: 0.6299 (ptmm) REVERT: C 930 MET cc_start: 0.7234 (mtt) cc_final: 0.6862 (mtp) REVERT: C 932 MET cc_start: 0.7398 (mmt) cc_final: 0.6724 (mtt) REVERT: C 963 ASP cc_start: 0.7014 (t70) cc_final: 0.6254 (t0) REVERT: C 990 ASP cc_start: 0.7638 (m-30) cc_final: 0.7350 (m-30) REVERT: C 1042 MET cc_start: 0.7694 (mtp) cc_final: 0.7343 (mmp) REVERT: C 1046 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6596 (mm-30) REVERT: C 1050 ASP cc_start: 0.6684 (m-30) cc_final: 0.6297 (m-30) REVERT: C 1084 MET cc_start: 0.5469 (mmt) cc_final: 0.4943 (mmp) REVERT: C 1122 ARG cc_start: 0.5730 (mtm-85) cc_final: 0.5433 (mtm110) REVERT: C 1128 ARG cc_start: 0.6153 (ttp80) cc_final: 0.5503 (ttm-80) REVERT: C 1129 GLN cc_start: 0.6018 (mt0) cc_final: 0.5610 (mm110) REVERT: C 1166 GLN cc_start: 0.6617 (mm-40) cc_final: 0.6114 (tm-30) REVERT: C 1234 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6935 (pp) REVERT: C 1314 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.5030 (tpt) REVERT: C 1365 MET cc_start: 0.7632 (ptm) cc_final: 0.7137 (ttm) REVERT: C 1465 ARG cc_start: 0.8014 (ptt180) cc_final: 0.7641 (ptt180) REVERT: D 129 MET cc_start: 0.6926 (mmm) cc_final: 0.6124 (tmt) REVERT: D 284 GLN cc_start: 0.6372 (mm-40) cc_final: 0.5812 (mt0) REVERT: D 368 ASN cc_start: 0.6722 (m110) cc_final: 0.6465 (m-40) REVERT: D 396 PHE cc_start: 0.7234 (t80) cc_final: 0.6683 (t80) REVERT: D 683 MET cc_start: 0.7133 (tpt) cc_final: 0.6572 (mmm) REVERT: D 696 ASN cc_start: 0.6141 (OUTLIER) cc_final: 0.5933 (m-40) REVERT: D 725 ASP cc_start: 0.7404 (m-30) cc_final: 0.6963 (m-30) REVERT: D 870 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6484 (mtt180) REVERT: D 922 LYS cc_start: 0.6794 (pttm) cc_final: 0.6297 (ptmm) REVERT: D 930 MET cc_start: 0.7242 (mtt) cc_final: 0.6861 (mtp) REVERT: D 932 MET cc_start: 0.7412 (mmt) cc_final: 0.6744 (mtt) REVERT: D 963 ASP cc_start: 0.7009 (t70) cc_final: 0.6237 (t0) REVERT: D 990 ASP cc_start: 0.7692 (m-30) cc_final: 0.7399 (m-30) REVERT: D 1042 MET cc_start: 0.7699 (mtp) cc_final: 0.7352 (mmp) REVERT: D 1046 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6603 (mm-30) REVERT: D 1050 ASP cc_start: 0.6674 (m-30) cc_final: 0.6288 (m-30) REVERT: D 1084 MET cc_start: 0.5502 (mmt) cc_final: 0.4972 (mmp) REVERT: D 1122 ARG cc_start: 0.5736 (mtm-85) cc_final: 0.5443 (mtm110) REVERT: D 1128 ARG cc_start: 0.6148 (ttp80) cc_final: 0.5499 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5997 (mt0) cc_final: 0.5588 (mm110) REVERT: D 1166 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6116 (tm-30) REVERT: D 1234 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6936 (pp) REVERT: D 1314 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.5055 (tpt) REVERT: D 1365 MET cc_start: 0.7609 (ptm) cc_final: 0.7133 (ttm) outliers start: 103 outliers final: 47 residues processed: 462 average time/residue: 0.7437 time to fit residues: 426.5995 Evaluate side-chains 412 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 349 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 346 THR 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 1105 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR 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 1105 THR Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET 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 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 1115 LEU Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR 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 1115 LEU Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 132 optimal weight: 8.9990 chunk 447 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 358 optimal weight: 0.2980 chunk 258 optimal weight: 5.9990 chunk 483 optimal weight: 0.7980 chunk 391 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 417 GLN A 813 HIS A1201 ASN A1261 GLN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS B 253 ASN B 598 GLN B 813 HIS B1201 ASN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN C 598 GLN C 813 HIS C1201 ASN ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS D 253 ASN D 598 GLN D 813 HIS D1201 ASN D1261 GLN ** D1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093858 restraints weight = 72731.346| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.41 r_work: 0.3186 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 41611 Z= 0.270 Angle : 0.751 11.895 56930 Z= 0.388 Chirality : 0.047 0.201 6668 Planarity : 0.006 0.069 7196 Dihedral : 9.136 89.892 6996 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.93 % Allowed : 15.32 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.11), residues: 5432 helix: 0.77 (0.09), residues: 3060 sheet: -1.20 (0.22), residues: 464 loop : -1.25 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1161 TYR 0.025 0.003 TYR D 420 PHE 0.018 0.003 PHE D 274 TRP 0.011 0.002 TRP D 842 HIS 0.009 0.002 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00636 (41608) covalent geometry : angle 0.75048 (56912) SS BOND : bond 0.00515 ( 3) SS BOND : angle 1.08817 ( 18) hydrogen bonds : bond 0.05923 ( 2348) hydrogen bonds : angle 4.64993 ( 6936) *********************** 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 503 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 358 time to evaluate : 1.635 Fit side-chains REVERT: A 129 MET cc_start: 0.7016 (mmm) cc_final: 0.6216 (tmt) REVERT: A 253 ASN cc_start: 0.6792 (OUTLIER) cc_final: 0.6308 (m110) REVERT: A 284 GLN cc_start: 0.6527 (mm-40) cc_final: 0.5912 (mt0) REVERT: A 368 ASN cc_start: 0.6807 (m110) cc_final: 0.6525 (m-40) REVERT: A 521 LEU cc_start: 0.5105 (tt) cc_final: 0.4842 (tt) REVERT: A 591 ILE cc_start: 0.4136 (tp) cc_final: 0.3789 (mm) REVERT: A 683 MET cc_start: 0.7026 (tpt) cc_final: 0.6428 (mmm) REVERT: A 696 ASN cc_start: 0.6006 (OUTLIER) cc_final: 0.5781 (m-40) REVERT: A 870 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6783 (mtt180) REVERT: A 930 MET cc_start: 0.7306 (mtt) cc_final: 0.6957 (mtp) REVERT: A 932 MET cc_start: 0.7467 (mmt) cc_final: 0.6827 (mtt) REVERT: A 963 ASP cc_start: 0.7133 (t70) cc_final: 0.6391 (t0) REVERT: A 990 ASP cc_start: 0.7633 (m-30) cc_final: 0.7388 (m-30) REVERT: A 1042 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7429 (mmp) REVERT: A 1050 ASP cc_start: 0.6702 (m-30) cc_final: 0.6238 (m-30) REVERT: A 1122 ARG cc_start: 0.5866 (mtm-85) cc_final: 0.5652 (mtm110) REVERT: A 1128 ARG cc_start: 0.6274 (ttp80) cc_final: 0.5631 (ttm-80) REVERT: