Starting phenix.real_space_refine on Thu Dec 26 04:10:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srd_40727/12_2024/8srd_40727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srd_40727/12_2024/8srd_40727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srd_40727/12_2024/8srd_40727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srd_40727/12_2024/8srd_40727.map" model { file = "/net/cci-nas-00/data/ceres_data/8srd_40727/12_2024/8srd_40727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srd_40727/12_2024/8srd_40727.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.076 sd= 1.011 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 21 5.21 5 S 248 5.16 5 C 27404 2.51 5 N 7344 2.21 5 O 7653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42686 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10508 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 22, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 251 Chain: "D" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10508 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 22, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 251 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 6, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 161 Unusual residues: {' MG': 5, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C Time building chain proxies: 39.10, per 1000 atoms: 0.92 Number of scatterers: 42686 At special positions: 0 Unit cell: (146.202, 146.202, 182.546, 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 248 16.00 P 16 15.00 Mg 21 11.99 O 7653 8.00 N 7344 7.00 C 27404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.02 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.02 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: 10.36 Conformation dependent library (CDL) restraints added in 5.7 seconds 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10304 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 36 sheets defined 57.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.772A 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 187 through 201 Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.501A pdb=" N MET A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.735A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.684A pdb=" N ASN A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.653A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 406 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.666A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.621A pdb=" N ARG A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.629A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.661A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 641 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 678 removed outlier: 3.959A pdb=" N LEU A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 699 through 707 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 788 through 799 removed outlier: 4.100A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 4.200A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 929 " --> pdb=" O GLY A 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.603A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 975 " --> pdb=" O PHE A 971 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1009 through 1012 removed outlier: 3.571A pdb=" N ARG A1012 " --> pdb=" O GLU A1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1009 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1047 removed outlier: 4.011A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1088 removed outlier: 4.211A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1129 Processing helix chain 'A' and resid 1131 through 1169 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1378 through 1392 Processing helix chain 'A' and resid 1403 through 1413 Processing helix chain 'A' and resid 1449 through 1453 Processing helix chain 'A' and resid 1478 through 1491 removed outlier: 3.502A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.772A 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 187 through 201 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.502A pdb=" N MET B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.735A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.683A pdb=" N ASN B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 406 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.665A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 removed outlier: 3.621A pdb=" N ARG B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.629A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.661A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 641 Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 678 removed outlier: 3.959A pdb=" N LEU B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 699 through 707 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 788 through 799 removed outlier: 4.101A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 Processing helix chain 'B' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 4.200A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.603A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 975 " --> pdb=" O PHE B 971 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1009 through 1012 removed outlier: 3.570A pdb=" N ARG B1012 " --> pdb=" O GLU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1009 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1047 removed outlier: 4.010A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 removed outlier: 4.211A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1129 Processing helix chain 'B' and resid 1131 through 1169 Processing helix chain 'B' and resid 1202 through 1206 Processing helix chain 'B' and resid 1378 through 1392 Processing helix chain 'B' and resid 1403 through 1413 Processing helix chain 'B' and resid 1449 through 1453 Processing helix chain 'B' and resid 1478 through 1491 removed outlier: 3.503A pdb=" N LEU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.772A 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 187 through 201 Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.501A pdb=" N MET C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.736A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 removed outlier: 3.684A pdb=" N ASN C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 406 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.665A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 503 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.621A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.629A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.662A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 641 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 678 removed outlier: 3.960A pdb=" N LEU C 673 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 699 through 707 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 788 through 799 removed outlier: 4.101A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 Processing helix chain 'C' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 4.201A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 929 " --> pdb=" O GLY C 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 940 " --> pdb=" O LYS C 936 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.603A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 975 " --> pdb=" O PHE C 971 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1009 through 1012 removed outlier: 3.570A pdb=" N ARG C1012 " --> pdb=" O GLU C1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1009 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1047 removed outlier: 4.012A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1088 removed outlier: 4.210A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1129 Processing helix chain 'C' and resid 1131 through 1169 Processing helix chain 'C' and resid 1202 through 1206 Processing helix chain 'C' and resid 1378 through 1392 Processing helix chain 'C' and resid 1403 through 1413 Processing helix chain 'C' and resid 1449 through 1453 Processing helix chain 'C' and resid 1478 through 1491 removed outlier: 3.503A pdb=" N LEU C1482 " --> pdb=" O SER C1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.772A 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 187 through 201 Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.501A pdb=" N MET D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.736A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 removed outlier: 3.683A pdb=" N ASN D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 406 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.665A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 503 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.622A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.630A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.662A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 641 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 678 removed outlier: 3.959A pdb=" N LEU D 673 " --> pdb=" O ALA D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 699 through 707 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 788 through 799 removed outlier: 4.100A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 Processing helix chain 'D' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 4.201A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE D 929 " --> pdb=" O GLY D 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 940 " --> pdb=" O LYS D 936 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.602A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 975 " --> pdb=" O PHE D 971 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1009 through 1012 removed outlier: 3.571A pdb=" N ARG D1012 " --> pdb=" O GLU D1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1009 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1047 removed outlier: 4.011A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D1066 " --> pdb=" O GLU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1088 removed outlier: 4.211A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1129 Processing helix chain 'D' and resid 1131 through 1169 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1403 through 1413 Processing helix chain 'D' and resid 1449 through 1453 Processing helix chain 'D' and resid 1478 through 1491 removed outlier: 3.501A pdb=" N LEU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 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: 7.549A pdb=" N TRP A 96 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A 182 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY A 149 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1200 removed outlier: 7.208A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 17.489A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.565A 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: 5.565A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.489A 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: 6.146A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 7.925A 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: 4.545A 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: 5.565A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.488A 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: 17.488A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.565A 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 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 58 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: 7.550A pdb=" N TRP B 96 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY B 182 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY B 149 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1199 through 1200 removed outlier: 7.208A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 17.488A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.741A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.565A 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: 5.565A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.741A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.488A 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: 6.146A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 7.785A 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: 4.545A 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 58 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: 7.549A pdb=" N TRP C 96 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 182 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY C 149 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1199 through 1200 removed outlier: 7.208A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 17.489A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.564A 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: 5.564A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.489A 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: 6.146A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 7.785A 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: 4.545A 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 58 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: 7.549A pdb=" N TRP D 96 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY D 182 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY D 149 " --> pdb=" O GLY D 182 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 6.146A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 7.924A 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: 4.545A 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 2311 hydrogen bonds defined for protein. 