A 1129 GLN cc_start: 0.6070 (mt0) cc_final: 0.5644 (mm110) REVERT: A 1166 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6298 (tm-30) REVERT: A 1234 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6955 (pp) REVERT: A 1361 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6395 (tt0) REVERT: A 1365 MET cc_start: 0.7632 (ptm) cc_final: 0.7103 (ttm) REVERT: A 1467 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7831 (ttm) REVERT: B 129 MET cc_start: 0.7040 (mmm) cc_final: 0.6230 (tmt) REVERT: B 253 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6312 (m110) REVERT: B 284 GLN cc_start: 0.6532 (mm-40) cc_final: 0.5908 (mt0) REVERT: B 368 ASN cc_start: 0.6797 (m110) cc_final: 0.6519 (m-40) REVERT: B 521 LEU cc_start: 0.5190 (tt) cc_final: 0.4928 (tt) REVERT: B 683 MET cc_start: 0.7024 (tpt) cc_final: 0.6423 (mmm) REVERT: B 696 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5764 (m-40) REVERT: B 870 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6762 (mtt180) REVERT: B 930 MET cc_start: 0.7380 (mtt) cc_final: 0.7021 (mtp) REVERT: B 932 MET cc_start: 0.7451 (mmt) cc_final: 0.6809 (mtt) REVERT: B 963 ASP cc_start: 0.7115 (t70) cc_final: 0.6396 (t0) REVERT: B 990 ASP cc_start: 0.7654 (m-30) cc_final: 0.7408 (m-30) REVERT: B 1042 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7429 (mmp) REVERT: B 1050 ASP cc_start: 0.6691 (m-30) cc_final: 0.6219 (m-30) REVERT: B 1084 MET cc_start: 0.5417 (mmt) cc_final: 0.5053 (mmp) REVERT: B 1122 ARG cc_start: 0.5857 (mtm-85) cc_final: 0.5639 (mtm110) REVERT: B 1128 ARG cc_start: 0.6263 (ttp80) cc_final: 0.5631 (ttm-80) REVERT: B 1129 GLN cc_start: 0.6072 (mt0) cc_final: 0.5643 (mm110) REVERT: B 1166 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6288 (tm-30) REVERT: B 1234 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6954 (pp) REVERT: B 1361 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: B 1365 MET cc_start: 0.7601 (ptm) cc_final: 0.7132 (ttm) REVERT: B 1467 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7885 (ttm) REVERT: C 129 MET cc_start: 0.7053 (mmm) cc_final: 0.6247 (tmt) REVERT: C 253 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6297 (m110) REVERT: C 284 GLN cc_start: 0.6526 (mm-40) cc_final: 0.5914 (mt0) REVERT: C 368 ASN cc_start: 0.6820 (m110) cc_final: 0.6558 (m-40) REVERT: C 521 LEU cc_start: 0.5165 (tt) cc_final: 0.4914 (tt) REVERT: C 683 MET cc_start: 0.7037 (tpt) cc_final: 0.6431 (mmm) REVERT: C 696 ASN cc_start: 0.6005 (OUTLIER) cc_final: 0.5776 (m-40) REVERT: C 870 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6785 (mtt180) REVERT: C 930 MET cc_start: 0.7323 (mtt) cc_final: 0.6976 (mtp) REVERT: C 932 MET cc_start: 0.7459 (mmt) cc_final: 0.6819 (mtt) REVERT: C 963 ASP cc_start: 0.7111 (t70) cc_final: 0.6397 (t0) REVERT: C 990 ASP cc_start: 0.7630 (m-30) cc_final: 0.7385 (m-30) REVERT: C 1042 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7416 (mmp) REVERT: C 1050 ASP cc_start: 0.6694 (m-30) cc_final: 0.6206 (m-30) REVERT: C 1084 MET cc_start: 0.5418 (mmt) cc_final: 0.5051 (mmp) REVERT: C 1122 ARG cc_start: 0.5848 (mtm-85) cc_final: 0.5631 (mtm110) REVERT: C 1128 ARG cc_start: 0.6285 (ttp80) cc_final: 0.5658 (ttm-80) REVERT: C 1129 GLN cc_start: 0.6034 (mt0) cc_final: 0.5605 (mm110) REVERT: C 1166 GLN cc_start: 0.6634 (mm-40) cc_final: 0.6279 (tm-30) REVERT: C 1234 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6959 (pp) REVERT: C 1361 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: C 1365 MET cc_start: 0.7594 (ptm) cc_final: 0.7140 (ttm) REVERT: D 129 MET cc_start: 0.7109 (mmm) cc_final: 0.6266 (tmt) REVERT: D 253 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6293 (m110) REVERT: D 284 GLN cc_start: 0.6513 (mm-40) cc_final: 0.5891 (mt0) REVERT: D 521 LEU cc_start: 0.5200 (tt) cc_final: 0.4942 (tt) REVERT: D 591 ILE cc_start: 0.4144 (tp) cc_final: 0.3797 (mm) REVERT: D 683 MET cc_start: 0.7025 (tpt) cc_final: 0.6426 (mmm) REVERT: D 696 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5777 (m-40) REVERT: D 870 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6783 (mtt180) REVERT: D 930 MET cc_start: 0.7375 (mtt) cc_final: 0.7013 (mtp) REVERT: D 932 MET cc_start: 0.7451 (mmt) cc_final: 0.6810 (mtt) REVERT: D 963 ASP cc_start: 0.7097 (t70) cc_final: 0.6370 (t0) REVERT: D 990 ASP cc_start: 0.7727 (m-30) cc_final: 0.7430 (m-30) REVERT: D 1042 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7431 (mmp) REVERT: D 1050 ASP cc_start: 0.6698 (m-30) cc_final: 0.6219 (m-30) REVERT: D 1122 ARG cc_start: 0.5869 (mtm-85) cc_final: 0.5653 (mtm110) REVERT: D 1128 ARG cc_start: 0.6273 (ttp80) cc_final: 0.5639 (ttm-80) REVERT: D 1129 GLN cc_start: 0.6065 (mt0) cc_final: 0.5633 (mm110) REVERT: D 1166 GLN cc_start: 0.6629 (mm-40) cc_final: 0.6280 (tm-30) REVERT: D 1234 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6977 (pp) REVERT: D 1361 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6370 (tt0) REVERT: D 1365 MET cc_start: 0.7591 (ptm) cc_final: 0.7123 (ttm) REVERT: D 1467 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7890 (ttm) outliers start: 145 outliers final: 72 residues processed: 468 average time/residue: 0.6786 time to fit residues: 398.2660 Evaluate side-chains 440 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 341 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 240 HIS 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 346 THR 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 621 LEU 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 1042 MET Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1361 GLN Chi-restraints excluded: chain A residue 1467 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR 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 621 LEU 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 1042 MET Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain B residue 1361 GLN Chi-restraints excluded: chain B residue 1467 MET Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 240 HIS 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 346 THR 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 621 LEU 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 1042 MET Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain C residue 1361 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR 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 621 LEU 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 1042 