6741 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: 21.37 Time building geometry restraints manager: 11.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6875 1.31 - 1.44: 11697 1.44 - 1.56: 24604 1.56 - 1.69: 56 1.69 - 1.82: 436 Bond restraints: 43668 Sorted by residual: bond pdb=" C PRO C 978 " pdb=" O PRO C 978 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C PRO A 978 " pdb=" O PRO A 978 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C PRO B 978 " pdb=" O PRO B 978 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C PRO D 978 " pdb=" O PRO D 978 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" N THR B 357 " pdb=" CA THR B 357 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.27e-02 6.20e+03 1.39e+01 ... (remaining 43663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 50629 2.35 - 4.70: 7154 4.70 - 7.05: 1334 7.05 - 9.40: 219 9.40 - 11.75: 36 Bond angle restraints: 59372 Sorted by residual: angle pdb=" N PRO C 244 " pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 110.70 121.76 -11.06 1.22e+00 6.72e-01 8.21e+01 angle pdb=" N PRO B 244 " pdb=" CA PRO B 244 " pdb=" C PRO B 244 " ideal model delta sigma weight residual 110.70 121.76 -11.06 1.22e+00 6.72e-01 8.21e+01 angle pdb=" N PRO D 244 " pdb=" CA PRO D 244 " pdb=" C PRO D 244 " ideal model delta sigma weight residual 110.70 121.73 -11.03 1.22e+00 6.72e-01 8.17e+01 angle pdb=" N PRO A 244 " pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 110.70 121.73 -11.03 1.22e+00 6.72e-01 8.17e+01 angle pdb=" N VAL D 844 " pdb=" CA VAL D 844 " pdb=" C VAL D 844 " ideal model delta sigma weight residual 110.53 103.33 7.20 9.40e-01 1.13e+00 5.87e+01 ... (remaining 59367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 24308 17.80 - 35.61: 1941 35.61 - 53.41: 381 53.41 - 71.21: 96 71.21 - 89.02: 60 Dihedral angle restraints: 26786 sinusoidal: 10878 harmonic: 15908 Sorted by residual: dihedral pdb=" C ASP B 611 " pdb=" N ASP B 611 " pdb=" CA ASP B 611 " pdb=" CB ASP B 611 " ideal model delta harmonic sigma weight residual -122.60 -139.61 17.01 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C ASP D 611 " pdb=" N ASP D 611 " pdb=" CA ASP D 611 " pdb=" CB ASP D 611 " ideal model delta harmonic sigma weight residual -122.60 -139.58 16.98 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" C ASP A 611 " pdb=" N ASP A 611 " pdb=" CA ASP A 611 " pdb=" CB ASP A 611 " ideal model delta harmonic sigma weight residual -122.60 -139.54 16.94 0 2.50e+00 1.60e-01 4.59e+01 ... (remaining 26783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 5528 0.121 - 0.241: 1016 0.241 - 0.362: 160 0.362 - 0.482: 32 0.482 - 0.603: 4 Chirality restraints: 6740 Sorted by residual: chirality pdb=" CA ASP B 611 " pdb=" N ASP B 611 " pdb=" C ASP B 611 " pdb=" CB ASP B 611 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" CA ASP D 611 " pdb=" N ASP D 611 " pdb=" C ASP D 611 " pdb=" CB ASP D 611 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.04e+00 chirality pdb=" CA ASP A 611 " pdb=" N ASP A 611 " pdb=" C ASP A 611 " pdb=" CB ASP A 611 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 ... (remaining 6737 not shown) Planarity restraints: 7504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 649 " -0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C PRO A 649 " 0.088 2.00e-02 2.50e+03 pdb=" O PRO A 649 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS A 650 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 649 " 0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C PRO C 649 " -0.088 2.00e-02 2.50e+03 pdb=" O PRO C 649 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS C 650 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 649 " -0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C PRO D 649 " 0.087 2.00e-02 2.50e+03 pdb=" O PRO D 649 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS D 650 " -0.029 2.00e-02 2.50e+03 ... (remaining 7501 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 383 2.60 - 3.17: 33247 3.17 - 3.75: 65807 3.75 - 4.32: 91845 4.32 - 4.90: 153559 Nonbonded interactions: 344841 Sorted by model distance: nonbonded pdb=" SG CYS C 997 " pdb=" SG CYS C1006 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.024 3.760 nonbonded pdb="MG MG C1704 " pdb=" O2B APR C1708 " model vdw 2.051 2.170 nonbonded pdb="MG MG B1704 " pdb=" O2B APR B1708 " model vdw 2.051 2.170 nonbonded pdb="MG MG A1704 " pdb=" O2B APR A1708 " model vdw 2.051 2.170 ... (remaining 344836 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 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'B' and (resid 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'C' and (resid 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'D' and (resid 51 through 1494 or resid 6004 through 6006 or resid 6009)) \ } 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: 4.590 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: 0.050 Extract box with map and model: 1.640 Check model and map are aligned: 0.280 Set scattering table: 0.320 Process input model: 110.800 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 0.090 43668 Z= 0.750 Angle : 1.759 11.751 59372 Z= 1.160 Chirality : 0.098 0.603 6740 Planarity : 0.011 0.055 7504 Dihedral : 14.224 89.018 16476 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.94 % Allowed : 3.29 % Favored : 95.77 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 5432 helix: 0.61 (0.09), residues: 2916 sheet: -0.87 (0.23), residues: 408 loop : -1.21 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B1052 HIS 0.035 0.002 HIS D 903 PHE 0.070 0.005 PHE D 941 TYR 0.055 0.004 TYR B 504 ARG 0.016 0.001 ARG C1452 *********************** 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 1104 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 1064 time to evaluate : 5.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.6967 (m-30) cc_final: 0.6572 (t0) REVERT: A 81 MET cc_start: 0.7325 (ptm) cc_final: 0.7064 (ptm) REVERT: A 156 LEU cc_start: 0.6909 (tp) cc_final: 0.6681 (OUTLIER) REVERT: A 166 LYS cc_start: 0.6819 (ttpt) cc_final: 0.6469 (ptmm) REVERT: A 174 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.6810 (ptp-170) REVERT: A 225 MET cc_start: 0.7325 (mtp) cc_final: 0.7072 (mtp) REVERT: A 251 ASP cc_start: 0.7589 (t0) cc_final: 0.7215 (t0) REVERT: A 284 GLN cc_start: 0.7079 (mt0) cc_final: 0.6723 (mt0) REVERT: A 306 LEU cc_start: 0.7478 (tp) cc_final: 0.7191 (tm) REVERT: A 356 GLN cc_start: 0.6737 (mt0) cc_final: 0.6018 (mm-40) REVERT: A 440 HIS cc_start: 0.4767 (p90) cc_final: 0.4541 (p-80) REVERT: A 456 MET cc_start: 0.5947 (mtt) cc_final: 0.5698 (mtt) REVERT: A 477 LYS cc_start: 0.6110 (mttm) cc_final: 0.5881 (mppt) REVERT: A 560 MET cc_start: 0.6744 (mmm) cc_final: 0.6498 (mmm) REVERT: A 592 GLN cc_start: 0.5410 (tt0) cc_final: 0.4921 (pt0) REVERT: A 594 ARG cc_start: 0.5745 (mtp180) cc_final: 0.5534 (mtp85) REVERT: A 638 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5200 (pt0) REVERT: A 654 GLU cc_start: 0.6119 (tp30) cc_final: 0.5850 (tp30) REVERT: A 663 LYS cc_start: 0.6115 (mmmt) cc_final: 0.5246 (mttm) REVERT: A 694 MET cc_start: 0.6631 (mtm) cc_final: 0.6417 (mtp) REVERT: A 725 ASP cc_start: 0.7345 (m-30) cc_final: 0.6852 (m-30) REVERT: A 731 LYS cc_start: 0.6692 (ttpt) cc_final: 0.6294 (mmpt) REVERT: A 829 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6010 (mm-30) REVERT: A 833 SER cc_start: 0.6288 (t) cc_final: 0.5882 (p) REVERT: A 854 MET cc_start: 0.6462 (mtm) cc_final: 0.6231 (mtt) REVERT: A 870 ARG cc_start: 0.6665 (mtt180) cc_final: 0.6372 (mtt180) REVERT: A 875 MET cc_start: 0.6744 (ptt) cc_final: 0.6469 (ptt) REVERT: A 932 MET cc_start: 0.6612 (mmt) cc_final: 0.6223 (mmt) REVERT: A 969 ARG cc_start: 0.6482 (mtm110) cc_final: 0.6101 (mtm-85) REVERT: A 972 ILE cc_start: 0.7306 (mt) cc_final: 0.6869 (mm) REVERT: A 998 LEU cc_start: 0.6660 (mt) cc_final: 0.6299 (mm) REVERT: A 1005 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5026 (tt0) REVERT: A 1043 LYS cc_start: 0.6901 (mttp) cc_final: 0.6585 (mttp) REVERT: A 1046 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6524 (pt0) REVERT: A 1049 GLU cc_start: 0.5823 (mm-30) cc_final: 0.5604 (mm-30) REVERT: A 1050 ASP cc_start: 0.6515 (m-30) cc_final: 0.5973 (m-30) REVERT: A 1062 GLU cc_start: 0.6707 (tt0) cc_final: 0.6242 (tt0) REVERT: A 1068 PHE cc_start: 0.6109 (t80) cc_final: 0.5869 (t80) REVERT: A 1081 MET cc_start: 0.5662 (mtm) cc_final: 0.5271 (mtp) REVERT: A 1122 ARG cc_start: 0.5843 (mtm-85) cc_final: 0.4829 (mtm-85) REVERT: A 1125 GLU cc_start: 0.5812 (mt-10) cc_final: 0.4656 (pp20) REVERT: A 1128 ARG cc_start: 0.6304 (tmm160) cc_final: 0.5893 (tmm160) REVERT: A 1149 MET cc_start: 0.7643 (mtp) cc_final: 0.7378 (mtm) REVERT: A 1150 MET cc_start: 0.7560 (tpp) cc_final: 0.7349 (mtp) REVERT: A 1152 GLN cc_start: 0.7387 (mt0) cc_final: 0.7046 (mt0) REVERT: A 1160 PHE cc_start: 0.7390 (m-10) cc_final: 0.7104 (m-10) REVERT: A 1248 TYR cc_start: 0.6876 (t80) cc_final: 0.6659 (t80) REVERT: A 1304 ARG cc_start: 0.7714 (ptp-170) cc_final: 0.7084 (mtp180) REVERT: A 1377 GLU cc_start: 0.6632 (pt0) cc_final: 0.6247 (pt0) REVERT: A 1389 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 1445 GLU cc_start: 0.6987 (pm20) cc_final: 0.6772 (mp0) REVERT: A 1456 GLN cc_start: 0.7333 (tm-30) cc_final: 0.7043 (pt0) REVERT: A 1463 HIS cc_start: 0.6939 (m90) cc_final: 0.6228 (t-170) REVERT: A 1491 ASN cc_start: 0.8134 (t0) cc_final: 0.7852 (t0) REVERT: B 74 ASP cc_start: 0.6947 (m-30) cc_final: 0.6554 (t0) REVERT: B 81 MET cc_start: 0.7347 (ptm) cc_final: 0.7088 (ptm) REVERT: B 156 LEU cc_start: 0.6881 (tp) cc_final: 0.6667 (mt) REVERT: B 166 LYS cc_start: 0.6790 (ttpt) cc_final: 0.6412 (ptmm) REVERT: B 174 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.6825 (ptp-170) REVERT: B 225 MET cc_start: 0.7339 (mtp) cc_final: 0.7084 (mtp) REVERT: B 251 ASP cc_start: 0.7585 (t0) cc_final: 0.7213 (t0) REVERT: B 284 GLN cc_start: 0.7073 (mt0) cc_final: 0.6714 (mt0) REVERT: B 306 LEU cc_start: 0.7474 (tp) cc_final: 0.7188 (tm) REVERT: B 356 GLN cc_start: 0.6735 (mt0) cc_final: 0.6026 (mm-40) REVERT: B 440 HIS cc_start: 0.4764 (p90) cc_final: 0.4541 (p-80) REVERT: B 456 MET cc_start: 0.5950 (mtt) cc_final: 0.5698 (mtt) REVERT: B 477 LYS cc_start: 0.6108 (mttm) cc_final: 0.5880 (mppt) REVERT: B 560 MET cc_start: 0.6731 (mmm) cc_final: 0.6486 (mmm) REVERT: B 577 ASP cc_start: 0.6231 (t0) cc_final: 0.5838 (t70) REVERT: B 592 GLN cc_start: 0.5461 (tt0) cc_final: 0.4957 (pt0) REVERT: B 594 ARG cc_start: 0.5743 (mtp180) cc_final: 0.5535 (mtp85) REVERT: B 638 GLU cc_start: 0.5820 (mt-10) cc_final: 0.5192 (pt0) REVERT: B 654 GLU cc_start: 0.6112 (tp30) cc_final: 0.5837 (tp30) REVERT: B 663 LYS cc_start: 0.6310 (mmmt) cc_final: 0.5390 (mttm) REVERT: B 694 MET cc_start: 0.6596 (mtm) cc_final: 0.6384 (mtp) REVERT: B 725 ASP cc_start: 0.7360 (m-30) cc_final: 0.6879 (m-30) REVERT: B 731 LYS cc_start: 0.6685 (ttpt) cc_final: 0.6298 (mmpt) REVERT: B 829 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6027 (mm-30) REVERT: B 833 SER cc_start: 0.6256 (t) cc_final: 0.5877 (p) REVERT: B 854 MET cc_start: 0.6443 (mtm) cc_final: 0.6219 (mtt) REVERT: B 870 ARG cc_start: 0.6673 (mtt180) cc_final: 0.6408 (mtt180) REVERT: B 875 MET cc_start: 0.6760 (ptt) cc_final: 0.6441 (ptp) REVERT: B 932 MET cc_start: 0.6540 (mmt) cc_final: 0.6155 (mmt) REVERT: B 969 ARG cc_start: 0.6478 (mtm110) cc_final: 0.6069 (mtm-85) REVERT: B 972 ILE cc_start: 0.7309 (mt) cc_final: 0.6873 (mm) REVERT: B 998 LEU cc_start: 0.6669 (mt) cc_final: 0.6334 (mm) REVERT: B 1005 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5055 (tt0) REVERT: B 1043 LYS cc_start: 0.6923 (mttp) cc_final: 0.6588 (mttp) REVERT: B 1046 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6487 (pt0) REVERT: B 1049 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5683 (mm-30) REVERT: B 1050 ASP cc_start: 0.6474 (m-30) cc_final: 0.5925 (m-30) REVERT: B 1062 GLU cc_start: 0.6679 (tt0) cc_final: 0.6198 (tt0) REVERT: B 1068 PHE cc_start: 0.6136 (t80) cc_final: 0.5884 (t80) REVERT: B 1081 MET cc_start: 0.5665 (mtm) cc_final: 0.5224 (mtp) REVERT: B 1122 ARG cc_start: 0.5852 (mtm-85) cc_final: 0.4841 (mtm-85) REVERT: B 1125 GLU cc_start: 0.5762 (mt-10) cc_final: 0.4634 (pp20) REVERT: B 1128 ARG cc_start: 0.6262 (tmm160) cc_final: 0.5827 (tmm160) REVERT: B 1149 MET cc_start: 0.7671 (mtp) cc_final: 0.7446 (mtm) REVERT: B 1150 MET cc_start: 0.7546 (tpp) cc_final: 0.7269 (mtp) REVERT: B 1152 GLN cc_start: 0.7372 (mt0) cc_final: 0.7022 (mt0) REVERT: B 1160 PHE cc_start: 0.7341 (m-10) cc_final: 0.7124 (m-10) REVERT: B 1248 TYR cc_start: 0.6889 (t80) cc_final: 0.6652 (t80) REVERT: B 1272 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6389 (pttt) REVERT: B 1304 ARG cc_start: 0.7724 (ptp-170) cc_final: 0.7101 (mtp180) REVERT: B 1377 GLU cc_start: 0.6640 (pt0) cc_final: 0.6252 (pt0) REVERT: B 1389 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7476 (mt-10) REVERT: B 1445 GLU cc_start: 0.6986 (pm20) cc_final: 0.6752 (mp0) REVERT: B 1456 GLN cc_start: 0.7336 (tm-30) cc_final: 0.7047 (pt0) REVERT: B 1463 HIS cc_start: 0.6931 (m90) cc_final: 0.6238 (t-170) REVERT: B 1491 ASN cc_start: 0.8146 (t0) cc_final: 0.7863 (t0) REVERT: C 74 ASP cc_start: 0.6973 (m-30) cc_final: 0.6584 (t0) REVERT: C 81 MET cc_start: 0.7362 (ptm) cc_final: 0.7099 (ptm) REVERT: C 156 LEU cc_start: 0.6880 (tp) cc_final: 0.6668 (mt) REVERT: C 166 LYS cc_start: 0.6789 (ttpt) cc_final: 0.6413 (ptmm) REVERT: C 174 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.6825 (ptp-170) REVERT: C 225 MET cc_start: 0.7355 (mtp) cc_final: 0.7103 (mtp) REVERT: C 251 ASP cc_start: 0.7582 (t0) cc_final: 0.7268 (t0) REVERT: C 284 GLN cc_start: 0.7074 (mt0) cc_final: 0.6417 (mp10) REVERT: C 306 LEU cc_start: 0.7474 (tp) cc_final: 0.7191 (tm) REVERT: C 356 GLN cc_start: 0.6778 (mt0) cc_final: 0.6073 (mm-40) REVERT: C 440 HIS cc_start: 0.4769 (p90) cc_final: 0.4543 (p-80) REVERT: C 456 MET cc_start: 0.5950 (mtt) cc_final: 0.5699 (mtt) REVERT: C 477 LYS cc_start: 0.6115 (mttm) cc_final: 0.5889 (mppt) REVERT: C 560 MET cc_start: 0.6743 (mmm) cc_final: 0.6498 (mmm) REVERT: C 592 GLN cc_start: 0.5412 (tt0) cc_final: 0.4916 (pt0) REVERT: C 594 ARG cc_start: 0.5736 (mtp180) cc_final: 0.5535 (mtp85) REVERT: C 638 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5189 (pt0) REVERT: C 654 GLU cc_start: 0.6098 (tp30) cc_final: 0.5824 (tp30) REVERT: C 663 LYS cc_start: 0.6300 (mmmt) cc_final: 0.5386 (mttm) REVERT: C 694 MET cc_start: 0.6620 (mtm) cc_final: 0.6408 (mtp) REVERT: C 725 ASP cc_start: 0.7362 (m-30) cc_final: 0.6882 (m-30) REVERT: C 731 LYS cc_start: 0.6671 (ttpt) cc_final: 0.6274 (mmpt) REVERT: C 829 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6024 (mm-30) REVERT: C 833 SER cc_start: 0.6268 (t) cc_final: 0.5889 (p) REVERT: C 854 MET cc_start: 0.6445 (mtm) cc_final: 0.6221 (mtt) REVERT: C 870 ARG cc_start: 0.6672 (mtt180) cc_final: 0.6409 (mtt180) REVERT: C 875 MET cc_start: 0.6737 (ptt) cc_final: 0.6413 (ptp) REVERT: C 932 MET cc_start: 0.6537 (mmt) cc_final: 0.6161 (mmt) REVERT: C 969 ARG cc_start: 0.6486 (mtm110) cc_final: 0.6079 (mtm-85) REVERT: C 972 ILE cc_start: 0.7309 (mt) cc_final: 0.6885 (mm) REVERT: C 998 LEU cc_start: 0.6663 (mt) cc_final: 0.6335 (mm) REVERT: C 1005 GLU cc_start: 0.6042 (mt-10) cc_final: 0.5044 (tt0) REVERT: C 1043 LYS cc_start: 0.6927 (mttp) cc_final: 0.6590 (mttp) REVERT: C 1046 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6545 (pt0) REVERT: C 1049 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5676 (mm-30) REVERT: C 1050 ASP cc_start: 0.6463 (m-30) cc_final: 0.5918 (m-30) REVERT: C 1062 GLU cc_start: 0.6708 (tt0) cc_final: 0.6232 (tt0) REVERT: C 1068 PHE cc_start: 0.6136 (t80) cc_final: 0.5890 (t80) REVERT: C 1081 MET cc_start: 0.5666 (mtm) cc_final: 0.5222 (mtp) REVERT: C 1122 ARG cc_start: 0.5851 (mtm-85) cc_final: 0.4838 (mtm-85) REVERT: C 1125 GLU cc_start: 0.5790 (mt-10) cc_final: 0.4663 (pp20) REVERT: C 1128 ARG cc_start: 0.6271 (tmm160) cc_final: 0.5858 (tmm160) REVERT: C 1149 MET cc_start: 0.7630 (mtp) cc_final: 0.7405 (mtm) REVERT: C 1150 MET cc_start: 0.7548 (tpp) cc_final: 0.7264 (mtp) REVERT: C 1152 GLN cc_start: 0.7356 (mt0) cc_final: 0.6992 (mt0) REVERT: C 1160 PHE cc_start: 0.7343 (m-10) cc_final: 0.7131 (m-10) REVERT: C 1248 TYR cc_start: 0.6895 (t80) cc_final: 0.6647 (t80) REVERT: C 1272 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6393 (pttt) REVERT: C 1304 ARG cc_start: 0.7737 (ptp-170) cc_final: 0.7104 (mtp180) REVERT: C 1377 GLU cc_start: 0.6635 (pt0) cc_final: 0.6247 (pt0) REVERT: C 1389 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 1445 GLU cc_start: 0.7040 (pm20) cc_final: 0.6766 (mp0) REVERT: C 1456 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7056 (pt0) REVERT: C 1463 HIS cc_start: 0.6928 (m90) cc_final: 0.6232 (t-170) REVERT: C 1491 ASN cc_start: 0.8147 (t0) cc_final: 0.7859 (t0) REVERT: D 74 ASP cc_start: 0.6945 (m-30) cc_final: 0.6554 (t0) REVERT: D 81 MET cc_start: 0.7352 (ptm) cc_final: 0.7093 (ptm) REVERT: D 156 LEU cc_start: 0.6881 (tp) cc_final: 0.6667 (mt) REVERT: D 166 LYS cc_start: 0.6788 (ttpt) cc_final: 0.6410 (ptmm) REVERT: D 174 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.6822 (ptp-170) REVERT: D 225 MET cc_start: 0.7339 (mtp) cc_final: 0.7086 (mtp) REVERT: D 251 ASP cc_start: 0.7584 (t0) cc_final: 0.7213 (t0) REVERT: D 284 GLN cc_start: 0.7072 (mt0) cc_final: 0.6713 (mt0) REVERT: D 306 LEU cc_start: 0.7473 (tp) cc_final: 0.7190 (tm) REVERT: D 356 GLN cc_start: 0.6736 (mt0) cc_final: 0.6028 (mm-40) REVERT: D 440 HIS cc_start: 0.4767 (p90) cc_final: 0.4540 (p-80) REVERT: D 456 MET cc_start: 0.5948 (mtt) cc_final: 0.5697 (mtt) REVERT: D 477 LYS cc_start: 0.6108 (mttm) cc_final: 0.5880 (mppt) REVERT: D 560 MET cc_start: 0.6734 (mmm) cc_final: 0.6489 (mmm) REVERT: D 577 ASP cc_start: 0.6230 (t0) cc_final: 0.5835 (t70) REVERT: D 592 GLN cc_start: 0.5454 (tt0) cc_final: 0.4953 (pt0) REVERT: D 594 ARG cc_start: 0.5744 (mtp180) cc_final: 0.5535 (mtp85) REVERT: D 638 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5192 (pt0) REVERT: D 654 GLU cc_start: 0.6110 (tp30) cc_final: 0.5835 (tp30) REVERT: D 663 LYS cc_start: 0.6302 (mmmt) cc_final: 0.5387 (mttm) REVERT: D 694 MET cc_start: 0.6598 (mtm) cc_final: 0.6386 (mtp) REVERT: D 725 ASP cc_start: 0.7360 (m-30) cc_final: 0.6880 (m-30) REVERT: D 731 LYS cc_start: 0.6681 (ttpt) cc_final: 0.6294 (mmpt) REVERT: D 829 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6025 (mm-30) REVERT: D 833 SER cc_start: 0.6257 (t) cc_final: 0.5876 (p) REVERT: D 854 MET cc_start: 0.6445 (mtm) cc_final: 0.6220 (mtt) REVERT: D 870 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6407 (mtt180) REVERT: D 875 MET cc_start: 0.6737 (ptt) cc_final: 0.6416 (ptp) REVERT: D 932 MET cc_start: 0.6543 (mmt) cc_final: 0.6157 (mmt) REVERT: D 969 ARG cc_start: 0.6484 (mtm110) cc_final: 0.6077 (mtm-85) REVERT: D 972 ILE cc_start: 0.7307 (mt) cc_final: 0.6873 (mm) REVERT: D 998 LEU cc_start: 0.6668 (mt) cc_final: 0.6333 (mm) REVERT: D 1005 GLU cc_start: 0.6048 (mt-10) cc_final: 0.5054 (tt0) REVERT: D 1043 LYS cc_start: 0.6922 (mttp) cc_final: 0.6587 (mttp) REVERT: D 1046 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6558 (pt0) REVERT: D 1049 GLU cc_start: 0.5888 (mm-30) cc_final: 0.5681 (mm-30) REVERT: D 1050 ASP cc_start: 0.6472 (m-30) cc_final: 0.5927 (m-30) REVERT: D 1062 GLU cc_start: 0.6678 (tt0) cc_final: 0.6201 (tt0) REVERT: D 1068 PHE cc_start: 0.6145 (t80) cc_final: 0.5902 (t80) REVERT: D 1081 MET cc_start: 0.5663 (mtm) cc_final: 0.5223 (mtp) REVERT: D 1122 ARG cc_start: 0.5851 (mtm-85) cc_final: 0.4838 (mtm-85) REVERT: D 1125 GLU cc_start: 0.5761 (mt-10) cc_final: 0.4634 (pp20) REVERT: D 1128 ARG cc_start: 0.6262 (tmm160) cc_final: 0.5827 (tmm160) REVERT: D 1149 MET cc_start: 0.7668 (mtp) cc_final: 0.7415 (mtm) REVERT: D 1150 MET cc_start: 0.7544 (tpp) cc_final: 0.7261 (mtp) REVERT: D 1152 GLN cc_start: 0.7373 (mt0) cc_final: 0.7027 (mt0) REVERT: D 1248 TYR cc_start: 0.6887 (t80) cc_final: 0.6648 (t80) REVERT: D 1272 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6391 (pttt) REVERT: D 1304 ARG cc_start: 0.7720 (ptp-170) cc_final: 0.7100 (mtp180) REVERT: D 1377 GLU cc_start: 0.6638 (pt0) cc_final: 0.6250 (pt0) REVERT: D 1389 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 1445 GLU cc_start: 0.6987 (pm20) cc_final: 0.6751 (mp0) REVERT: D 1456 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7050 (pt0) REVERT: D 1463 HIS cc_start: 0.6931 (m90) cc_final: 0.6236 (t-170) REVERT: D 1491 ASN cc_start: 0.8144 (t0) cc_final: 0.7861 (t0) outliers start: 40 outliers final: 5 residues processed: 1092 average time/residue: 1.7852 time to fit residues: 2336.6959 Evaluate side-chains 628 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 621 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 1272 LYS Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 1272 LYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 1272 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 459 optimal weight: 5.9990 chunk 412 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 278 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 426 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 317 optimal weight: 0.8980 chunk 494 optimal weight: 0.6980 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 73 GLN A 368 ASN A 450 ASN A 457 HIS A 514 HIS A 893 GLN A1056 ASN A1129 GLN B 73 GLN B 368 ASN B 450 ASN B 457 HIS B 514 HIS B 893 GLN B1045 GLN B1056 ASN B1129 GLN C 73 GLN C 368 ASN C 450 ASN C 457 HIS C 514 HIS C 893 GLN C 957 GLN C 992 ASN C1045 GLN C1056 ASN C1129 GLN D 73 GLN D 368 ASN D 450 ASN D 457 HIS D 514 HIS D 893 GLN D 957 GLN D 992 ASN D1045 GLN D1056 ASN D1129 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43668 Z= 0.204 Angle : 0.582 8.067 59372 Z= 0.309 Chirality : 0.041 0.212 6740 Planarity : 0.004 0.045 7504 Dihedral : 9.066 88.981 7068 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.66 % Allowed : 9.69 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.11), residues: 5432 helix: 1.76 (0.09), residues: 2968 sheet: -0.49 (0.23), residues: 396 loop : -1.02 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 726 HIS 0.008 0.001 HIS A 514 PHE 0.021 0.002 PHE C1083 TYR 0.018 0.002 TYR A 979 ARG 0.005 0.001 ARG D 159 *********************** 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 797 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 684 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7120 (m-30) cc_final: 0.6739 (t0) REVERT: A 174 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.6814 (mtm180) REVERT: A 284 GLN cc_start: 0.7176 (mt0) cc_final: 0.6801 (mt0) REVERT: A 352 GLN cc_start: 0.7469 (tt0) cc_final: 0.6377 (mt0) REVERT: A 356 GLN cc_start: 0.6995 (mt0) cc_final: 0.6334 (mm-40) REVERT: A 365 GLN cc_start: 0.6518 (mt0) cc_final: 0.5447 (mp10) REVERT: A 410 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5819 (mtpt) REVERT: A 456 MET cc_start: 0.5570 (mtt) cc_final: 0.5262 (mtp) REVERT: A 473 ILE cc_start: 0.7263 (mt) cc_final: 0.6975 (mp) REVERT: A 477 LYS cc_start: 0.6357 (mttm) cc_final: 0.6157 (mppt) REVERT: A 560 MET cc_start: 0.6422 (mmm) cc_final: 0.6142 (mmm) REVERT: A 594 ARG cc_start: 0.5663 (mtp180) cc_final: 0.5435 (mtp85) REVERT: A 618 HIS cc_start: 0.5499 (t70) cc_final: 0.4452 (m170) REVERT: A 638 GLU cc_start: 0.5692 (mt-10) cc_final: 0.4990 (pt0) REVERT: A 663 LYS cc_start: 0.6392 (mmmt) cc_final: 0.5628 (mttm) REVERT: A 666 GLU cc_start: 0.6160 (pt0) cc_final: 0.5671 (tt0) REVERT: A 682 HIS cc_start: 0.6214 (t-90) cc_final: 0.6013 (t70) REVERT: A 694 MET cc_start: 0.6387 (mtm) cc_final: 0.6175 (mtp) REVERT: A 725 ASP cc_start: 0.7497 (m-30) cc_final: 0.7142 (m-30) REVERT: A 731 LYS cc_start: 0.6823 (ttpt) cc_final: 0.6396 (mmmt) REVERT: A 829 GLU cc_start: 0.6883 (mt-10) cc_final: 0.5908 (mm-30) REVERT: A 833 SER cc_start: 0.5986 (t) cc_final: 0.5372 (p) REVERT: A 870 ARG cc_start: 0.6450 (mtt180) cc_final: 0.6067 (mtp85) REVERT: A 875 MET cc_start: 0.6287 (ptt) cc_final: 0.5994 (ptp) REVERT: A 932 MET cc_start: 0.6163 (mmt) cc_final: 0.5936 (mmt) REVERT: A 969 ARG cc_start: 0.6165 (mtm110) cc_final: 0.5782 (mtm-85) REVERT: A 998 LEU cc_start: 0.6652 (mt) cc_final: 0.6196 (mm) REVERT: A 1005 GLU cc_start: 0.6308 (mt-10) cc_final: 0.5276 (tt0) REVERT: A 1043 LYS cc_start: 0.6923 (mttp) cc_final: 0.6622 (mttt) REVERT: A 1046 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6441 (pt0) REVERT: A 1050 ASP cc_start: 0.6256 (m-30) cc_final: 0.5833 (m-30) REVERT: A 1062 GLU cc_start: 0.6529 (tt0) cc_final: 0.6079 (tt0) REVERT: A 1064 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6606 (mttt) REVERT: A 1085 ARG cc_start: 0.4617 (ttt90) cc_final: 0.4343 (tpt90) REVERT: A 1105 THR cc_start: 0.6239 (m) cc_final: 0.5869 (p) REVERT: A 1122 ARG cc_start: 0.5568 (mtm-85) cc_final: 0.4967 (mtm-85) REVERT: A 1125 GLU cc_start: 0.5426 (mt-10) cc_final: 0.4586 (pp20) REVERT: A 1145 GLN cc_start: 0.7330 (tt0) cc_final: 0.6578 (mt0) REVERT: A 1152 GLN cc_start: 0.6949 (mt0) cc_final: 0.6555 (mt0) REVERT: A 1244 MET cc_start: 0.5995 (ptp) cc_final: 0.5738 (ptp) REVERT: A 1272 LYS cc_start: 0.6789 (mmtm) cc_final: 0.6575 (pttp) REVERT: A 1377 GLU cc_start: 0.6778 (pt0) cc_final: 0.6252 (pt0) REVERT: A 1389 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 1445 GLU cc_start: 0.7148 (pm20) cc_final: 0.6822 (pt0) REVERT: A 1463 HIS cc_start: 0.7063 (m90) cc_final: 0.6225 (t-170) REVERT: A 1491 ASN cc_start: 0.8182 (t0) cc_final: 0.7949 (t0) REVERT: B 74 ASP cc_start: 0.7138 (m-30) cc_final: 0.6770 (t0) REVERT: B 174 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.6801 (mtm180) REVERT: B 284 GLN cc_start: 0.7165 (mt0) cc_final: 0.6784 (mt0) REVERT: B 352 GLN cc_start: 0.7438 (tt0) cc_final: 0.6453 (mt0) REVERT: B 356 GLN cc_start: 0.6992 (mt0) cc_final: 0.6326 (mm-40) REVERT: B 365 GLN cc_start: 0.6517 (mt0) cc_final: 0.5444 (mp10) REVERT: B 410 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5831 (mtpt) REVERT: B 456 MET cc_start: 0.5563 (mtt) cc_final: 0.5250 (mtp) REVERT: B 473 ILE cc_start: 0.7273 (mt) cc_final: 0.6979 (mp) REVERT: B 477 LYS cc_start: 0.6354 (mttm) cc_final: 0.6154 (mppt) REVERT: B 560 MET cc_start: 0.6422 (mmm) cc_final: 0.6143 (mmm) REVERT: B 594 ARG cc_start: 0.5657 (mtp180) cc_final: 0.5440 (mtp85) REVERT: B 618 HIS cc_start: 0.5484 (t70) cc_final: 0.4452 (m170) REVERT: B 638 GLU cc_start: 0.5654 (mt-10) cc_final: 0.5018 (pt0) REVERT: B 663 LYS cc_start: 0.6389 (mmmt) cc_final: 0.5606 (mttm) REVERT: B 666 GLU cc_start: 0.6185 (pt0) cc_final: 0.5835 (tt0) REVERT: B 682 HIS cc_start: 0.6222 (t-90) cc_final: 0.6021 (t70) REVERT: B 694 MET cc_start: 0.6364 (mtm) cc_final: 0.6155 (mtp) REVERT: B 725 ASP cc_start: 0.7463 (m-30) cc_final: 0.7079 (m-30) REVERT: B 731 LYS cc_start: 0.6661 (ttpt) cc_final: 0.6294 (mmmt) REVERT: B 829 GLU cc_start: 0.6894 (mt-10) cc_final: 0.5939 (mm-30) REVERT: B 833 SER cc_start: 0.5935 (t) cc_final: 0.5338 (p) REVERT: B 849 GLU cc_start: 0.6791 (tp30) cc_final: 0.6491 (tp30) REVERT: B 870 ARG cc_start: 0.6456 (mtt180) cc_final: 0.6074 (mtp85) REVERT: B 875 MET cc_start: 0.6294 (ptt) cc_final: 0.6007 (ptp) REVERT: B 932 MET cc_start: 0.6131 (mmt) cc_final: 0.5903 (mmt) REVERT: B 969 ARG cc_start: 0.6158 (mtm110) cc_final: 0.5755 (mtm-85) REVERT: B 998 LEU cc_start: 0.6676 (mt) cc_final: 0.6222 (mm) REVERT: B 1005 GLU cc_start: 0.6288 (mt-10) cc_final: 0.5256 (tt0) REVERT: B 1043 LYS cc_start: 0.6953 (mttp) cc_final: 0.6636 (mttt) REVERT: B 1046 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6423 (pt0) REVERT: B 1050 ASP cc_start: 0.6295 (m-30) cc_final: 0.5867 (m-30) REVERT: B 1062 GLU cc_start: 0.6526 (tt0) cc_final: 0.6083 (tt0) REVERT: B 1064 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6527 (mttt) REVERT: B 1085 ARG cc_start: 0.4640 (ttt90) cc_final: 0.4316 (tpt170) REVERT: B 1105 THR cc_start: 0.6233 (m) cc_final: 0.5858 (p) REVERT: B 1122 ARG cc_start: 0.5586 (mtm-85) cc_final: 0.5016 (mtm-85) REVERT: B 1125 GLU cc_start: 0.5411 (mt-10) cc_final: 0.4580 (pp20) REVERT: B 1145 GLN cc_start: 0.7239 (tt0) cc_final: 0.6512 (mt0) REVERT: B 1152 GLN cc_start: 0.6974 (mt0) cc_final: 0.6604 (mt0) REVERT: B 1244 MET cc_start: 0.5998 (ptp) cc_final: 0.5744 (ptp) REVERT: B 1377 GLU cc_start: 0.6807 (pt0) cc_final: 0.6269 (pt0) REVERT: B 1389 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7249 (mt-10) REVERT: B 1445 GLU cc_start: 0.7203 (pm20) cc_final: 0.6803 (pt0) REVERT: B 1463 HIS cc_start: 0.7063 (m90) cc_final: 0.6222 (t-170) REVERT: B 1491 ASN cc_start: 0.8185 (t0) cc_final: 0.7951 (t0) REVERT: C 74 ASP cc_start: 0.7135 (m-30) cc_final: 0.6767 (t0) REVERT: C 174 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6803 (mtm180) REVERT: C 284 GLN cc_start: 0.7152 (mt0) cc_final: 0.6774 (mt0) REVERT: C 352 GLN cc_start: 0.7440 (tt0) cc_final: 0.6459 (mt0) REVERT: C 356 GLN cc_start: 0.6997 (mt0) cc_final: 0.6329 (mm-40) REVERT: C 365 GLN cc_start: 0.6519 (mt0) cc_final: 0.5446 (mp10) REVERT: C 410 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5827 (mtpt) REVERT: C 456 MET cc_start: 0.5576 (mtt) cc_final: 0.5289 (mtp) REVERT: C 473 ILE cc_start: 0.7274 (mt) cc_final: 0.6985 (mp) REVERT: C 477 LYS cc_start: 0.6364 (mttm) cc_final: 0.6161 (mppt) REVERT: C 560 MET cc_start: 0.6419 (mmm) cc_final: 0.6140 (mmm) REVERT: C 594 ARG cc_start: 0.5653 (mtp180) cc_final: 0.5437 (mtp85) REVERT: C 618 HIS cc_start: 0.5465 (t70) cc_final: 0.4418 (m170) REVERT: C 638 GLU cc_start: 0.5687 (mt-10) cc_final: 0.4979 (pt0) REVERT: C 663 LYS cc_start: 0.6388 (mmmt) cc_final: 0.5631 (mttm) REVERT: C 666 GLU cc_start: 0.6117 (pt0) cc_final: 0.5781 (tt0) REVERT: C 682 HIS cc_start: 0.6223 (t-90) cc_final: 0.6022 (t70) REVERT: C 694 MET cc_start: 0.6369 (mtm) cc_final: 0.6158 (mtp) REVERT: C 725 ASP cc_start: 0.7463 (m-30) cc_final: 0.7059 (m-30) REVERT: C 731 LYS cc_start: 0.6660 (ttpt) cc_final: 0.6278 (mmmt) REVERT: C 829 GLU cc_start: 0.6893 (mt-10) cc_final: 0.5939 (mm-30) REVERT: C 833 SER cc_start: 0.5938 (t) cc_final: 0.5342 (p) REVERT: C 849 GLU cc_start: 0.6797 (tp30) cc_final: 0.6497 (tp30) REVERT: C 870 ARG cc_start: 0.6454 (mtt180) cc_final: 0.6071 (mtp85) REVERT: C 875 MET cc_start: 0.6292 (ptt) cc_final: 0.6004 (ptp) REVERT: C 932 MET cc_start: 0.6126 (mmt) cc_final: 0.5904 (mmt) REVERT: C 969 ARG cc_start: 0.6186 (mtm110) cc_final: 0.5784 (mtm-85) REVERT: C 998 LEU cc_start: 0.6729 (mt) cc_final: 0.6329 (mm) REVERT: C 1005 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5233 (tt0) REVERT: C 1043 LYS cc_start: 0.6958 (mttp) cc_final: 0.6640 (mttt) REVERT: C 1046 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6423 (pt0) REVERT: C 1050 ASP cc_start: 0.6347 (m-30) cc_final: 0.5922 (m-30) REVERT: C 1062 GLU cc_start: 0.6526 (tt0) cc_final: 0.6070 (tt0) REVERT: C 1064 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6528 (mttt) REVERT: C 1085 ARG cc_start: 0.4633 (ttt90) cc_final: 0.4319 (tpt170) REVERT: C 1105 THR cc_start: 0.6234 (m) cc_final: 0.5858 (p) REVERT: C 1145 GLN cc_start: 0.7312 (tt0) cc_final: 0.6544 (mt0) REVERT: C 1152 GLN cc_start: 0.6982 (mt0) cc_final: 0.6604 (mt0) REVERT: C 1244 MET cc_start: 0.6060 (ptp) cc_final: 0.5839 (ptp) REVERT: C 1377 GLU cc_start: 0.6805 (pt0) cc_final: 0.6268 (pt0) REVERT: C 1389 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7257 (mt-10) REVERT: C 1445 GLU cc_start: 0.7202 (pm20) cc_final: 0.6797 (pt0) REVERT: C 1463 HIS cc_start: 0.7058 (m90) cc_final: 0.6216 (t-170) REVERT: C 1491 ASN cc_start: 0.8187 (t0) cc_final: 0.7950 (t0) REVERT: D 74 ASP cc_start: 0.7136 (m-30) cc_final: 0.6767 (t0) REVERT: D 174 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6801 (mtm180) REVERT: D 284 GLN cc_start: 0.7157 (mt0) cc_final: 0.6773 (mt0) REVERT: D 352 GLN cc_start: 0.7439 (tt0) cc_final: 0.6456 (mt0) REVERT: D 356 GLN cc_start: 0.6992 (mt0) cc_final: 0.6326 (mm-40) REVERT: D 365 GLN cc_start: 0.6516 (mt0) cc_final: 0.5445 (mp10) REVERT: D 410 LYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5828 (mtpt) REVERT: D 456 MET cc_start: 0.5568 (mtt) cc_final: 0.5259 (mtp) REVERT: D 473 ILE cc_start: 0.7273 (mt) cc_final: 0.6981 (mp) REVERT: D 477 LYS cc_start: 0.6357 (mttm) cc_final: 0.6156 (mppt) REVERT: D 560 MET cc_start: 0.6422 (mmm) cc_final: 0.6143 (mmm) REVERT: D 594 ARG cc_start: 0.5655 (mtp180) cc_final: 0.5438 (mtp85) REVERT: D 618 HIS cc_start: 0.5481 (t70) cc_final: 0.4448 (m170) REVERT: D 638 GLU cc_start: 0.5671 (mt-10) cc_final: 0.5007 (pt0) REVERT: D 663 LYS cc_start: 0.6392 (mmmt) cc_final: 0.5608 (mttm) REVERT: D 666 GLU cc_start: 0.6189 (pt0) cc_final: 0.5694 (tt0) REVERT: D 682 HIS cc_start: 0.6222 (t-90) cc_final: 0.6020 (t70) REVERT: D 694 MET cc_start: 0.6368 (mtm) cc_final: 0.6151 (mtp) REVERT: D 725 ASP cc_start: 0.7462 (m-30) cc_final: 0.7059 (m-30) REVERT: D 731 LYS cc_start: 0.6663 (ttpt) cc_final: 0.6294 (mmmt) REVERT: D 829 GLU cc_start: 0.6893 (mt-10) cc_final: 0.5939 (mm-30) REVERT: D 833 SER cc_start: 0.5937 (t) cc_final: 0.5337 (p) REVERT: D 849 GLU cc_start: 0.6790 (tp30) cc_final: 0.6490 (tp30) REVERT: D 870 ARG cc_start: 0.6458 (mtt180) cc_final: 0.6076 (mtp85) REVERT: D 875 MET cc_start: 0.6289 (ptt) cc_final: 0.6004 (ptp) REVERT: D 932 MET cc_start: 0.6129 (mmt) cc_final: 0.5899 (mmt) REVERT: D 969 ARG cc_start: 0.6154 (mtm110) cc_final: 0.5754 (mtm-85) REVERT: D 998 LEU cc_start: 0.6728 (mt) cc_final: 0.6321 (mm) REVERT: D 1005 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5241 (tt0) REVERT: D 1043 LYS cc_start: 0.6955 (mttp) cc_final: 0.6640 (mttt) REVERT: D 1046 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6422 (pt0) REVERT: D 1050 ASP cc_start: 0.6302 (m-30) cc_final: 0.5870 (m-30) REVERT: D 1062 GLU cc_start: 0.6525 (tt0) cc_final: 0.6073 (tt0) REVERT: D 1064 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6528 (mttt) REVERT: D 1085 ARG cc_start: 0.4639 (ttt90) cc_final: 0.4316 (tpt170) REVERT: D 1105 THR cc_start: 0.6234 (m) cc_final: 0.5858 (p) REVERT: D 1145 GLN cc_start: 0.7308 (tt0) cc_final: 0.6549 (mt0) REVERT: D 1152 GLN cc_start: 0.6981 (mt0) cc_final: 0.6588 (mt0) REVERT: D 1244 MET cc_start: 0.6059 (ptp) cc_final: 0.5835 (ptp) REVERT: D 1377 GLU cc_start: 0.6807 (pt0) cc_final: 0.6273 (pt0) REVERT: D 1389 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7271 (mt-10) REVERT: D 1445 GLU cc_start: 0.7203 (pm20) cc_final: 0.6802 (pt0) REVERT: D 1463 HIS cc_start: 0.7063 (m90) cc_final: 0.6221 (t-170) REVERT: D 1491 ASN cc_start: 0.8185 (t0) cc_final: 0.7951 (t0) outliers start: 113 outliers final: 24 residues processed: 768 average time/residue: 1.8173 time to fit residues: 1675.0023 Evaluate side-chains 585 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 553 time to evaluate : 4.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 274 optimal weight: 0.0470 chunk 153 optimal weight: 1.9990 chunk 411 optimal weight: 0.0570 chunk 336 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 494 optimal weight: 0.9980 chunk 534 optimal weight: 3.9990 chunk 440 optimal weight: 4.9990 chunk 490 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 397 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 514 HIS A 893 GLN A 957 GLN A 992 ASN A1456 GLN B 417 GLN B 514 HIS B 893 GLN B 957 GLN B 992 ASN B1282 ASN B1456 GLN C 514 HIS C 893 GLN C1282 ASN C1456 GLN D 417 GLN D 514 HIS D 893 GLN D1456 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43668 Z= 0.218 Angle : 0.563 9.380 59372 Z= 0.296 Chirality : 0.041 0.175 6740 Planarity : 0.004 0.045 7504 Dihedral : 8.497 88.089 7056 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.17 % Allowed : 11.03 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 5432 helix: 1.99 (0.09), residues: 2984 sheet: -0.57 (0.24), residues: 372 loop : -0.72 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 726 HIS 0.011 0.001 HIS C 514 PHE 0.018 0.002 PHE B1068 TYR 0.020 0.002 TYR C 216 ARG 0.005 0.001 ARG D1008 *********************** 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 762 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 627 time to evaluate : 4.