MET Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Chi-restraints excluded: chain D residue 1361 GLN Chi-restraints excluded: chain D residue 1467 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 70 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 363 optimal weight: 0.9990 chunk 505 optimal weight: 0.7980 chunk 365 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 514 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A1261 GLN ** A1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN B1261 GLN ** B1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN ** C1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 368 ASN D 598 GLN D1261 GLN ** D1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096219 restraints weight = 72324.398| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.40 r_work: 0.3233 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 41611 Z= 0.113 Angle : 0.511 8.530 56930 Z= 0.264 Chirality : 0.038 0.154 6668 Planarity : 0.004 0.058 7196 Dihedral : 8.636 88.876 6996 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.82 % Allowed : 17.11 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.11), residues: 5432 helix: 1.74 (0.09), residues: 3008 sheet: -1.16 (0.24), residues: 380 loop : -0.90 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1126 TYR 0.035 0.002 TYR A 110 PHE 0.011 0.001 PHE D 274 TRP 0.009 0.001 TRP B1124 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00240 (41608) covalent geometry : angle 0.51057 (56912) SS BOND : bond 0.00116 ( 3) SS BOND : angle 0.23045 ( 18) hydrogen bonds : bond 0.04049 ( 2348) hydrogen bonds : angle 4.00529 ( 6936) *********************** 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 474 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 370 time to evaluate : 1.605 Fit side-chains REVERT: A 129 MET cc_start: 0.6813 (mmm) cc_final: 0.6101 (tmt) REVERT: A 248 THR cc_start: 0.7281 (m) cc_final: 0.6685 (p) REVERT: A 284 GLN cc_start: 0.6554 (mm-40) cc_final: 0.5930 (mt0) REVERT: A 368 ASN cc_start: 0.6784 (m110) cc_final: 0.6485 (m-40) REVERT: A 396 PHE cc_start: 0.7195 (t80) cc_final: 0.6553 (t80) REVERT: A 591 ILE cc_start: 0.4276 (tp) cc_final: 0.3961 (mm) REVERT: A 683 MET cc_start: 0.7028 (tpt) cc_final: 0.6431 (mmm) REVERT: A 696 ASN cc_start: 0.6086 (t0) cc_final: 0.5749 (t0) REVERT: A 725 ASP cc_start: 0.7438 (m-30) cc_final: 0.6990 (m-30) REVERT: A 870 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6534 (mtt180) REVERT: A 922 LYS cc_start: 0.6735 (pttm) cc_final: 0.6249 (ptmm) REVERT: A 930 MET cc_start: 0.7295 (mtt) cc_final: 0.6872 (mtp) REVERT: A 932 MET cc_start: 0.7387 (mmt) cc_final: 0.6739 (mtt) REVERT: A 963 ASP cc_start: 0.6970 (t70) cc_final: 0.6199 (t0) REVERT: A 1042 MET cc_start: 0.7774 (mtp) cc_final: 0.7409 (mmp) REVERT: A 1050 ASP cc_start: 0.6688 (m-30) cc_final: 0.6256 (m-30) REVERT: A 1084 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.5012 (mmp) REVERT: A 1085 ARG cc_start: 0.4165 (tpt170) cc_final: 0.3890 (tpp80) REVERT: A 1122 ARG cc_start: 0.5685 (mtm-85) cc_final: 0.5414 (mtm110) REVERT: A 1128 ARG cc_start: 0.6225 (ttp80) cc_final: 0.5572 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5934 (mt0) cc_final: 0.5535 (mm110) REVERT: A 1234 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6800 (pp) REVERT: A 1314 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.4966 (tpt) REVERT: A 1365 MET cc_start: 0.7499 (ptm) cc_final: 0.7241 (ttm) REVERT: A 1467 MET cc_start: 0.8433 (mtp) cc_final: 0.7851 (ttm) REVERT: B 112 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6722 (ttp-170) REVERT: B 129 MET cc_start: 0.6825 (mmm) cc_final: 0.6104 (tmt) REVERT: B 248 THR cc_start: 0.7264 (m) cc_final: 0.6686 (p) REVERT: B 284 GLN cc_start: 0.6555 (mm-40) cc_final: 0.5912 (mt0) REVERT: B 368 ASN cc_start: 0.6776 (m110) cc_final: 0.6477 (m-40) REVERT: B 396 PHE cc_start: 0.7186 (t80) cc_final: 0.6492 (t80) REVERT: B 521 LEU cc_start: 0.5142 (tt) cc_final: 0.4875 (tt) REVERT: B 591 ILE cc_start: 0.4321 (tp) cc_final: 0.3860 (mp) REVERT: B 657 LYS cc_start: 0.4732 (tttm) cc_final: 0.4263 (tptt) REVERT: B 683 MET cc_start: 0.7052 (tpt) cc_final: 0.6476 (mmm) REVERT: B 696 ASN cc_start: 0.6078 (t0) cc_final: 0.5741 (t0) REVERT: B 725 ASP cc_start: 0.7443 (m-30) cc_final: 0.6996 (m-30) REVERT: B 870 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6565 (mtt180) REVERT: B 922 LYS cc_start: 0.6740 (pttm) cc_final: 0.6244 (ptmm) REVERT: B 930 MET cc_start: 0.7267 (mtt) cc_final: 0.6862 (mtp) REVERT: B 932 MET cc_start: 0.7383 (mmt) cc_final: 0.6730 (mtt) REVERT: B 963 ASP cc_start: 0.6990 (t70) cc_final: 0.6224 (t0) REVERT: B 1042 MET cc_start: 0.7772 (mtp) cc_final: 0.7411 (mmp) REVERT: B 1050 ASP cc_start: 0.6682 (m-30) cc_final: 0.6252 (m-30) REVERT: B 1084 MET cc_start: 0.5425 (mmt) cc_final: 0.4960 (mmp) REVERT: B 1085 ARG cc_start: 0.4172 (tpt170) cc_final: 0.3896 (tpp80) REVERT: B 1122 ARG cc_start: 0.5820 (mtm-85) cc_final: 0.5526 (mtm110) REVERT: B 1128 ARG cc_start: 0.6246 (ttp80) cc_final: 0.5595 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5919 (mt0) cc_final: 0.5531 (mm110) REVERT: B 1234 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6786 (pp) REVERT: B 1314 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.4944 (tpt) REVERT: B 1365 MET cc_start: 0.7498 (ptm) cc_final: 0.7267 (ttm) REVERT: B 1467 MET cc_start: 0.8444 (mtp) cc_final: 0.7858 (ttm) REVERT: C 129 MET cc_start: 0.7005 (mmm) cc_final: 0.6198 (tmt) REVERT: C 284 GLN cc_start: 0.6583 (mm-40) cc_final: 0.5964 (mt0) REVERT: C 368 ASN cc_start: 0.6794 (m110) cc_final: 0.6481 (m-40) REVERT: C 396 PHE cc_start: 0.7196 (t80) cc_final: 0.6601 (t80) REVERT: C 591 ILE cc_start: 0.4335 (tp) cc_final: 0.4046 (mm) REVERT: C 657 LYS cc_start: 0.4736 (tttm) cc_final: 0.4268 (tptt) REVERT: C 683 MET cc_start: 0.7036 (tpt) cc_final: 0.6436 (mmm) REVERT: C 696 ASN cc_start: 0.6081 (t0) cc_final: 0.5741 (t0) REVERT: C 725 ASP cc_start: 0.7485 (m-30) cc_final: 0.7026 (m-30) REVERT: C 870 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6553 (mtt180) REVERT: C 922 LYS cc_start: 0.6747 (pttm) cc_final: 0.6244 (ptmm) REVERT: C 930 MET cc_start: 0.7301 (mtt) cc_final: 0.6873 (mtp) REVERT: C 932 MET cc_start: 0.7378 (mmt) cc_final: 0.6728 (mtt) REVERT: C 963 ASP cc_start: 0.7003 (t70) cc_final: 0.6278 (t0) REVERT: C 1042 MET cc_start: 0.7762 (mtp) cc_final: 0.7405 (mmp) REVERT: C 1050 ASP cc_start: 0.6685 (m-30) cc_final: 0.6249 (m-30) REVERT: C 1084 MET cc_start: 0.5403 (mmt) cc_final: 0.4943 (mmp) REVERT: C 1085 ARG cc_start: 0.4167 (tpt170) cc_final: 0.3891 (tpp80) REVERT: C 1122 ARG cc_start: 0.5802 (mtm-85) cc_final: 0.5512 (mtm110) REVERT: C 1128 ARG cc_start: 0.6252 (ttp80) cc_final: 0.5602 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5944 (mt0) cc_final: 0.5550 (mm110) REVERT: C 1144 VAL cc_start: 0.7501 (t) cc_final: 0.7183 (t) REVERT: C 1234 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6805 (pp) REVERT: C 1314 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.4890 (tpt) REVERT: C 1365 MET cc_start: 0.7491 (ptm) cc_final: 0.7252 (ttm) REVERT: D 112 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6734 (ttp-170) REVERT: D 129 MET cc_start: 0.6836 (mmm) cc_final: 0.6097 (tmt) REVERT: D 284 GLN cc_start: 0.6573 (mm-40) cc_final: 0.5953 (mt0) REVERT: D 396 PHE cc_start: 0.7199 (t80) cc_final: 0.6544 (t80) REVERT: D 521 LEU cc_start: 0.5125 (tt) cc_final: 0.4870 (tt) REVERT: D 591 ILE cc_start: 0.4334 (tp) cc_final: 0.4027 (mm) REVERT: D 683 MET cc_start: 0.7035 (tpt) cc_final: 0.6430 (mmm) REVERT: D 696 ASN cc_start: 0.6051 (OUTLIER) cc_final: 0.5699 (t0) REVERT: D 725 ASP cc_start: 0.7455 (m-30) cc_final: 0.7009 (m-30) REVERT: D 870 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6563 (mtt180) REVERT: D 922 LYS cc_start: 0.6728 (pttm) cc_final: 0.6236 (ptmm) REVERT: D 930 MET cc_start: 0.7252 (mtt) cc_final: 0.6846 (mtp) REVERT: D 932 MET cc_start: 0.7383 (mmt) cc_final: 0.6731 (mtt) REVERT: D 963 ASP cc_start: 0.7001 (t70) cc_final: 0.6268 (t0) REVERT: D 990 ASP cc_start: 0.7560 (m-30) cc_final: 0.7287 (m-30) REVERT: D 1042 MET cc_start: 0.7740 (mtp) cc_final: 0.7383 (mmp) REVERT: D 1050 ASP cc_start: 0.6671 (m-30) cc_final: 0.6228 (m-30) REVERT: D 1084 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.5006 (mmp) REVERT: D 1085 ARG cc_start: 0.4154 (tpt170) cc_final: 0.3884 (tpp80) REVERT: D 1122 ARG cc_start: 0.5685 (mtm-85) cc_final: 0.5411 (mtm110) REVERT: D 1128 ARG cc_start: 0.6244 (ttp80) cc_final: 0.5592 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5938 (mt0) cc_final: 0.5533 (mm110) REVERT: D 1234 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6822 (pp) REVERT: D 1314 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.4897 (tpt) REVERT: D 1365 MET cc_start: 0.7489 (ptm) cc_final: 0.7263 (ttm) REVERT: D 1467 MET cc_start: 0.8450 (mtp) cc_final: 0.7868 (ttm) outliers start: 104 outliers final: 44 residues processed: 452 average time/residue: 0.6472 time to fit residues: 362.1213 Evaluate side-chains 406 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 345 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 346 THR 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 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1084 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 346 THR 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 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 346 THR 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 870 ARG Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 346 THR 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 1084 MET Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 448 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 351 optimal weight: 0.9980 chunk 408 optimal weight: 10.0000 chunk 397 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 454 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A1276 ASN B 82 HIS B 598 GLN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1276 ASN C 598 GLN C1276 ASN D 82 HIS D 368 ASN D 598 GLN D1276 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.127058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094984 restraints weight = 72116.615| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.40 r_work: 0.3208 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41611 Z= 0.160 Angle : 0.588 10.134 56930 Z= 0.301 Chirality : 0.041 0.171 6668 Planarity : 0.005 0.057 7196 Dihedral : 8.712 88.221 6996 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 17.14 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.11), residues: 5432 helix: 1.48 (0.09), residues: 3028 sheet: -1.23 (0.22), residues: 456 loop : -1.08 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 916 TYR 0.028 0.002 TYR A 110 PHE 0.017 0.002 PHE B 268 TRP 0.008 0.001 TRP A 842 HIS 0.005 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00367 (41608) covalent geometry : angle 0.58817 (56912) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.47662 ( 18) hydrogen bonds : bond 0.04693 ( 2348) hydrogen bonds : angle 4.16708 ( 6936) *********************** 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 478 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 366 time to evaluate : 1.914 Fit side-chains REVERT: A 76 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5796 (tpp) REVERT: A 129 MET cc_start: 0.6896 (mmm) cc_final: 0.6139 (tmt) REVERT: A 199 LEU cc_start: 0.6053 (tp) cc_final: 0.5850 (tt) REVERT: A 284 GLN cc_start: 0.6694 (mm-40) cc_final: 0.6030 (mt0) REVERT: A 368 ASN cc_start: 0.6883 (m110) cc_final: 0.6588 (m-40) REVERT: A 591 ILE cc_start: 0.4329 (tp) cc_final: 0.3965 (mm) REVERT: A 683 MET cc_start: 0.7031 (tpt) cc_final: 0.6473 (mmm) REVERT: A 696 ASN cc_start: 0.6089 (OUTLIER) cc_final: 0.5756 (t0) REVERT: A 725 ASP cc_start: 0.7525 (m-30) cc_final: 0.7049 (m-30) REVERT: A 870 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6554 (mtt180) REVERT: A 922 LYS cc_start: 0.6745 (pttm) cc_final: 0.6264 (ptmm) REVERT: A 930 MET cc_start: 0.7337 (mtt) cc_final: 0.6926 (mtp) REVERT: A 932 MET cc_start: 0.7382 (mmt) cc_final: 0.6729 (mtt) REVERT: A 963 ASP cc_start: 0.7052 (t70) cc_final: 0.6246 (t0) REVERT: A 1042 MET cc_start: 0.7751 (mtp) cc_final: 0.7383 (mmp) REVERT: A 1050 ASP cc_start: 0.6651 (m-30) cc_final: 0.6218 (m-30) REVERT: A 1084 MET cc_start: 0.5345 (mpt) cc_final: 0.4997 (mmp) REVERT: A 1122 ARG cc_start: 0.5836 (mtm-85) cc_final: 0.5540 (mtm110) REVERT: A 1128 ARG cc_start: 0.6322 (ttp80) cc_final: 0.5625 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5890 (mt0) cc_final: 0.5472 (mm110) REVERT: A 1234 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6833 (pp) REVERT: A 1314 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.5440 (tpt) REVERT: A 1365 MET cc_start: 0.7535 (ptm) cc_final: 0.7187 (ttm) REVERT: A 1467 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7792 (ttm) REVERT: B 112 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6662 (ttp-170) REVERT: B 129 MET cc_start: 0.6889 (mmm) cc_final: 0.6144 (tmt) REVERT: B 284 GLN cc_start: 0.6680 (mm-40) cc_final: 0.6019 (mt0) REVERT: B 368 ASN cc_start: 0.6838 (m110) cc_final: 0.6454 (m110) REVERT: B 521 LEU cc_start: 0.5008 (tt) cc_final: 0.4738 (tt) REVERT: B 591 ILE cc_start: 0.4274 (tp) cc_final: 0.3956 (mm) REVERT: B 683 MET cc_start: 0.7042 (tpt) cc_final: 0.6441 (mmm) REVERT: B 696 ASN cc_start: 0.6047 (OUTLIER) cc_final: 0.5706 (t0) REVERT: B 725 ASP cc_start: 0.7537 (m-30) cc_final: 0.7060 (m-30) REVERT: B 870 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6563 (mtt180) REVERT: B 922 LYS cc_start: 0.6778 (pttm) cc_final: 0.6293 (ptmm) REVERT: B 930 MET cc_start: 0.7340 (mtt) cc_final: 0.6927 (mtp) REVERT: B 932 MET cc_start: 0.7379 (mmt) cc_final: 0.6722 (mtt) REVERT: B 963 ASP cc_start: 0.7055 (t70) cc_final: 0.6253 (t0) REVERT: B 1042 MET cc_start: 0.7755 (mtp) cc_final: 0.7385 (mmp) REVERT: B 1050 ASP cc_start: 0.6653 (m-30) cc_final: 0.6211 (m-30) REVERT: B 1084 MET cc_start: 0.5495 (mmt) cc_final: 0.5165 (mmp) REVERT: B 1085 ARG cc_start: 0.4260 (tpt170) cc_final: 0.3972 (tpp80) REVERT: B 1122 ARG cc_start: 0.5850 (mtm-85) cc_final: 0.5550 (mtm110) REVERT: B 1128 ARG cc_start: 0.6324 (ttp80) cc_final: 0.5628 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5915 (mt0) cc_final: 0.5473 (mm110) REVERT: B 1234 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6838 (pp) REVERT: B 1314 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.5403 (tpt) REVERT: B 1365 MET cc_start: 0.7534 (ptm) cc_final: 0.7204 (ttm) REVERT: B 1467 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7901 (ttm) REVERT: C 129 MET cc_start: 0.6887 (mmm) cc_final: 0.6169 (tmt) REVERT: C 284 GLN cc_start: 0.6687 (mm-40) cc_final: 0.6023 (mt0) REVERT: C 368 ASN cc_start: 0.6900 (m110) cc_final: 0.6328 (t0) REVERT: C 591 ILE cc_start: 0.4273 (tp) cc_final: 0.3966 (mm) REVERT: C 683 MET cc_start: 0.7067 (tpt) cc_final: 0.6478 (mmm) REVERT: C 696 ASN cc_start: 0.6051 (OUTLIER) cc_final: 0.5713 (t0) REVERT: C 725 ASP cc_start: 0.7528 (m-30) cc_final: 0.7049 (m-30) REVERT: C 870 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6577 (mtt180) REVERT: C 922 LYS cc_start: 0.6780 (pttm) cc_final: 0.6297 (ptmm) REVERT: C 930 MET cc_start: 0.7351 (mtt) cc_final: 0.6938 (mtp) REVERT: C 932 MET cc_start: 0.7376 (mmt) cc_final: 0.6717 (mtt) REVERT: C 963 ASP cc_start: 0.7081 (t70) cc_final: 0.6316 (t0) REVERT: C 1042 MET cc_start: 0.7725 (mtp) cc_final: 0.7367 (mmp) REVERT: C 1050 ASP cc_start: 0.6659 (m-30) cc_final: 0.6217 (m-30) REVERT: C 1084 MET cc_start: 0.5505 (mmt) cc_final: 0.5178 (mmp) REVERT: C 1085 ARG cc_start: 0.4267 (tpt170) cc_final: 0.3977 (tpp80) REVERT: C 1122 ARG cc_start: 0.5765 (mtm-85) cc_final: 0.5483 (mtm110) REVERT: C 1128 ARG cc_start: 0.6329 (ttp80) cc_final: 0.5628 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5879 (mt0) cc_final: 0.5468 (mm110) REVERT: C 1166 GLN cc_start: 0.6582 (mm-40) cc_final: 0.6187 (tm-30) REVERT: C 1234 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6846 (pp) REVERT: C 1314 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.5396 (tpt) REVERT: C 1365 MET cc_start: 0.7508 (ptm) cc_final: 0.7296 (ttm) REVERT: D 112 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6656 (ttp-170) REVERT: D 129 MET cc_start: 0.6869 (mmm) cc_final: 0.6135 (tmt) REVERT: D 284 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6019 (mt0) REVERT: D 521 LEU cc_start: 0.5008 (tt) cc_final: 0.4741 (tt) REVERT: D 591 ILE cc_start: 0.4275 (tp) cc_final: 0.3955 (mm) REVERT: D 683 MET cc_start: 0.7064 (tpt) cc_final: 0.6479 (mmm) REVERT: D 696 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.5643 (t0) REVERT: D 725 ASP cc_start: 0.7528 (m-30) cc_final: 0.7051 (m-30) REVERT: D 870 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6555 (mtt180) REVERT: D 922 LYS cc_start: 0.6750 (pttm) cc_final: 0.6267 (ptmm) REVERT: D 930 MET cc_start: 0.7346 (mtt) cc_final: 0.6935 (mtp) REVERT: D 932 MET cc_start: 0.7380 (mmt) cc_final: 0.6721 (mtt) REVERT: D 963 ASP cc_start: 0.7062 (t70) cc_final: 0.6299 (t0) REVERT: D 990 ASP cc_start: 0.7591 (m-30) cc_final: 0.7293 (m-30) REVERT: D 1042 MET cc_start: 0.7728 (mtp) cc_final: 0.7362 (mmp) REVERT: D 1050 ASP cc_start: 0.6641 (m-30) cc_final: 0.6195 (m-30) REVERT: D 1084 MET cc_start: 0.5392 (mpt) cc_final: 0.5059 (mmp) REVERT: D 1122 ARG cc_start: 0.5818 (mtm-85) cc_final: 0.5522 (mtm110) REVERT: D 1128 ARG cc_start: 0.6318 (ttp80) cc_final: 0.5616 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5883 (mt0) cc_final: 0.5459 (mm110) REVERT: D 1234 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6808 (pp) REVERT: D 1314 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.5493 (tpt) REVERT: D 1365 MET cc_start: 0.7513 (ptm) cc_final: 0.7288 (ttm) REVERT: D 1467 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7893 (ttm) outliers start: 112 outliers final: 61 residues processed: 449 average time/residue: 0.7304 time to fit residues: 406.1438 Evaluate side-chains 433 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 350 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR 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 621 LEU 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 1105 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1467 MET Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR 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 621 LEU 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 989 ASP Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain B residue 1467 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR 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 621 LEU 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 989 ASP Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR 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 1105 THR Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Chi-restraints excluded: chain D residue 1467 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 393 optimal weight: 0.9980 chunk 385 optimal weight: 1.9990 chunk 448 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 467 optimal weight: 0.8980 chunk 490 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 535 optimal weight: 0.5980 chunk 543 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A1276 