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5472 (ppp) cc_final: 0.5005 (ppp) REVERT: A 74 ASP cc_start: 0.7152 (m-30) cc_final: 0.6765 (t0) REVERT: A 78 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6850 (ptp-170) REVERT: A 139 ASP cc_start: 0.7595 (m-30) cc_final: 0.7118 (m-30) REVERT: A 174 ARG cc_start: 0.7349 (mtm-85) cc_final: 0.6638 (mtm180) REVERT: A 284 GLN cc_start: 0.7086 (mt0) cc_final: 0.6770 (mt0) REVERT: A 352 GLN cc_start: 0.7621 (tt0) cc_final: 0.6512 (mt0) REVERT: A 356 GLN cc_start: 0.7277 (mt0) cc_final: 0.6577 (mm-40) REVERT: A 365 GLN cc_start: 0.6504 (mt0) cc_final: 0.5447 (mp10) REVERT: A 456 MET cc_start: 0.5684 (mtt) cc_final: 0.5469 (mtp) REVERT: A 473 ILE cc_start: 0.7196 (mt) cc_final: 0.6893 (mp) REVERT: A 506 ARG cc_start: 0.6190 (mtp85) cc_final: 0.5920 (ttt-90) REVERT: A 560 MET cc_start: 0.6389 (mmm) cc_final: 0.6144 (mmm) REVERT: A 618 HIS cc_start: 0.5566 (t70) cc_final: 0.4659 (m170) REVERT: A 663 LYS cc_start: 0.6276 (mmmt) cc_final: 0.5492 (mttp) REVERT: A 666 GLU cc_start: 0.6161 (pt0) cc_final: 0.5775 (tt0) REVERT: A 682 HIS cc_start: 0.6482 (t-90) cc_final: 0.6192 (t70) REVERT: A 731 LYS cc_start: 0.6900 (ttpt) cc_final: 0.6531 (mttp) REVERT: A 829 GLU cc_start: 0.6871 (mt-10) cc_final: 0.5936 (mm-30) REVERT: A 832 ILE cc_start: 0.6914 (mm) cc_final: 0.6651 (mt) REVERT: A 833 SER cc_start: 0.6081 (t) cc_final: 0.5250 (p) REVERT: A 849 GLU cc_start: 0.6892 (tp30) cc_final: 0.6573 (tp30) REVERT: A 870 ARG cc_start: 0.6315 (mtt180) cc_final: 0.5962 (mtt90) REVERT: A 875 MET cc_start: 0.6538 (ptt) cc_final: 0.6144 (ptp) REVERT: A 930 MET cc_start: 0.7252 (mtm) cc_final: 0.6886 (mtt) REVERT: A 969 ARG cc_start: 0.6357 (mtm110) cc_final: 0.5845 (mtm-85) REVERT: A 1039 ASP cc_start: 0.7300 (m-30) cc_final: 0.7042 (m-30) REVERT: A 1062 GLU cc_start: 0.6626 (tt0) cc_final: 0.6319 (tt0) REVERT: A 1064 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6394 (mttt) REVERT: A 1085 ARG cc_start: 0.4849 (ttt90) cc_final: 0.4360 (tpt170) REVERT: A 1105 THR cc_start: 0.6082 (m) cc_final: 0.5623 (p) REVERT: A 1127 GLU cc_start: 0.5713 (mt-10) cc_final: 0.5454 (pt0) REVERT: A 1145 GLN cc_start: 0.7250 (tt0) cc_final: 0.6521 (mt0) REVERT: A 1152 GLN cc_start: 0.6935 (mt0) cc_final: 0.6511 (mt0) REVERT: A 1233 LEU cc_start: 0.7352 (mm) cc_final: 0.7016 (pt) REVERT: A 1272 LYS cc_start: 0.6714 (mmtm) cc_final: 0.6511 (pttp) REVERT: A 1377 GLU cc_start: 0.6807 (pt0) cc_final: 0.6138 (pt0) REVERT: A 1389 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 1445 GLU cc_start: 0.7208 (pm20) cc_final: 0.6853 (pt0) REVERT: A 1460 ASP cc_start: 0.7408 (t70) cc_final: 0.7198 (t0) REVERT: A 1463 HIS cc_start: 0.7253 (m90) cc_final: 0.6465 (t-170) REVERT: A 1480 ARG cc_start: 0.7286 (ttp-170) cc_final: 0.6990 (mmm-85) REVERT: B 70 MET cc_start: 0.5439 (ppp) cc_final: 0.4969 (ppp) REVERT: B 74 ASP cc_start: 0.7131 (m-30) cc_final: 0.6750 (t0) REVERT: B 78 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6877 (ptp-170) REVERT: B 139 ASP cc_start: 0.7595 (m-30) cc_final: 0.7117 (m-30) REVERT: B 174 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.6637 (mtm180) REVERT: B 225 MET cc_start: 0.7357 (mtp) cc_final: 0.7083 (mtp) REVERT: B 239 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7127 (mmm) REVERT: B 284 GLN cc_start: 0.7100 (mt0) cc_final: 0.6786 (mt0) REVERT: B 352 GLN cc_start: 0.7625 (tt0) cc_final: 0.6512 (mt0) REVERT: B 356 GLN cc_start: 0.7300 (mt0) cc_final: 0.6596 (mm-40) REVERT: B 365 GLN cc_start: 0.6496 (mt0) cc_final: 0.5460 (mp10) REVERT: B 456 MET cc_start: 0.5679 (mtt) cc_final: 0.5457 (mtp) REVERT: B 473 ILE cc_start: 0.7191 (mt) cc_final: 0.6912 (mp) REVERT: B 506 ARG cc_start: 0.6323 (mtp85) cc_final: 0.6038 (ttt-90) REVERT: B 560 MET cc_start: 0.6384 (mmm) cc_final: 0.6140 (mmm) REVERT: B 592 GLN cc_start: 0.5503 (OUTLIER) cc_final: 0.5151 (tp-100) REVERT: B 618 HIS cc_start: 0.5530 (t70) cc_final: 0.4673 (m170) REVERT: B 663 LYS cc_start: 0.6350 (mmmt) cc_final: 0.5583 (mttt) REVERT: B 666 GLU cc_start: 0.6211 (pt0) cc_final: 0.5982 (tt0) REVERT: B 682 HIS cc_start: 0.6370 (t-90) cc_final: 0.6086 (t70) REVERT: B 731 LYS cc_start: 0.6872 (ttpt) cc_final: 0.6485 (mttp) REVERT: B 829 GLU cc_start: 0.6893 (mt-10) cc_final: 0.5966 (mm-30) REVERT: B 832 ILE cc_start: 0.6923 (mm) cc_final: 0.6652 (mt) REVERT: B 833 SER cc_start: 0.6082 (t) cc_final: 0.5256 (p) REVERT: B 849 GLU cc_start: 0.6962 (tp30) cc_final: 0.6607 (tp30) REVERT: B 870 ARG cc_start: 0.6299 (mtt180) cc_final: 0.5946 (mtt90) REVERT: B 875 MET cc_start: 0.6549 (ptt) cc_final: 0.6160 (ptp) REVERT: B 969 ARG cc_start: 0.6374 (mtm110) cc_final: 0.5831 (mtm-85) REVERT: B 1039 ASP cc_start: 0.7228 (m-30) cc_final: 0.6988 (m-30) REVERT: B 1046 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6302 (pt0) REVERT: B 1062 GLU cc_start: 0.6656 (tt0) cc_final: 0.6301 (tt0) REVERT: B 1064 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6421 (mttt) REVERT: B 1085 ARG cc_start: 0.4809 (ttt90) cc_final: 0.4339 (tpt170) REVERT: B 1105 THR cc_start: 0.6067 (m) cc_final: 0.5602 (p) REVERT: B 1127 GLU cc_start: 0.5757 (mt-10) cc_final: 0.5494 (pt0) REVERT: B 1145 GLN cc_start: 0.7277 (tt0) cc_final: 0.6511 (mt0) REVERT: B 1152 GLN cc_start: 0.6880 (mt0) cc_final: 0.6435 (mt0) REVERT: B 1233 LEU cc_start: 0.7325 (mm) cc_final: 0.7013 (pt) REVERT: B 1377 GLU cc_start: 0.6845 (pt0) cc_final: 0.6183 (pt0) REVERT: B 1389 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 1445 GLU cc_start: 0.7198 (pm20) cc_final: 0.6769 (pt0) REVERT: B 1460 ASP cc_start: 0.7402 (t70) cc_final: 0.7192 (t0) REVERT: B 1463 HIS cc_start: 0.7252 (m90) cc_final: 0.6463 (t-170) REVERT: B 1480 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.7011 (mmm-85) REVERT: C 70 MET cc_start: 0.5516 (ppp) cc_final: 0.5028 (ppp) REVERT: C 74 ASP cc_start: 0.7129 (m-30) cc_final: 0.6765 (t0) REVERT: C 78 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6943 (ptp-170) REVERT: C 94 THR cc_start: 0.6453 (p) cc_final: 0.5846 (t) REVERT: C 139 ASP cc_start: 0.7597 (m-30) cc_final: 0.7119 (m-30) REVERT: C 174 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.6644 (mtm180) REVERT: C 225 MET cc_start: 0.7381 (mtp) cc_final: 0.7139 (mtp) REVERT: C 239 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: C 284 GLN cc_start: 0.7100 (mt0) cc_final: 0.6784 (mt0) REVERT: C 352 GLN cc_start: 0.7615 (tt0) cc_final: 0.6512 (mt0) REVERT: C 356 GLN cc_start: 0.7303 (mt0) cc_final: 0.6598 (mm-40) REVERT: C 365 GLN cc_start: 0.6497 (mt0) cc_final: 0.5460 (mp10) REVERT: C 473 ILE cc_start: 0.7124 (mt) cc_final: 0.6841 (mp) REVERT: C 506 ARG cc_start: 0.6324 (mtp85) cc_final: 0.6036 (ttt-90) REVERT: C 560 MET cc_start: 0.6388 (mmm) cc_final: 0.6143 (mmm) REVERT: C 618 HIS cc_start: 0.5537 (t70) cc_final: 0.4635 (m170) REVERT: C 663 LYS cc_start: 0.6275 (mmmt) cc_final: 0.5495 (mttt) REVERT: C 666 GLU cc_start: 0.6154 (pt0) cc_final: 0.5819 (tt0) REVERT: C 682 HIS cc_start: 0.6449 (t-90) cc_final: 0.6157 (t70) REVERT: C 731 LYS cc_start: 0.6871 (ttpt) cc_final: 0.6486 (mttp) REVERT: C 829 GLU cc_start: 0.6898 (mt-10) cc_final: 0.5969 (mm-30) REVERT: C 832 ILE cc_start: 0.6910 (mm) cc_final: 0.6641 (mt) REVERT: C 833 SER cc_start: 0.6082 (t) cc_final: 0.5260 (p) REVERT: C 849 GLU cc_start: 0.6885 (tp30) cc_final: 0.6567 (tp30) REVERT: C 870 ARG cc_start: 0.6300 (mtt180) cc_final: 0.5947 (mtt90) REVERT: C 875 MET cc_start: 0.6561 (ptt) cc_final: 0.6170 (ptp) REVERT: C 969 ARG cc_start: 0.6386 (mtm110) cc_final: 0.5844 (mtm-85) REVERT: C 1039 ASP cc_start: 0.7229 (m-30) cc_final: 0.6987 (m-30) REVERT: C 1046 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6282 (pt0) REVERT: C 1062 GLU cc_start: 0.6652 (tt0) cc_final: 0.6345 (tt0) REVERT: C 1064 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6419 (mttt) REVERT: C 1085 ARG cc_start: 0.4817 (ttt90) cc_final: 0.4335 (tpt170) REVERT: C 1105 THR cc_start: 0.6079 (m) cc_final: 0.5617 (p) REVERT: C 1127 GLU cc_start: 0.5768 (mt-10) cc_final: 0.5509 (pt0) REVERT: C 1145 GLN cc_start: 0.7254 (tt0) cc_final: 0.6514 (mt0) REVERT: C 1152 GLN cc_start: 0.6867 (mt0) cc_final: 0.6438 (mt0) REVERT: C 1233 LEU cc_start: 0.7324 (mm) cc_final: 0.7013 (pt) REVERT: C 1377 GLU cc_start: 0.6839 (pt0) cc_final: 0.6176 (pt0) REVERT: C 1389 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7136 (mt-10) REVERT: C 1445 GLU cc_start: 0.7203 (pm20) cc_final: 0.6732 (pt0) REVERT: C 1460 ASP cc_start: 0.7399 (t70) cc_final: 0.7189 (t0) REVERT: C 1463 HIS cc_start: 0.7230 (m90) cc_final: 0.6444 (t-170) REVERT: C 1480 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.7019 (mmm-85) REVERT: D 70 MET cc_start: 0.5436 (ppp) cc_final: 0.4953 (ppp) REVERT: D 74 ASP cc_start: 0.7130 (m-30) cc_final: 0.6749 (t0) REVERT: D 78 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6946 (ptp-170) REVERT: D 94 THR cc_start: 0.6455 (p) cc_final: 0.5850 (t) REVERT: D 139 ASP cc_start: 0.7597 (m-30) cc_final: 0.7119 (m-30) REVERT: D 174 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.6639 (mtm180) REVERT: D 225 MET cc_start: 0.7368 (mtp) cc_final: 0.7123 (mtp) REVERT: D 239 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7126 (mmm) REVERT: D 284 GLN cc_start: 0.7101 (mt0) cc_final: 0.6786 (mt0) REVERT: D 352 GLN cc_start: 0.7615 (tt0) cc_final: 0.6512 (mt0) REVERT: D 356 GLN cc_start: 0.7298 (mt0) cc_final: 0.6595 (mm-40) REVERT: D 365 GLN cc_start: 0.6496 (mt0) cc_final: 0.5459 (mp10) REVERT: D 456 MET cc_start: 0.5668 (mtt) cc_final: 0.5432 (mtp) REVERT: D 473 ILE cc_start: 0.7194 (mt) cc_final: 0.6913 (mp) REVERT: D 506 ARG cc_start: 0.6255 (mtp85) cc_final: 0.5976 (ttt-90) REVERT: D 560 MET cc_start: 0.6392 (mmm) cc_final: 0.6147 (mmm) REVERT: D 618 HIS cc_start: 0.5564 (t70) cc_final: 0.4657 (m170) REVERT: D 663 LYS cc_start: 0.6347 (mmmt) cc_final: 0.5582 (mttt) REVERT: D 666 GLU cc_start: 0.6215 (pt0) cc_final: 0.5981 (tt0) REVERT: D 682 HIS cc_start: 0.6452 (t-90) cc_final: 0.6164 (t70) REVERT: D 731 LYS cc_start: 0.6872 (ttpt) cc_final: 0.6485 (mttp) REVERT: D 829 GLU cc_start: 0.6895 (mt-10) cc_final: 0.5967 (mm-30) REVERT: D 832 ILE cc_start: 0.6924 (mm) cc_final: 0.6654 (mt) REVERT: D 833 SER cc_start: 0.6079 (t) cc_final: 0.5255 (p) REVERT: D 849 GLU cc_start: 0.6963 (tp30) cc_final: 0.6608 (tp30) REVERT: D 870 ARG cc_start: 0.6298 (mtt180) cc_final: 0.5946 (mtt90) REVERT: D 875 MET cc_start: 0.6551 (ptt) cc_final: 0.6160 (ptp) REVERT: D 969 ARG cc_start: 0.6381 (mtm110) cc_final: 0.5841 (mtm-85) REVERT: D 1039 ASP cc_start: 0.7230 (m-30) cc_final: 0.6992 (m-30) REVERT: D 1046 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6301 (pt0) REVERT: D 1062 GLU cc_start: 0.6617 (tt0) cc_final: 0.6280 (tt0) REVERT: D 1064 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6420 (mttt) REVERT: D 1085 ARG cc_start: 0.4810 (ttt90) cc_final: 0.4339 (tpt170) REVERT: D 1105 THR cc_start: 0.6066 (m) cc_final: 0.5600 (p) REVERT: D 1127 GLU cc_start: 0.5770 (mt-10) cc_final: 0.5511 (pt0) REVERT: D 1145 GLN cc_start: 0.7251 (tt0) cc_final: 0.6518 (mt0) REVERT: D 1152 GLN cc_start: 0.6889 (mt0) cc_final: 0.6462 (mt0) REVERT: D 1233 LEU cc_start: 0.7325 (mm) cc_final: 0.7014 (pt) REVERT: D 1377 GLU cc_start: 0.6839 (pt0) cc_final: 0.6196 (pt0) REVERT: D 1445 GLU cc_start: 0.7200 (pm20) cc_final: 0.6730 (pt0) REVERT: D 1460 ASP cc_start: 0.7402 (t70) cc_final: 0.7190 (t0) REVERT: D 1463 HIS cc_start: 0.7251 (m90) cc_final: 0.6463 (t-170) REVERT: D 1480 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.6985 (mmm-85) outliers start: 135 outliers final: 43 residues processed: 723 average time/residue: 1.8118 time to fit residues: 1576.6671 Evaluate side-chains 566 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 511 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1453 LEU Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain C residue 1453 LEU Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain D residue 1453 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 488 optimal weight: 5.9990 chunk 372 optimal weight: 0.0870 chunk 256 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 332 optimal weight: 0.7980 chunk 496 optimal weight: 0.9980 chunk 525 optimal weight: 0.0170 chunk 259 optimal weight: 2.9990 chunk 470 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1491 ASN B 514 HIS B 893 GLN B1491 ASN C 514 HIS C 893 GLN C1491 ASN D 514 HIS D 893 GLN D1491 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43668 Z= 0.156 Angle : 0.483 7.847 59372 Z= 0.254 Chirality : 0.038 0.168 6740 Planarity : 0.004 0.046 7504 Dihedral : 8.200 86.395 7056 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.82 % Allowed : 13.08 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.11), residues: 5432 helix: 2.12 (0.09), residues: 2992 sheet: -0.71 (0.24), residues: 376 loop : -0.61 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 726 HIS 0.009 0.001 HIS A 514 PHE 0.022 0.001 PHE B1068 TYR 0.011 0.001 TYR D 917 ARG 0.007 0.000 ARG B 594 *********************** 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 652 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 532 time to evaluate : 5.