ASN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1276 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN C1276 ASN D1276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.128146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096335 restraints weight = 72320.341| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.40 r_work: 0.3230 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41611 Z= 0.116 Angle : 0.518 8.005 56930 Z= 0.265 Chirality : 0.038 0.150 6668 Planarity : 0.004 0.086 7196 Dihedral : 8.541 88.455 6996 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.30 % Allowed : 18.14 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.11), residues: 5432 helix: 1.87 (0.09), residues: 2996 sheet: -1.22 (0.24), residues: 388 loop : -0.92 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 916 TYR 0.032 0.002 TYR C 110 PHE 0.017 0.001 PHE B 268 TRP 0.009 0.001 TRP C1309 HIS 0.004 0.001 HIS A 886 Details of bonding type rmsd covalent geometry : bond 0.00251 (41608) covalent geometry : angle 0.51757 (56912) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.22392 ( 18) hydrogen bonds : bond 0.03989 ( 2348) hydrogen bonds : angle 3.92960 ( 6936) *********************** 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 449 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 364 time to evaluate : 1.678 Fit side-chains REVERT: A 76 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5730 (tpp) REVERT: A 129 MET cc_start: 0.6817 (mmm) cc_final: 0.6107 (tmt) REVERT: A 284 GLN cc_start: 0.6667 (mm-40) cc_final: 0.6025 (mt0) REVERT: A 368 ASN cc_start: 0.6776 (m110) cc_final: 0.6228 (t0) REVERT: A 591 ILE cc_start: 0.4473 (tp) cc_final: 0.4025 (mp) REVERT: A 621 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7001 (tm) REVERT: A 683 MET cc_start: 0.7071 (tpt) cc_final: 0.6521 (mmm) REVERT: A 696 ASN cc_start: 0.6099 (OUTLIER) cc_final: 0.5759 (t0) REVERT: A 725 ASP cc_start: 0.7426 (m-30) cc_final: 0.6981 (m-30) REVERT: A 870 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6543 (mtt180) REVERT: A 916 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7523 (tpt170) REVERT: A 922 LYS cc_start: 0.6747 (pttm) cc_final: 0.6264 (ptmm) REVERT: A 930 MET cc_start: 0.7325 (mtt) cc_final: 0.6899 (mtp) REVERT: A 932 MET cc_start: 0.7456 (mmt) cc_final: 0.6820 (mtt) REVERT: A 1042 MET cc_start: 0.7762 (mtp) cc_final: 0.7397 (mmp) REVERT: A 1050 ASP cc_start: 0.6648 (m-30) cc_final: 0.6234 (m-30) REVERT: A 1084 MET cc_start: 0.5509 (mpt) cc_final: 0.5079 (mmp) REVERT: A 1122 ARG cc_start: 0.5743 (mtm-85) cc_final: 0.5455 (mtm110) REVERT: A 1128 ARG cc_start: 0.6253 (ttp80) cc_final: 0.5602 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5898 (mt0) cc_final: 0.5447 (mm110) REVERT: A 1234 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6712 (pp) REVERT: A 1314 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.4914 (tpt) REVERT: A 1345 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7728 (tp) REVERT: A 1467 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7795 (ttm) REVERT: B 112 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6693 (ttp-170) REVERT: B 129 MET cc_start: 0.6782 (mmm) cc_final: 0.6095 (tmt) REVERT: B 284 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6051 (mt0) REVERT: B 368 ASN cc_start: 0.6793 (m110) cc_final: 0.6235 (t0) REVERT: B 521 LEU cc_start: 0.5063 (tt) cc_final: 0.4830 (tt) REVERT: B 591 ILE cc_start: 0.4334 (tp) cc_final: 0.4016 (mm) REVERT: B 683 MET cc_start: 0.7051 (tpt) cc_final: 0.6509 (mmm) REVERT: B 696 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5711 (t0) REVERT: B 725 ASP cc_start: 0.7400 (m-30) cc_final: 0.6957 (m-30) REVERT: B 870 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6479 (mtt180) REVERT: B 916 ARG cc_start: 0.7732 (tpt170) cc_final: 0.7453 (tmt90) REVERT: B 922 LYS cc_start: 0.6765 (pttm) cc_final: 0.6284 (ptmm) REVERT: B 930 MET cc_start: 0.7327 (mtt) cc_final: 0.6840 (mtp) REVERT: B 932 MET cc_start: 0.7455 (mmt) cc_final: 0.6810 (mtt) REVERT: B 1042 MET cc_start: 0.7761 (mtp) cc_final: 0.7395 (mmp) REVERT: B 1050 ASP cc_start: 0.6671 (m-30) cc_final: 0.6234 (m-30) REVERT: B 1084 MET cc_start: 0.5582 (mmt) cc_final: 0.5127 (mmp) REVERT: B 1085 ARG cc_start: 0.4299 (tpt170) cc_final: 0.3989 (tpp80) REVERT: B 1122 ARG cc_start: 0.5847 (mtm-85) cc_final: 0.5551 (mtm110) REVERT: B 1128 ARG cc_start: 0.6262 (ttp80) cc_final: 0.5609 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5887 (mt0) cc_final: 0.5443 (mm110) REVERT: B 1234 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6723 (pp) REVERT: B 1314 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.4953 (tpt) REVERT: B 1467 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7827 (ttm) REVERT: C 129 MET cc_start: 0.6700 (mmm) cc_final: 0.6134 (tmt) REVERT: C 284 GLN cc_start: 0.6661 (mm-40) cc_final: 0.6023 (mt0) REVERT: C 368 ASN cc_start: 0.6780 (m110) cc_final: 0.6241 (t0) REVERT: C 396 PHE cc_start: 0.7178 (t80) cc_final: 0.6471 (t80) REVERT: C 591 ILE cc_start: 0.4357 (tp) cc_final: 0.4057 (mm) REVERT: C 621 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7006 (tm) REVERT: C 657 LYS cc_start: 0.4783 (tttm) cc_final: 0.4278 (tptt) REVERT: C 683 MET cc_start: 0.7099 (tpt) cc_final: 0.6540 (mmm) REVERT: C 696 ASN cc_start: 0.6093 (OUTLIER) cc_final: 0.5750 (t0) REVERT: C 725 ASP cc_start: 0.7421 (m-30) cc_final: 0.6971 (m-30) REVERT: C 870 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6568 (mtt180) REVERT: C 916 ARG cc_start: 0.7825 (tmm-80) cc_final: 0.7502 (tpt170) REVERT: C 922 LYS cc_start: 0.6752 (pttm) cc_final: 0.6277 (ptmm) REVERT: C 930 MET cc_start: 0.7362 (mtt) cc_final: 0.6856 (mtp) REVERT: C 932 MET cc_start: 0.7503 (mmt) cc_final: 0.6880 (mtt) REVERT: C 1042 MET cc_start: 0.7737 (mtp) cc_final: 0.7383 (mmp) REVERT: C 1050 ASP cc_start: 0.6669 (m-30) cc_final: 0.6256 (m-30) REVERT: C 1084 MET cc_start: 0.5582 (mmt) cc_final: 0.5135 (mmp) REVERT: C 1085 ARG cc_start: 0.4305 (tpt170) cc_final: 0.3994 (tpp80) REVERT: C 1122 ARG cc_start: 0.5692 (mtm-85) cc_final: 0.5413 (mtm110) REVERT: C 1128 ARG cc_start: 0.6306 (ttp80) cc_final: 0.5649 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5898 (mt0) cc_final: 0.5456 (mm110) REVERT: C 1234 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6743 (pp) REVERT: C 1314 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.4954 (tpt) REVERT: D 112 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6702 (ttp-170) REVERT: D 129 MET cc_start: 0.6638 (mmm) cc_final: 0.6072 (tmt) REVERT: D 284 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6016 (mt0) REVERT: D 396 PHE cc_start: 0.7198 (t80) cc_final: 0.6487 (t80) REVERT: D 521 LEU cc_start: 0.5064 (tt) cc_final: 0.4830 (tt) REVERT: D 591 ILE cc_start: 0.4421 (tp) cc_final: 0.4091 (mm) REVERT: D 621 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6986 (tm) REVERT: D 683 MET cc_start: 0.7046 (tpt) cc_final: 0.6490 (mmm) REVERT: D 696 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.5634 (t0) REVERT: D 725 ASP cc_start: 0.7434 (m-30) cc_final: 0.6991 (m-30) REVERT: D 870 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6541 (mtt180) REVERT: D 916 ARG cc_start: 0.7823 (tmm-80) cc_final: 0.7524 (tpt170) REVERT: D 922 LYS cc_start: 0.6727 (pttm) cc_final: 0.6246 (ptmm) REVERT: D 930 MET cc_start: 0.7337 (mtt) cc_final: 0.6847 (mtp) REVERT: D 932 MET cc_start: 0.7463 (mmt) cc_final: 0.6827 (mtt) REVERT: D 990 ASP cc_start: 0.7548 (m-30) cc_final: 0.7276 (m-30) REVERT: D 1042 MET cc_start: 0.7747 (mtp) cc_final: 0.7389 (mmp) REVERT: D 1050 ASP cc_start: 0.6654 (m-30) cc_final: 0.6240 (m-30) REVERT: D 1084 MET cc_start: 0.5513 (mpt) cc_final: 0.5080 (mmp) REVERT: D 1122 ARG cc_start: 0.5751 (mtm-85) cc_final: 0.5460 (mtm110) REVERT: D 1128 ARG cc_start: 0.6251 (ttp80) cc_final: 0.5598 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5905 (mt0) cc_final: 0.5450 (mm110) REVERT: D 1234 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6731 (pp) REVERT: D 1314 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.4912 (tpt) REVERT: D 1467 MET cc_start: 0.8437 (mtp) cc_final: 0.7912 (ttm) outliers start: 85 outliers final: 44 residues processed: 429 average time/residue: 0.7379 time to fit residues: 390.3250 Evaluate side-chains 421 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 352 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR 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 621 LEU 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 1105 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1467 MET Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR 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 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain B residue 1467 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR 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 621 LEU 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 1105 THR Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR 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 621 LEU 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 1115 LEU Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 375 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 295 optimal weight: 1.9990 chunk 523 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 0.0050 chunk 518 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 472 optimal weight: 0.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095954 restraints weight = 71806.903| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.39 r_work: 0.3226 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41611 Z= 0.122 Angle : 0.532 10.913 56930 Z= 0.270 Chirality : 0.039 0.151 6668 Planarity : 0.004 0.076 7196 Dihedral : 8.521 88.736 6996 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.25 % Allowed : 18.47 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.11), residues: 5432 helix: 1.85 (0.09), residues: 3000 sheet: -1.07 (0.22), residues: 428 loop : -0.96 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.032 0.002 TYR B 420 PHE 0.018 0.001 PHE D 268 TRP 0.008 0.001 TRP C1309 HIS 0.004 0.001 HIS C 886 Details of bonding type rmsd covalent geometry : bond 0.00269 (41608) covalent geometry : angle 0.53198 (56912) SS BOND : bond 0.00122 ( 3) SS BOND : angle 0.26552 ( 18) hydrogen bonds : bond 0.04072 ( 2348) hydrogen bonds : angle 3.92525 ( 6936) ********************** 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 451 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 368 time to evaluate : 1.718 Fit side-chains REVERT: A 76 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5732 (tpp) REVERT: A 129 MET cc_start: 0.6740 (mmm) cc_final: 0.6066 (tmt) REVERT: A 284 GLN cc_start: 0.6676 (mm-40) cc_final: 0.5992 (mt0) REVERT: A 368 ASN cc_start: 0.6753 (m110) cc_final: 0.6211 (t0) REVERT: A 591 ILE cc_start: 0.4516 (tp) cc_final: 0.4036 (mp) REVERT: A 683 MET cc_start: 0.7044 (tpt) cc_final: 0.6485 (mmm) REVERT: A 696 ASN cc_start: 0.6091 (OUTLIER) cc_final: 0.5747 (t0) REVERT: A 725 ASP cc_start: 0.7410 (m-30) cc_final: 0.6956 (m-30) REVERT: A 870 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6522 (mtt180) REVERT: A 922 LYS cc_start: 0.6759 (pttm) cc_final: 0.6251 (ptmm) REVERT: A 930 MET cc_start: 0.7330 (mtt) cc_final: 0.6915 (mtp) REVERT: A 932 MET cc_start: 0.7510 (mmt) cc_final: 0.6888 (mtt) REVERT: A 963 ASP cc_start: 0.6953 (t70) cc_final: 0.6183 (t0) REVERT: A 1042 MET cc_start: 0.7726 (mtp) cc_final: 0.7366 (mmp) REVERT: A 1050 ASP cc_start: 0.6675 (m-30) cc_final: 0.6223 (m-30) REVERT: A 1084 MET cc_start: 0.5581 (mpt) cc_final: 0.5165 (mmp) REVERT: A 1122 ARG cc_start: 0.5758 (mtm-85) cc_final: 0.5468 (mtm110) REVERT: A 1128 ARG cc_start: 0.6259 (ttp80) cc_final: 0.5619 (ttm-80) REVERT: A 1129 GLN cc_start: 0.5887 (mt0) cc_final: 0.5437 (mm110) REVERT: A 1234 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6754 (pp) REVERT: A 1314 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.4983 (tpt) REVERT: A 1345 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 1467 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7865 (ttm) REVERT: B 81 MET cc_start: 0.4970 (ttp) cc_final: 0.4267 (mtp) REVERT: B 112 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6628 (ttp-170) REVERT: B 129 MET cc_start: 0.6731 (mmm) cc_final: 0.6061 (tmt) REVERT: B 284 GLN cc_start: 0.6674 (mm-40) cc_final: 0.6039 (mt0) REVERT: B 368 ASN cc_start: 0.6772 (m110) cc_final: 0.6211 (t0) REVERT: B 521 LEU cc_start: 0.5078 (tt) cc_final: 0.4817 (tt) REVERT: B 591 ILE cc_start: 0.4445 (tp) cc_final: 0.3999 (mp) REVERT: B 683 MET cc_start: 0.7053 (tpt) cc_final: 0.6508 (mmm) REVERT: B 696 ASN cc_start: 0.6083 (OUTLIER) cc_final: 0.5729 (t0) REVERT: B 725 ASP cc_start: 0.7426 (m-30) cc_final: 0.6968 (m-30) REVERT: B 870 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6530 (mtt180) REVERT: B 916 ARG