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7121 (m-30) cc_final: 0.6773 (t0) REVERT: A 78 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6869 (ptp-170) REVERT: A 139 ASP cc_start: 0.7601 (m-30) cc_final: 0.7132 (m-30) REVERT: A 284 GLN cc_start: 0.7115 (mt0) cc_final: 0.6783 (mt0) REVERT: A 352 GLN cc_start: 0.7526 (tt0) cc_final: 0.6575 (mt0) REVERT: A 356 GLN cc_start: 0.7164 (mt0) cc_final: 0.6580 (mm-40) REVERT: A 365 GLN cc_start: 0.6509 (mt0) cc_final: 0.5468 (mp10) REVERT: A 473 ILE cc_start: 0.7183 (mt) cc_final: 0.6889 (mp) REVERT: A 506 ARG cc_start: 0.6006 (mtp85) cc_final: 0.5793 (ttt-90) REVERT: A 577 ASP cc_start: 0.6174 (t0) cc_final: 0.5820 (t70) REVERT: A 618 HIS cc_start: 0.5412 (t70) cc_final: 0.4647 (m170) REVERT: A 663 LYS cc_start: 0.6358 (mmmt) cc_final: 0.5545 (mmtp) REVERT: A 666 GLU cc_start: 0.6054 (pt0) cc_final: 0.5816 (tt0) REVERT: A 682 HIS cc_start: 0.6219 (t-90) cc_final: 0.5931 (t70) REVERT: A 731 LYS cc_start: 0.6879 (ttpt) cc_final: 0.6453 (mptt) REVERT: A 829 GLU cc_start: 0.6863 (mt-10) cc_final: 0.5975 (mm-30) REVERT: A 832 ILE cc_start: 0.6833 (mm) cc_final: 0.6568 (mt) REVERT: A 849 GLU cc_start: 0.6940 (tp30) cc_final: 0.6622 (tp30) REVERT: A 870 ARG cc_start: 0.6309 (mtt180) cc_final: 0.5948 (mtt90) REVERT: A 875 MET cc_start: 0.6500 (ptt) cc_final: 0.6178 (ptp) REVERT: A 1039 ASP cc_start: 0.7276 (m-30) cc_final: 0.7039 (m-30) REVERT: A 1062 GLU cc_start: 0.6613 (tt0) cc_final: 0.6263 (tt0) REVERT: A 1064 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6430 (mttt) REVERT: A 1085 ARG cc_start: 0.4864 (ttt90) cc_final: 0.4377 (tpt170) REVERT: A 1105 THR cc_start: 0.5985 (m) cc_final: 0.5522 (p) REVERT: A 1127 GLU cc_start: 0.5714 (mt-10) cc_final: 0.5462 (pt0) REVERT: A 1145 GLN cc_start: 0.7196 (tt0) cc_final: 0.6527 (mt0) REVERT: A 1150 MET cc_start: 0.7205 (mmt) cc_final: 0.6932 (mtp) REVERT: A 1152 GLN cc_start: 0.6882 (mt0) cc_final: 0.6395 (mt0) REVERT: A 1233 LEU cc_start: 0.7175 (mm) cc_final: 0.6823 (pt) REVERT: A 1377 GLU cc_start: 0.6802 (pt0) cc_final: 0.6315 (pt0) REVERT: A 1389 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 1445 GLU cc_start: 0.7211 (pm20) cc_final: 0.6825 (pt0) REVERT: A 1460 ASP cc_start: 0.7368 (t70) cc_final: 0.7155 (t0) REVERT: A 1480 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.7080 (mmm-85) REVERT: B 74 ASP cc_start: 0.7107 (m-30) cc_final: 0.6762 (t0) REVERT: B 78 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6812 (ptp-170) REVERT: B 139 ASP cc_start: 0.7601 (m-30) cc_final: 0.7133 (m-30) REVERT: B 284 GLN cc_start: 0.7117 (mt0) cc_final: 0.6838 (mt0) REVERT: B 352 GLN cc_start: 0.7531 (tt0) cc_final: 0.6536 (mt0) REVERT: B 356 GLN cc_start: 0.7181 (mt0) cc_final: 0.6521 (mm-40) REVERT: B 365 GLN cc_start: 0.6500 (mt0) cc_final: 0.5462 (mp10) REVERT: B 473 ILE cc_start: 0.7153 (mt) cc_final: 0.6865 (mp) REVERT: B 506 ARG cc_start: 0.6013 (mtp85) cc_final: 0.5719 (ttt-90) REVERT: B 577 ASP cc_start: 0.6166 (t0) cc_final: 0.5782 (t70) REVERT: B 618 HIS cc_start: 0.5363 (t70) cc_final: 0.4581 (m170) REVERT: B 663 LYS cc_start: 0.6402 (mmmt) cc_final: 0.5609 (mmtp) REVERT: B 682 HIS cc_start: 0.6191 (t-90) cc_final: 0.5906 (t70) REVERT: B 731 LYS cc_start: 0.6826 (ttpt) cc_final: 0.6388 (mptt) REVERT: B 829 GLU cc_start: 0.6875 (mt-10) cc_final: 0.5992 (mm-30) REVERT: B 832 ILE cc_start: 0.6841 (mm) cc_final: 0.6568 (mt) REVERT: B 849 GLU cc_start: 0.6942 (tp30) cc_final: 0.6609 (tp30) REVERT: B 870 ARG cc_start: 0.6307 (mtt180) cc_final: 0.5946 (mtt90) REVERT: B 875 MET cc_start: 0.6505 (ptt) cc_final: 0.6188 (ptp) REVERT: B 969 ARG cc_start: 0.6484 (mtm110) cc_final: 0.5929 (mtm-85) REVERT: B 1039 ASP cc_start: 0.7286 (m-30) cc_final: 0.7055 (m-30) REVERT: B 1062 GLU cc_start: 0.6677 (tt0) cc_final: 0.6343 (tt0) REVERT: B 1064 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6435 (mttt) REVERT: B 1085 ARG cc_start: 0.4803 (ttt90) cc_final: 0.4341 (tpt170) REVERT: B 1105 THR cc_start: 0.5984 (m) cc_final: 0.5521 (p) REVERT: B 1127 GLU cc_start: 0.5742 (mt-10) cc_final: 0.5489 (pt0) REVERT: B 1145 GLN cc_start: 0.7199 (tt0) cc_final: 0.6494 (mt0) REVERT: B 1152 GLN cc_start: 0.6889 (mt0) cc_final: 0.6423 (mt0) REVERT: B 1233 LEU cc_start: 0.7140 (mm) cc_final: 0.6804 (pt) REVERT: B 1389 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7113 (mt-10) REVERT: B 1445 GLU cc_start: 0.7170 (pm20) cc_final: 0.6748 (pt0) REVERT: B 1460 ASP cc_start: 0.7375 (t70) cc_final: 0.7156 (t0) REVERT: B 1480 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.7068 (mmm-85) REVERT: C 74 ASP cc_start: 0.7109 (m-30) cc_final: 0.6766 (t0) REVERT: C 78 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6934 (ptp-170) REVERT: C 139 ASP cc_start: 0.7599 (m-30) cc_final: 0.7131 (m-30) REVERT: C 284 GLN cc_start: 0.7118 (mt0) cc_final: 0.6837 (mt0) REVERT: C 352 GLN cc_start: 0.7537 (tt0) cc_final: 0.6550 (mt0) REVERT: C 356 GLN cc_start: 0.7182 (mt0) cc_final: 0.6523 (mm-40) REVERT: C 365 GLN cc_start: 0.6501 (mt0) cc_final: 0.5463 (mp10) REVERT: C 473 ILE cc_start: 0.7106 (mt) cc_final: 0.6836 (mp) REVERT: C 506 ARG cc_start: 0.6035 (mtp85) cc_final: 0.5714 (ttt-90) REVERT: C 577 ASP cc_start: 0.6124 (t0) cc_final: 0.5767 (t70) REVERT: C 618 HIS cc_start: 0.5465 (t70) cc_final: 0.4666 (m170) REVERT: C 663 LYS cc_start: 0.6359 (mmmt) cc_final: 0.5550 (mmtp) REVERT: C 682 HIS cc_start: 0.6194 (t-90) cc_final: 0.5911 (t70) REVERT: C 731 LYS cc_start: 0.6825 (ttpt) cc_final: 0.6388 (mptt) REVERT: C 829 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6003 (mm-30) REVERT: C 832 ILE cc_start: 0.6840 (mm) cc_final: 0.6558 (mt) REVERT: C 849 GLU cc_start: 0.6931 (tp30) cc_final: 0.6597 (tp30) REVERT: C 870 ARG cc_start: 0.6308 (mtt180) cc_final: 0.5946 (mtt90) REVERT: C 875 MET cc_start: 0.6498 (ptt) cc_final: 0.6179 (ptp) REVERT: C 969 ARG cc_start: 0.6491 (mtm110) cc_final: 0.5928 (mtm-85) REVERT: C 998 LEU cc_start: 0.6778 (mt) cc_final: 0.6568 (OUTLIER) REVERT: C 1039 ASP cc_start: 0.7291 (m-30) cc_final: 0.7049 (m-30) REVERT: C 1062 GLU cc_start: 0.6676 (tt0) cc_final: 0.6336 (tt0) REVERT: C 1064 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6434 (mttt) REVERT: C 1085 ARG cc_start: 0.4876 (ttt90) cc_final: 0.4373 (tpt170) REVERT: C 1105 THR cc_start: 0.6004 (m) cc_final: 0.5531 (p) REVERT: C 1127 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5670 (pt0) REVERT: C 1145 GLN cc_start: 0.7182 (tt0) cc_final: 0.6516 (mt0) REVERT: C 1152 GLN cc_start: 0.6880 (mt0) cc_final: 0.6473 (mt0) REVERT: C 1233 LEU cc_start: 0.7106 (mm) cc_final: 0.6769 (pt) REVERT: C 1389 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7101 (mt-10) REVERT: C 1445 GLU cc_start: 0.7173 (pm20) cc_final: 0.6746 (pt0) REVERT: C 1460 ASP cc_start: 0.7371 (t70) cc_final: 0.7154 (t0) REVERT: C 1480 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.7068 (mmm-85) REVERT: D 74 ASP cc_start: 0.7108 (m-30) cc_final: 0.6763 (t0) REVERT: D 78 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6937 (ptp-170) REVERT: D 139 ASP cc_start: 0.7600 (m-30) cc_final: 0.7133 (m-30) REVERT: D 284 GLN cc_start: 0.7117 (mt0) cc_final: 0.6837 (mt0) REVERT: D 352 GLN cc_start: 0.7534 (tt0) cc_final: 0.6547 (mt0) REVERT: D 356 GLN cc_start: 0.7178 (mt0) cc_final: 0.6520 (mm-40) REVERT: D 365 GLN cc_start: 0.6500 (mt0) cc_final: 0.5462 (mp10) REVERT: D 473 ILE cc_start: 0.7158 (mt) cc_final: 0.6888 (mp) REVERT: D 506 ARG cc_start: 0.6013 (mtp85) cc_final: 0.5718 (ttt-90) REVERT: D 618 HIS cc_start: 0.5410 (t70) cc_final: 0.4645 (m170) REVERT: D 663 LYS cc_start: 0.6402 (mmmt) cc_final: 0.5609 (mmtp) REVERT: D 682 HIS cc_start: 0.6191 (t-90) cc_final: 0.5907 (t70) REVERT: D 731 LYS cc_start: 0.6826 (ttpt) cc_final: 0.6473 (mttp) REVERT: D 829 GLU cc_start: 0.6875 (mt-10) cc_final: 0.5992 (mm-30) REVERT: D 832 ILE cc_start: 0.6840 (mm) cc_final: 0.6567 (mt) REVERT: D 849 GLU cc_start: 0.6942 (tp30) cc_final: 0.6610 (tp30) REVERT: D 870 ARG cc_start: 0.6306 (mtt180) cc_final: 0.5947 (mtt90) REVERT: D 875 MET cc_start: 0.6498 (ptt) cc_final: 0.6181 (ptp) REVERT: D 998 LEU cc_start: 0.6791 (mt) cc_final: 0.6584 (OUTLIER) REVERT: D 1039 ASP cc_start: 0.7301 (m-30) cc_final: 0.7066 (m-30) REVERT: D 1062 GLU cc_start: 0.6678 (tt0) cc_final: 0.6344 (tt0) REVERT: D 1064 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6432 (mttt) REVERT: D 1085 ARG cc_start: 0.4807 (ttt90) cc_final: 0.4342 (tpt170) REVERT: D 1105 THR cc_start: 0.6004 (m) cc_final: 0.5531 (p) REVERT: D 1127 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5667 (pt0) REVERT: D 1145 GLN cc_start: 0.7204 (tt0) cc_final: 0.6526 (mt0) REVERT: D 1150 MET cc_start: 0.7625 (tpp) cc_final: 0.7091 (mtp) REVERT: D 1152 GLN cc_start: 0.6874 (mt0) cc_final: 0.6442 (mt0) REVERT: D 1233 LEU cc_start: 0.7140 (mm) cc_final: 0.6805 (pt) REVERT: D 1377 GLU cc_start: 0.6796 (pt0) cc_final: 0.6181 (pt0) REVERT: D 1445 GLU cc_start: 0.7174 (pm20) cc_final: 0.6750 (pt0) REVERT: D 1460 ASP cc_start: 0.7373 (t70) cc_final: 0.7155 (t0) REVERT: D 1480 ARG cc_start: 0.7362 (ttp-170) cc_final: 0.7068 (mmm-85) outliers start: 120 outliers final: 40 residues processed: 626 average time/residue: 1.8874 time to fit residues: 1422.6935 Evaluate side-chains 537 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 491 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 437 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 391 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 448 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 268 optimal weight: 0.4980 chunk 471 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 813 HIS A 893 GLN A1255 HIS B 514 HIS B 813 HIS B 893 GLN B1255 HIS C 514 HIS C 813 HIS C 893 GLN C1255 HIS D 514 HIS D 813 HIS D 893 GLN D1255 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 43668 Z= 0.324 Angle : 0.613 8.615 59372 Z= 0.322 Chirality : 0.043 0.193 6740 Planarity : 0.005 0.048 7504 Dihedral : 8.739 86.988 7056 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 3.74 % Allowed : 12.96 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5432 helix: 1.80 (0.09), residues: 3000 sheet: -0.85 (0.24), residues: 388 loop : -0.67 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1216 HIS 0.012 0.002 HIS A 514 PHE 0.025 0.002 PHE D 604 TYR 0.022 0.002 TYR A 917 ARG 0.008 0.001 ARG C 594 *********************** 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 654 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 495 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5635 (ttm110) REVERT: A 70 MET cc_start: 0.5450 (ppp) cc_final: 0.4709 (ppp) REVERT: A 74 ASP cc_start: 0.7241 (m-30) cc_final: 0.6722 (t0) REVERT: A 139 ASP cc_start: 0.7627 (m-30) cc_final: 0.7196 (m-30) REVERT: A 240 HIS cc_start: 0.6667 (m-70) cc_final: 0.6284 (m170) REVERT: A 284 GLN cc_start: 0.7168 (mt0) cc_final: 0.6929 (mt0) REVERT: A 352 GLN cc_start: 0.7552 (tt0) cc_final: 0.6688 (mt0) REVERT: A 356 GLN cc_start: 0.7140 (mt0) cc_final: 0.6700 (mm-40) REVERT: A 365 GLN cc_start: 0.6593 (mt0) cc_final: 0.5513 (mp10) REVERT: A 475 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6631 (mm-30) REVERT: A 506 ARG cc_start: 0.6036 (mtp85) cc_final: 0.5665 (ttt-90) REVERT: A 618 HIS cc_start: 0.5542 (t70) cc_final: 0.4531 (m170) REVERT: A 663 LYS cc_start: 0.6476 (mmmt) cc_final: 0.5710 (mttt) REVERT: A 666 GLU cc_start: 0.6336 (pt0) cc_final: 0.6012 (tt0) REVERT: A 682 HIS cc_start: 0.6353 (t-90) cc_final: 0.6038 (t-90) REVERT: A 731 LYS cc_start: 0.6770 (ttpt) cc_final: 0.6370 (mttp) REVERT: A 803 TYR cc_start: 0.7537 (t80) cc_final: 0.7334 (t80) REVERT: A 829 GLU cc_start: 0.6703 (mt-10) cc_final: 0.5899 (mm-30) REVERT: A 832 ILE cc_start: 0.6636 (mm) cc_final: 0.6414 (mt) REVERT: A 849 GLU cc_start: 0.7157 (tp30) cc_final: 0.6747 (tp30) REVERT: A 875 MET cc_start: 0.6627 (ptt) cc_final: 0.6351 (ptt) REVERT: A 1062 GLU cc_start: 0.6576 (tt0) cc_final: 0.6199 (tt0) REVERT: A 1064 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6515 (mttt) REVERT: A 1085 ARG cc_start: 0.4786 (ttt90) cc_final: 0.4313 (tpt170) REVERT: A 1105 THR cc_start: 0.6091 (m) cc_final: 0.5616 (p) REVERT: A 1127 GLU cc_start: 0.5965 (mt-10) cc_final: 0.5531 (pt0) REVERT: A 1145 GLN cc_start: 0.7258 (tt0) cc_final: 0.6555 (mt0) REVERT: A 1150 MET cc_start: 0.7321 (mmt) cc_final: 0.6998 (mtp) REVERT: A 1152 GLN cc_start: 0.6790 (mt0) cc_final: 0.6402 (mt0) REVERT: A 1233 LEU cc_start: 0.7269 (mm) cc_final: 0.6844 (tp) REVERT: A 1394 MET cc_start: 0.6920 (mtt) cc_final: 0.6704 (mtt) REVERT: A 1445 GLU cc_start: 0.7298 (pm20) cc_final: 0.6871 (pt0) REVERT: A 1460 ASP cc_start: 0.7026 (t70) cc_final: 0.6785 (t0) REVERT: A 1480 ARG cc_start: 0.7587 (ttp-170) cc_final: 0.7189 (ttp80) REVERT: B 70 MET cc_start: 0.5466 (ppp) cc_final: 0.4764 (ppp) REVERT: B 74 ASP cc_start: 0.7223 (m-30) cc_final: 0.6713 (t0) REVERT: B 139 ASP cc_start: 0.7630 (m-30) cc_final: 0.7197 (m-30) REVERT: B 240 HIS cc_start: 0.6665 (m-70) cc_final: 0.6221 (m-70) REVERT: B 284 GLN cc_start: 0.7169 (mt0) cc_final: 0.6929 (mt0) REVERT: B 352 GLN cc_start: 0.7547 (tt0) cc_final: 0.6688 (mt0) REVERT: B 356 GLN cc_start: 0.7118 (mt0) cc_final: 0.6683 (mm-40) REVERT: B 365 GLN cc_start: 0.6592 (mt0) cc_final: 0.5518 (mp10) REVERT: B 506 ARG cc_start: 0.6061 (mtp85) cc_final: 0.5670 (ttt-90) REVERT: B 592 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5404 (tp-100) REVERT: B 618 HIS cc_start: 0.5550 (t70) cc_final: 0.4545 (m170) REVERT: B 663 LYS cc_start: 0.6688 (mmmt) cc_final: 0.6209 (mptt) REVERT: B 682 HIS cc_start: 0.6375 (t-90) cc_final: 0.6061 (t-90) REVERT: B 731 LYS cc_start: 0.6868 (ttpt) cc_final: 0.6438 (mttp) REVERT: B 829 GLU cc_start: 0.6697 (mt-10) cc_final: 0.5829 (mm-30) REVERT: B 832 ILE cc_start: 0.6654 (mm) cc_final: 0.6410 (mt) REVERT: B 849 GLU cc_start: 0.7167 (tp30) cc_final: 0.6793 (tp30) REVERT: B 875 MET cc_start: 0.6611 (ptt) cc_final: 0.6332 (ptt) REVERT: B 969 ARG cc_start: 0.6628 (mtm110) cc_final: 0.6112 (mtm-85) REVERT: B 1005 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5826 (mt-10) REVERT: B 1062 GLU cc_start: 0.6577 (tt0) cc_final: 0.6200 (tt0) REVERT: B 1064 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6508 (mttt) REVERT: B 1085 ARG cc_start: 0.4831 (ttt90) cc_final: 0.4329 (tpt170) REVERT: B 1105 THR cc_start: 0.6026 (m) cc_final: 0.5549 (p) REVERT: B 1127 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5632 (pt0) REVERT: B 1145 GLN cc_start: 0.7265 (tt0) cc_final: 0.6529 (mt0) REVERT: B 1152 GLN cc_start: 0.6863 (mt0) cc_final: 0.6511 (mt0) REVERT: B 1233 LEU cc_start: 0.7268 (mm) cc_final: 0.6841 (tp) REVERT: B 1445 GLU cc_start: 0.7284 (pm20) cc_final: 0.6809 (pt0) REVERT: B 1460 ASP cc_start: 0.7019 (t70) cc_final: 0.6778 (t0) REVERT: B 1480 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.7179 (ttp80) REVERT: C 69 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5627 (ttm110) REVERT: C 70 MET cc_start: 0.5483 (ppp) cc_final: 0.4752 (ppp) REVERT: C 74 ASP cc_start: 0.7234 (m-30) cc_final: 0.6717 (t0) REVERT: C 98 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7508 (p) REVERT: C 139 ASP cc_start: 0.7628 (m-30) cc_final: 0.7197 (m-30) REVERT: C 240 HIS cc_start: 0.6645 (m-70) cc_final: 0.6202 (m-70) REVERT: C 284 GLN cc_start: 0.7171 (mt0) cc_final: 0.6933 (mt0) REVERT: C 352 GLN cc_start: 0.7536 (tt0) cc_final: 0.6696 (mt0) REVERT: C 356 GLN cc_start: 0.7120 (mt0) cc_final: 0.6684 (mm-40) REVERT: C 365 GLN cc_start: 0.6594 (mt0) cc_final: 0.5520 (mp10) REVERT: C 475 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6623 (mm-30) REVERT: C 506 ARG cc_start: 0.6058 (mtp85) cc_final: 0.5660 (ttt-90) REVERT: C 577 ASP cc_start: 0.6129 (t0) cc_final: 0.5731 (t70) REVERT: C 618 HIS cc_start: 0.5592 (t70) cc_final: 0.4554 (m170) REVERT: C 663 LYS cc_start: 0.6662 (mmmt) cc_final: 0.5739 (mttt) REVERT: C 682 HIS cc_start: 0.6376 (t-90) cc_final: 0.6062 (t-90) REVERT: C 731 LYS cc_start: 0.6866 (ttpt) cc_final: 0.6437 (mttp) REVERT: C 829 GLU cc_start: 0.6703 (mt-10) cc_final: 0.5848 (mm-30) REVERT: C 832 ILE cc_start: 0.6651 (mm) cc_final: 0.6411 (mt) REVERT: C 849 GLU cc_start: 0.7162 (tp30) cc_final: 0.6764 (tp30) REVERT: C 875 MET cc_start: 0.6613 (ptt) cc_final: 0.6335 (ptt) REVERT: C 969 ARG cc_start: 0.6637 (mtm110) cc_final: 0.6113 (mtm-85) REVERT: C 1062 GLU cc_start: 0.6577 (tt0) cc_final: 0.6198 (tt0) REVERT: C 1064 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6519 (mttt) REVERT: C 1085 ARG cc_start: 0.4802 (ttt90) cc_final: 0.4366 (tpt170) REVERT: C 1105 THR cc_start: 0.6121 (m) cc_final: 0.5640 (p) REVERT: C 1127 GLU cc_start: 0.5924 (mt-10) cc_final: 0.5492 (pt0) REVERT: C 1145 GLN cc_start: 0.7238 (tt0) cc_final: 0.6586 (mt0) REVERT: C 1152 GLN cc_start: 0.6814 (mt0) cc_final: 0.6456 (mt0) REVERT: C 1233 LEU cc_start: 0.7268 (mm) cc_final: 0.6870 (tp) REVERT: C 1394 MET cc_start: 0.6921 (mtt) cc_final: 0.6704 (mtt) REVERT: C 1445 GLU cc_start: 0.7288 (pm20) cc_final: 0.6812 (pt0) REVERT: C 1460 ASP cc_start: 0.7019 (t70) cc_final: 0.6781 (t0) REVERT: C 1480 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7173 (ttp80) REVERT: D 70 MET cc_start: 0.5464 (ppp) cc_final: 0.4762 (ppp) REVERT: D 74 ASP cc_start: 0.7247 (m-30) cc_final: 0.6739 (t0) REVERT: D 139 ASP cc_start: 0.7629 (m-30) cc_final: 0.7196 (m-30) REVERT: D 240 HIS cc_start: 0.6663 (m-70) cc_final: 0.6247 (m-70) REVERT: D 284 GLN cc_start: 0.7168 (mt0) cc_final: 0.6927 (mt0) REVERT: D 352 GLN cc_start: 0.7547 (tt0) cc_final: 0.6688 (mt0) REVERT: D 356 GLN cc_start: 0.7118 (mt0) cc_final: 0.6683 (mm-40) REVERT: D 365 GLN cc_start: 0.6592 (mt0) cc_final: 0.5520 (mp10) REVERT: D 475 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6641 (mm-30) REVERT: D 506 ARG cc_start: 0.6037 (mtp85) cc_final: 0.5664 (ttt-90) REVERT: D 618 HIS cc_start: 0.5650 (t70) cc_final: 0.4551 (m170) REVERT: D 663 LYS cc_start: 0.6687 (mmmt) cc_final: 0.5766 (mttt) REVERT: D 682 HIS cc_start: 0.6344 (t-90) cc_final: 0.6028 (t-90) REVERT: D 731 LYS cc_start: 0.6868 (ttpt) cc_final: 0.6437 (mttp) REVERT: D 829 GLU cc_start: 0.6700 (mt-10) cc_final: 0.5832 (mm-30) REVERT: D 832 ILE cc_start: 0.6652 (mm) cc_final: 0.6410 (mt) REVERT: D 849 GLU cc_start: 0.7167 (tp30) cc_final: 0.6763 (tp30) REVERT: D 875 MET cc_start: 0.6614 (ptt) cc_final: 0.6336 (ptt) REVERT: D 969 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6080 (mtm-85) REVERT: D 1062 GLU cc_start: 0.6562 (tt0) cc_final: 0.6186 (tt0) REVERT: D 1064 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6500 (mttt) REVERT: D 1085 ARG cc_start: 0.4814 (ttt90) cc_final: 0.4312 (tpt170) REVERT: D 1105 THR cc_start: 0.6119 (m) cc_final: 0.5639 (p) REVERT: D 1127 GLU cc_start: 0.5922 (mt-10) cc_final: 0.5489 (pt0) REVERT: D 1145 GLN cc_start: 0.7241 (tt0) cc_final: 0.6545 (mt0) REVERT: D 1150 MET cc_start: 0.7736 (tpp) cc_final: 0.7133 (mtp) REVERT: D 1152 GLN cc_start: 0.6776 (mt0) cc_final: 0.6426 (mt0) REVERT: D 1233 LEU cc_start: 0.7311 (mm) cc_final: 0.6869 (tp) REVERT: D 1394 MET cc_start: 0.6856 (mtt) cc_final: 0.6595 (mtt) REVERT: D 1445 GLU cc_start: 0.7289 (pm20) cc_final: 0.6812 (pt0) REVERT: D 1460 ASP cc_start: 0.7019 (t70) cc_final: 0.6780 (t0) REVERT: D 1480 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7179 (ttp80) outliers start: 159 outliers final: 63 residues processed: 610 average time/residue: 1.8765 time to fit residues: 1374.0162 Evaluate side-chains 533 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 461 time to evaluate : 5.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1277 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 176 optimal weight: 6.9990 chunk 473 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 526 optimal weight: 0.9990 chunk 436 optimal weight: 2.9990 chunk 243 optimal weight: 0.0040 chunk 43 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 276 optimal weight: 0.0870 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN B 448 ASN B 514 HIS B 893 GLN B1080 HIS C 514 HIS C 893 GLN C1080 HIS D 514 HIS D 893 GLN D1080 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43668 Z= 0.159 Angle : 0.489 7.900 59372 Z= 0.258 Chirality : 0.038 0.170 6740 Planarity : 0.004 0.046 7504 Dihedral : 8.186 84.637 7056 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 2.38 % Allowed : 15.05 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.12), residues: 5432 helix: 2.06 (0.09), residues: 2992 sheet: -1.03 (0.24), residues: 376 loop : -0.57 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.007 0.001 HIS A 514 PHE 0.016 0.001 PHE C1068 TYR 0.013 0.001 TYR B 799 ARG 0.010 0.000 ARG C 594 *********************** 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 592 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 491 time to evaluate : 5.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7153 (m-30) cc_final: 0.6721 (t0) REVERT: A 98 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7574 (p) REVERT: A 139 ASP cc_start: 0.7625 (m-30) cc_final: 0.7197 (m-30) REVERT: A 240 HIS cc_start: 0.6620 (m-70) cc_final: 0.6200 (m170) REVERT: A 284 GLN cc_start: 0.7129 (mt0) cc_final: 0.6870 (mt0) REVERT: A 352 GLN cc_start: 0.7511 (tt0) cc_final: 0.6646 (mt0) REVERT: A 356 GLN cc_start: 0.7122 (mt0) cc_final: 0.6711 (mm-40) REVERT: A 475 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6618 (mm-30) REVERT: A 506 ARG cc_start: 0.5979 (mtp85) cc_final: 0.5635 (ttt-90) REVERT: A 618 HIS cc_start: 0.5569 (t70) cc_final: 0.4651 (m170) REVERT: A 654 GLU cc_start: 0.5578 (tp30) cc_final: 0.5357 (tp30) REVERT: A 663 LYS cc_start: 0.6440 (mmmt) cc_final: 0.5670 (mttt) REVERT: A 666 GLU cc_start: 0.6190 (pt0) cc_final: 0.5944 (tt0) REVERT: A 682 HIS cc_start: 0.6269 (t-90) cc_final: 0.5954 (t-90) REVERT: A 731 LYS cc_start: 0.6998 (ttpt) cc_final: 0.6692 (tttp) REVERT: A 829 GLU cc_start: 0.6760 (mt-10) cc_final: 0.5948 (mm-30) REVERT: A 832 ILE cc_start: 0.6629 (mm) cc_final: 0.6216 (mt) REVERT: A 849 GLU cc_start: 0.7156 (tp30) cc_final: 0.6758 (tp30) REVERT: A 870 ARG cc_start: 0.6318 (mtt180) cc_final: 0.5923 (mtt90) REVERT: A 875 MET cc_start: 0.6543 (ptt) cc_final: 0.6207 (ptp) REVERT: A 969 ARG cc_start: 0.6896 (mtp180) cc_final: 0.6071 (mtm-85) REVERT: A 1039 ASP cc_start: 0.7378 (m-30) cc_final: 0.7095 (m-30) REVERT: A 1062 GLU cc_start: 0.6607 (tt0) cc_final: 0.6267 (tt0) REVERT: A 1064 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6354 (mttt) REVERT: A 1085 ARG cc_start: 0.4853 (ttt90) cc_final: 0.4322 (tpt170) REVERT: A 1105 THR cc_start: 0.6021 (m) cc_final: 0.5549 (p) REVERT: A 1126 ARG cc_start: 0.5494 (ttp-110) cc_final: 0.5277 (mtp-110) REVERT: A 1127 GLU cc_start: 0.5897 (mt-10) cc_final: 0.5474 (pt0) REVERT: A 1130 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5797 (mm-30) REVERT: A 1145 GLN cc_start: 0.7182 (tt0) cc_final: 0.6525 (mt0) REVERT: A 1150 MET cc_start: 0.7125 (mmt) cc_final: 0.6911 (mtp) REVERT: A 1152 GLN cc_start: 0.6757 (mt0) cc_final: 0.6395 (mt0) REVERT: A 1233 LEU cc_start: 0.7130 (mm) cc_final: 0.6759 (tp) REVERT: A 1244 MET cc_start: 0.5849 (ptp) cc_final: 0.5005 (mmt) REVERT: A 1394 MET cc_start: 0.6951 (mtt) cc_final: 0.6686 (mtt) REVERT: A 1445 GLU cc_start: 0.7299 (pm20) cc_final: 0.6870 (pt0) REVERT: A 1480 ARG cc_start: 0.7534 (ttp-170) cc_final: 0.7161 (ttp80) REVERT: B 74 ASP cc_start: 0.7184 (m-30) cc_final: 0.6717 (t0) REVERT: B 98 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7544 (p) REVERT: B 139 ASP cc_start: 0.7627 (m-30) cc_final: 0.7199 (m-30) REVERT: B 240 HIS cc_start: 0.6626 (m-70) cc_final: 0.6206 (m170) REVERT: B 284 GLN cc_start: 0.7140 (mt0) cc_final: 0.6884 (mt0) REVERT: B 352 GLN cc_start: 0.7549 (tt0) cc_final: 0.6672 (mt0) REVERT: B 356 GLN cc_start: 0.7107 (mt0) cc_final: 0.6663 (mm-40) REVERT: B 506 ARG cc_start: 0.5978 (mtp85) cc_final: 0.5636 (ttt-90) REVERT: B 618 HIS cc_start: 0.5516 (t70) cc_final: 0.4622 (m170) REVERT: B 654 GLU cc_start: 0.5574 (tp30) cc_final: 0.5350 (tp30) REVERT: B 663 LYS cc_start: 0.6645 (mmmt) cc_final: 0.5721 (mmtp) REVERT: B 682 HIS cc_start: 0.6278 (t-90) cc_final: 0.5957 (t-90) REVERT: B 731 LYS cc_start: 0.6893 (ttpt) cc_final: 0.6404 (mptt) REVERT: B 829 GLU cc_start: 0.6764 (mt-10) cc_final: 0.5954 (mm-30) REVERT: B 832 ILE cc_start: 0.6635 (mm) cc_final: 0.6220 (mt) REVERT: B 849 GLU cc_start: 0.7159 (tp30) cc_final: 0.6760 (tp30) REVERT: B 870 ARG cc_start: 0.6299 (mtt180) cc_final: 0.5905 (mtt90) REVERT: B 875 MET cc_start: 0.6542 (ptt) cc_final: 0.6208 (ptp) REVERT: B 969 ARG cc_start: 0.6593 (mtm110) cc_final: 0.6065 (mtm-85) REVERT: B 1005 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5748 (mt-10) REVERT: B 1039 ASP cc_start: 0.7471 (m-30) cc_final: 0.7207 (m-30) REVERT: B 1046 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: B 1062 GLU cc_start: 0.6608 (tt0) cc_final: 0.6269 (tt0) REVERT: B 1064 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6353 (mttt) REVERT: B 1085 ARG cc_start: 0.4847 (ttt90) cc_final: 0.4324 (tpt170) REVERT: B 1105 THR cc_start: 0.6050 (m) cc_final: 0.5578 (p) REVERT: B 1127 GLU cc_start: 0.5895 (mt-10) cc_final: 0.5496 (pt0) REVERT: B 1145 GLN cc_start: 0.7209 (tt0) cc_final: 0.6512 (mt0) REVERT: B 1152 