cc_start: 0.7752 (tpt170) cc_final: 0.7431 (tmm-80) REVERT: B 922 LYS cc_start: 0.6725 (pttm) cc_final: 0.6245 (ptmm) REVERT: B 930 MET cc_start: 0.7322 (mtt) cc_final: 0.6911 (mtp) REVERT: B 932 MET cc_start: 0.7519 (mmt) cc_final: 0.6886 (mtt) REVERT: B 963 ASP cc_start: 0.6967 (t70) cc_final: 0.6246 (t0) REVERT: B 1042 MET cc_start: 0.7734 (mtp) cc_final: 0.7370 (mmp) REVERT: B 1050 ASP cc_start: 0.6696 (m-30) cc_final: 0.6254 (m-30) REVERT: B 1084 MET cc_start: 0.5561 (mmt) cc_final: 0.5105 (mmp) REVERT: B 1085 ARG cc_start: 0.4258 (tpt170) cc_final: 0.3951 (tpp80) REVERT: B 1122 ARG cc_start: 0.5852 (mtm-85) cc_final: 0.5554 (mtm110) REVERT: B 1128 ARG cc_start: 0.6265 (ttp80) cc_final: 0.5623 (ttm-80) REVERT: B 1129 GLN cc_start: 0.5819 (mt0) cc_final: 0.5335 (mm110) REVERT: B 1234 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6693 (pp) REVERT: B 1314 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.4951 (tpt) REVERT: C 129 MET cc_start: 0.6623 (mmm) cc_final: 0.6217 (tmt) REVERT: C 284 GLN cc_start: 0.6666 (mm-40) cc_final: 0.5995 (mt0) REVERT: C 335 MET cc_start: 0.8548 (mtp) cc_final: 0.8346 (mtt) REVERT: C 591 ILE cc_start: 0.4339 (tp) cc_final: 0.3885 (mp) REVERT: C 683 MET cc_start: 0.7094 (tpt) cc_final: 0.6549 (mmm) REVERT: C 696 ASN cc_start: 0.6086 (OUTLIER) cc_final: 0.5742 (t0) REVERT: C 725 ASP cc_start: 0.7453 (m-30) cc_final: 0.6987 (m-30) REVERT: C 870 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6515 (mtt180) REVERT: C 922 LYS cc_start: 0.6783 (pttm) cc_final: 0.6287 (ptmm) REVERT: C 930 MET cc_start: 0.7328 (mtt) cc_final: 0.6915 (mtp) REVERT: C 932 MET cc_start: 0.7511 (mmt) cc_final: 0.6887 (mtt) REVERT: C 1042 MET cc_start: 0.7695 (mtp) cc_final: 0.7345 (mmp) REVERT: C 1050 ASP cc_start: 0.6699 (m-30) cc_final: 0.6249 (m-30) REVERT: C 1084 MET cc_start: 0.5562 (mmt) cc_final: 0.5106 (mmp) REVERT: C 1085 ARG cc_start: 0.4259 (tpt170) cc_final: 0.3949 (tpp80) REVERT: C 1122 ARG cc_start: 0.5718 (mtm-85) cc_final: 0.5436 (mtm110) REVERT: C 1128 ARG cc_start: 0.6275 (ttp80) cc_final: 0.5634 (ttm-80) REVERT: C 1129 GLN cc_start: 0.5877 (mt0) cc_final: 0.5435 (mm110) REVERT: C 1234 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6740 (pp) REVERT: C 1314 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.4942 (tpt) REVERT: D 81 MET cc_start: 0.5073 (ttp) cc_final: 0.4319 (mtp) REVERT: D 112 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6631 (ttp-170) REVERT: D 129 MET cc_start: 0.6520 (mmm) cc_final: 0.6112 (tmt) REVERT: D 284 GLN cc_start: 0.6670 (mm-40) cc_final: 0.5992 (mt0) REVERT: D 521 LEU cc_start: 0.5071 (tt) cc_final: 0.4809 (tt) REVERT: D 621 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6994 (tm) REVERT: D 683 MET cc_start: 0.7030 (tpt) cc_final: 0.6496 (mmm) REVERT: D 696 ASN cc_start: 0.5937 (OUTLIER) cc_final: 0.5601 (t0) REVERT: D 725 ASP cc_start: 0.7423 (m-30) cc_final: 0.6972 (m-30) REVERT: D 870 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6523 (mtt180) REVERT: D 922 LYS cc_start: 0.6746 (pttm) cc_final: 0.6265 (ptmm) REVERT: D 930 MET cc_start: 0.7329 (mtt) cc_final: 0.6913 (mtp) REVERT: D 932 MET cc_start: 0.7503 (mmt) cc_final: 0.6877 (mtt) REVERT: D 963 ASP cc_start: 0.6971 (t70) cc_final: 0.6211 (t0) REVERT: D 990 ASP cc_start: 0.7570 (m-30) cc_final: 0.7278 (m-30) REVERT: D 1042 MET cc_start: 0.7715 (mtp) cc_final: 0.7357 (mmp) REVERT: D 1050 ASP cc_start: 0.6689 (m-30) cc_final: 0.6237 (m-30) REVERT: D 1084 MET cc_start: 0.5582 (mpt) cc_final: 0.5165 (mmp) REVERT: D 1122 ARG cc_start: 0.5765 (mtm-85) cc_final: 0.5472 (mtm110) REVERT: D 1128 ARG cc_start: 0.6262 (ttp80) cc_final: 0.5618 (ttm-80) REVERT: D 1129 GLN cc_start: 0.5817 (mt0) cc_final: 0.5334 (mm110) REVERT: D 1234 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6731 (pp) REVERT: D 1314 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.4991 (tpt) REVERT: D 1467 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7876 (ttm) outliers start: 83 outliers final: 47 residues processed: 427 average time/residue: 0.7214 time to fit residues: 380.7986 Evaluate side-chains 434 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 364 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 346 THR 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 696 ASN Chi-restraints excluded: chain A residue 870 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1467 MET Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 THR 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 696 ASN Chi-restraints excluded: chain B residue 870 ARG Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 346 THR 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 664 LYS Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 870 ARG Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1234 ILE Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 346 THR 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 621 LEU 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 1115 LEU Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1314 MET Chi-restraints excluded: chain D residue 1467 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 304 optimal weight: 0.2980 chunk 534 optimal weight: 0.8980 chunk 535 optimal weight: 7.9990 chunk 541 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 598 GLN ** B1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095558 restraints weight = 72053.686| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.39 r_work: 0.3220 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41611 Z= 0.140 Angle : 0.560 10.966 56930 Z= 0.285 Chirality : 0.040 0.165 6668 Planarity : 0.005 0.085 7196 Dihedral : 8.596 88.530 6996 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.41 % Allowed : 18.38 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.11), residues: 5432 helix: 1.73 (0.09), residues: 3000 sheet: -1.13 (0.22), residues: 460 loop : -1.05 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 916 TYR 0.031 0.002 TYR B 420 PHE 0.022 0.002 PHE A 268 TRP 0.008 0.001 TRP B1309 HIS 0.007 0.001 HIS C1470 Details of bonding type rmsd covalent geometry : bond 0.00315 (41608) covalent geometry : angle 0.56002 (56912) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.36506 ( 18) hydrogen bonds : bond 0.04347 ( 2348) hydrogen bonds : angle 4.02082 ( 6936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18870.99 seconds wall clock time: 321 minutes 29.43 seconds (19289.43 seconds total)