GLN cc_start: 0.6819 (mt0) cc_final: 0.6460 (mt0) REVERT: B 1233 LEU cc_start: 0.7126 (mm) cc_final: 0.6751 (tp) REVERT: B 1445 GLU cc_start: 0.7327 (pm20) cc_final: 0.6886 (pt0) REVERT: B 1480 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.7142 (ttp80) REVERT: C 74 ASP cc_start: 0.7150 (m-30) cc_final: 0.6740 (t0) REVERT: C 94 THR cc_start: 0.6794 (p) cc_final: 0.6431 (p) REVERT: C 98 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7554 (p) REVERT: C 139 ASP cc_start: 0.7627 (m-30) cc_final: 0.7197 (m-30) REVERT: C 240 HIS cc_start: 0.6621 (m-70) cc_final: 0.6194 (m170) REVERT: C 284 GLN cc_start: 0.7131 (mt0) cc_final: 0.6874 (mt0) REVERT: C 352 GLN cc_start: 0.7549 (tt0) cc_final: 0.6672 (mt0) REVERT: C 356 GLN cc_start: 0.7108 (mt0) cc_final: 0.6663 (mm-40) REVERT: C 475 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6609 (mm-30) REVERT: C 506 ARG cc_start: 0.5850 (mtp85) cc_final: 0.5509 (ttt-90) REVERT: C 618 HIS cc_start: 0.5572 (t70) cc_final: 0.4635 (m170) REVERT: C 663 LYS cc_start: 0.6643 (mmmt) cc_final: 0.5698 (mttt) REVERT: C 682 HIS cc_start: 0.6279 (t-90) cc_final: 0.5959 (t-90) REVERT: C 731 LYS cc_start: 0.6886 (ttpt) cc_final: 0.6405 (mptt) REVERT: C 829 GLU cc_start: 0.6764 (mt-10) cc_final: 0.5957 (mm-30) REVERT: C 832 ILE cc_start: 0.6633 (mm) cc_final: 0.6220 (mt) REVERT: C 849 GLU cc_start: 0.7152 (tp30) cc_final: 0.6729 (tp30) REVERT: C 870 ARG cc_start: 0.6305 (mtt180) cc_final: 0.5911 (mtt90) REVERT: C 875 MET cc_start: 0.6542 (ptt) cc_final: 0.6208 (ptp) REVERT: C 969 ARG cc_start: 0.6599 (mtm110) cc_final: 0.6066 (mtm-85) REVERT: C 1039 ASP cc_start: 0.7471 (m-30) cc_final: 0.7205 (m-30) REVERT: C 1046 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6580 (mt-10) REVERT: C 1062 GLU cc_start: 0.6609 (tt0) cc_final: 0.6268 (tt0) REVERT: C 1064 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6354 (mttt) REVERT: C 1085 ARG cc_start: 0.4848 (ttt90) cc_final: 0.4358 (tpt170) REVERT: C 1105 THR cc_start: 0.6069 (m) cc_final: 0.5584 (p) REVERT: C 1127 GLU cc_start: 0.5913 (mt-10) cc_final: 0.5478 (pt0) REVERT: C 1145 GLN cc_start: 0.7154 (tt0) cc_final: 0.6562 (mt0) REVERT: C 1152 GLN cc_start: 0.6758 (mt0) cc_final: 0.6376 (mt0) REVERT: C 1233 LEU cc_start: 0.7091 (mm) cc_final: 0.6741 (tp) REVERT: C 1394 MET cc_start: 0.6954 (mtt) cc_final: 0.6687 (mtt) REVERT: C 1445 GLU cc_start: 0.7327 (pm20) cc_final: 0.6885 (pt0) REVERT: C 1460 ASP cc_start: 0.7071 (t70) cc_final: 0.6807 (t0) REVERT: C 1480 ARG cc_start: 0.7516 (ttp-170) cc_final: 0.7138 (ttp80) REVERT: D 74 ASP cc_start: 0.7149 (m-30) cc_final: 0.6739 (t0) REVERT: D 94 THR cc_start: 0.6795 (p) cc_final: 0.6433 (p) REVERT: D 98 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7515 (p) REVERT: D 139 ASP cc_start: 0.7628 (m-30) cc_final: 0.7198 (m-30) REVERT: D 240 HIS cc_start: 0.6624 (m-70) cc_final: 0.6205 (m170) REVERT: D 284 GLN cc_start: 0.7141 (mt0) cc_final: 0.6885 (mt0) REVERT: D 352 GLN cc_start: 0.7549 (tt0) cc_final: 0.6672 (mt0) REVERT: D 356 GLN cc_start: 0.7111 (mt0) cc_final: 0.6663 (mm-40) REVERT: D 475 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6619 (mm-30) REVERT: D 506 ARG cc_start: 0.5978 (mtp85) cc_final: 0.5635 (ttt-90) REVERT: D 618 HIS cc_start: 0.5565 (t70) cc_final: 0.4621 (m170) REVERT: D 654 GLU cc_start: 0.5574 (tp30) cc_final: 0.5351 (tp30) REVERT: D 663 LYS cc_start: 0.6645 (mmmt) cc_final: 0.5721 (mmtp) REVERT: D 682 HIS cc_start: 0.6274 (t-90) cc_final: 0.5956 (t-90) REVERT: D 731 LYS cc_start: 0.6893 (ttpt) cc_final: 0.6402 (mptt) REVERT: D 829 GLU cc_start: 0.6764 (mt-10) cc_final: 0.5944 (mm-30) REVERT: D 832 ILE cc_start: 0.6634 (mm) cc_final: 0.6219 (mt) REVERT: D 849 GLU cc_start: 0.7157 (tp30) cc_final: 0.6742 (tp30) REVERT: D 870 ARG cc_start: 0.6304 (mtt180) cc_final: 0.5911 (mtt90) REVERT: D 875 MET cc_start: 0.6543 (ptt) cc_final: 0.6210 (ptp) REVERT: D 969 ARG cc_start: 0.6868 (mtp180) cc_final: 0.6028 (mtm-85) REVERT: D 1039 ASP cc_start: 0.7476 (m-30) cc_final: 0.7211 (m-30) REVERT: D 1046 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: D 1062 GLU cc_start: 0.6607 (tt0) cc_final: 0.6268 (tt0) REVERT: D 1064 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6354 (mttt) REVERT: D 1085 ARG cc_start: 0.4849 (ttt90) cc_final: 0.4327 (tpt170) REVERT: D 1105 THR cc_start: 0.6068 (m) cc_final: 0.5583 (p) REVERT: D 1126 ARG cc_start: 0.5398 (mtp-110) cc_final: 0.5096 (mtp-110) REVERT: D 1127 GLU cc_start: 0.5910 (mt-10) cc_final: 0.5465 (pt0) REVERT: D 1130 GLU cc_start: 0.6454 (mt-10) cc_final: 0.5819 (mm-30) REVERT: D 1145 GLN cc_start: 0.7194 (tt0) cc_final: 0.6588 (mt0) REVERT: D 1150 MET cc_start: 0.7624 (tpp) cc_final: 0.7100 (mtp) REVERT: D 1152 GLN cc_start: 0.6774 (mt0) cc_final: 0.6414 (mt0) REVERT: D 1233 LEU cc_start: 0.7114 (mm) cc_final: 0.6741 (tp) REVERT: D 1394 MET cc_start: 0.6893 (mtt) cc_final: 0.6626 (mtt) REVERT: D 1445 GLU cc_start: 0.7328 (pm20) cc_final: 0.6884 (pt0) REVERT: D 1460 ASP cc_start: 0.7076 (t70) cc_final: 0.6813 (t0) REVERT: D 1480 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.7144 (ttp80) outliers start: 101 outliers final: 42 residues processed: 566 average time/residue: 1.8905 time to fit residues: 1287.0036 Evaluate side-chains 536 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 482 time to evaluate : 5.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 507 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 384 optimal weight: 0.0070 chunk 297 optimal weight: 4.9990 chunk 443 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 524 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 319 optimal weight: 10.0000 chunk 242 optimal weight: 0.6980 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN B 514 HIS B 893 GLN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 GLN D 514 HIS D 893 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 43668 Z= 0.364 Angle : 0.633 8.160 59372 Z= 0.330 Chirality : 0.044 0.212 6740 Planarity : 0.005 0.046 7504 Dihedral : 8.762 86.302 7056 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 3.13 % Allowed : 14.49 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.11), residues: 5432 helix: 1.73 (0.09), residues: 2992 sheet: -1.00 (0.24), residues: 388 loop : -0.67 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1216 HIS 0.007 0.001 HIS A 618 PHE 0.025 0.002 PHE A 604 TYR 0.023 0.002 TYR D 917 ARG 0.010 0.001 ARG A 594 *********************** 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 607 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 474 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5681 (ttm110) REVERT: A 74 ASP cc_start: 0.7315 (m-30) cc_final: 0.6822 (t0) REVERT: A 77 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6929 (mmtt) REVERT: A 98 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 139 ASP cc_start: 0.7654 (m-30) cc_final: 0.7264 (m-30) REVERT: A 240 HIS cc_start: 0.6781 (m-70) cc_final: 0.6377 (m90) REVERT: A 284 GLN cc_start: 0.7158 (mt0) cc_final: 0.6901 (mt0) REVERT: A 352 GLN cc_start: 0.7462 (tt0) cc_final: 0.6657 (mt0) REVERT: A 356 GLN cc_start: 0.7136 (mt0) cc_final: 0.6735 (mm-40) REVERT: A 365 GLN cc_start: 0.6593 (mt0) cc_final: 0.5500 (mp10) REVERT: A 433 GLU cc_start: 0.7202 (tt0) cc_final: 0.6857 (mm-30) REVERT: A 464 GLU cc_start: 0.5955 (tp30) cc_final: 0.5746 (mt-10) REVERT: A 506 ARG cc_start: 0.5835 (mtp85) cc_final: 0.5470 (ttt-90) REVERT: A 577 ASP cc_start: 0.6086 (t0) cc_final: 0.5680 (t70) REVERT: A 663 LYS cc_start: 0.6536 (mmmt) cc_final: 0.5771 (mttt) REVERT: A 666 GLU cc_start: 0.6351 (pt0) cc_final: 0.6015 (tt0) REVERT: A 682 HIS cc_start: 0.6341 (t-90) cc_final: 0.6013 (t-90) REVERT: A 731 LYS cc_start: 0.6932 (ttpt) cc_final: 0.6505 (mttp) REVERT: A 829 GLU cc_start: 0.6720 (mt-10) cc_final: 0.5920 (mm-30) REVERT: A 832 ILE cc_start: 0.6621 (mm) cc_final: 0.6241 (mt) REVERT: A 849 GLU cc_start: 0.7178 (tp30) cc_final: 0.6803 (tp30) REVERT: A 875 MET cc_start: 0.6634 (ptt) cc_final: 0.6307 (ptp) REVERT: A 969 ARG cc_start: 0.6883 (mtp180) cc_final: 0.6161 (mtm-85) REVERT: A 1046 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: A 1062 GLU cc_start: 0.6584 (tt0) cc_final: 0.6305 (tt0) REVERT: A 1064 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6504 (mttt) REVERT: A 1085 ARG cc_start: 0.4732 (ttt90) cc_final: 0.4279 (tpt170) REVERT: A 1105 THR cc_start: 0.6055 (m) cc_final: 0.5580 (p) REVERT: A 1130 GLU cc_start: 0.6404 (mt-10) cc_final: 0.5748 (mm-30) REVERT: A 1145 GLN cc_start: 0.7282 (tt0) cc_final: 0.6561 (mt0) REVERT: A 1150 MET cc_start: 0.7329 (mmt) cc_final: 0.7044 (mtp) REVERT: A 1152 GLN cc_start: 0.6769 (mt0) cc_final: 0.6442 (mt0) REVERT: A 1233 LEU cc_start: 0.7248 (mm) cc_final: 0.6873 (tp) REVERT: A 1244 MET cc_start: 0.5890 (ptp) cc_final: 0.5005 (mmt) REVERT: A 1445 GLU cc_start: 0.7435 (pm20) cc_final: 0.6982 (pt0) REVERT: A 1480 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7202 (ttp80) REVERT: B 74 ASP cc_start: 0.7315 (m-30) cc_final: 0.6823 (t0) REVERT: B 77 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6929 (mmtt) REVERT: B 98 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7622 (p) REVERT: B 139 ASP cc_start: 0.7658 (m-30) cc_final: 0.7265 (m-30) REVERT: B 240 HIS cc_start: 0.6804 (m-70) cc_final: 0.6374 (m-70) REVERT: B 284 GLN cc_start: 0.7160 (mt0) cc_final: 0.6904 (mt0) REVERT: B 352 GLN cc_start: 0.7501 (tt0) cc_final: 0.6625 (mt0) REVERT: B 356 GLN cc_start: 0.7039 (mt0) cc_final: 0.6682 (mm-40) REVERT: B 365 GLN cc_start: 0.6657 (mt0) cc_final: 0.5541 (mp10) REVERT: B 506 ARG cc_start: 0.5839 (mtp85) cc_final: 0.5476 (ttt-90) REVERT: B 577 ASP cc_start: 0.6088 (t0) cc_final: 0.5673 (t70) REVERT: B 663 LYS cc_start: 0.6674 (mmmt) cc_final: 0.5752 (mttt) REVERT: B 682 HIS cc_start: 0.6341 (t-90) cc_final: 0.6010 (t-90) REVERT: B 731 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6472 (mttp) REVERT: B 829 GLU cc_start: 0.6661 (mt-10) cc_final: 0.5887 (mm-30) REVERT: B 849 GLU cc_start: 0.7169 (tp30) cc_final: 0.6795 (tp30) REVERT: B 875 MET cc_start: 0.6635 (ptt) cc_final: 0.6308 (ptp) REVERT: B 969 ARG cc_start: 0.6631 (mtm110) cc_final: 0.6098 (mtm-85) REVERT: B 1005 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5662 (mt-10) REVERT: B 1046 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6518 (mt-10) REVERT: B 1062 GLU cc_start: 0.6585 (tt0) cc_final: 0.6306 (tt0) REVERT: B 1064 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6506 (mttt) REVERT: B 1085 ARG cc_start: 0.4810 (ttt90) cc_final: 0.4274 (tpt170) REVERT: B 1105 THR cc_start: 0.6057 (m) cc_final: 0.5580 (p) REVERT: B 1145 GLN cc_start: 0.7303 (tt0) cc_final: 0.6562 (mt0) REVERT: B 1152 GLN cc_start: 0.6817 (mt0) cc_final: 0.6504 (mt0) REVERT: B 1233 LEU cc_start: 0.7247 (mm) cc_final: 0.6865 (tp) REVERT: B 1244 MET cc_start: 0.5974 (ptp) cc_final: 0.5085 (mmt) REVERT: B 1445 GLU cc_start: 0.7381 (pm20) cc_final: 0.6919 (pt0) REVERT: B 1460 ASP cc_start: 0.7065 (t70) cc_final: 0.6809 (t0) REVERT: B 1480 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7189 (ttp80) REVERT: C 69 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5615 (ttm110) REVERT: C 70 MET cc_start: 0.5572 (ppp) cc_final: 0.4759 (ppp) REVERT: C 74 ASP cc_start: 0.7316 (m-30) cc_final: 0.6786 (t0) REVERT: C 77 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6861 (mmtt) REVERT: C 98 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7612 (p) REVERT: C 139 ASP cc_start: 0.7660 (m-30) cc_final: 0.7265 (m-30) REVERT: C 240 HIS cc_start: 0.6761 (m-70) cc_final: 0.6327 (m-70) REVERT: C 284 GLN cc_start: 0.7160 (mt0) cc_final: 0.6906 (mt0) REVERT: C 352 GLN cc_start: 0.7500 (tt0) cc_final: 0.6626 (mt0) REVERT: C 356 GLN cc_start: 0.7033 (mt0) cc_final: 0.6664 (mm-40) REVERT: C 365 GLN cc_start: 0.6633 (mt0) cc_final: 0.5541 (mp10) REVERT: C 464 GLU cc_start: 0.5937 (tp30) cc_final: 0.5723 (mt-10) REVERT: C 506 ARG cc_start: 0.5933 (mtp85) cc_final: 0.5562 (ttt-90) REVERT: C 577 ASP cc_start: 0.6089 (t0) cc_final: 0.5673 (t70) REVERT: C 663 LYS cc_start: 0.6643 (mmmt) cc_final: 0.5708 (mttt) REVERT: C 682 HIS cc_start: 0.6339 (t-90) cc_final: 0.6010 (t-90) REVERT: C 731 LYS cc_start: 0.6847 (ttpt) cc_final: 0.6471 (mttp) REVERT: C 829 GLU cc_start: 0.6666 (mt-10) cc_final: 0.5897 (mm-30) REVERT: C 849 GLU cc_start: 0.7183 (tp30) cc_final: 0.6809 (tp30) REVERT: C 875 MET cc_start: 0.6637 (ptt) cc_final: 0.6307 (ptp) REVERT: C 969 ARG cc_start: 0.6632 (mtm110) cc_final: 0.6097 (mtm-85) REVERT: C 1046 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: C 1062 GLU cc_start: 0.6588 (tt0) cc_final: 0.6308 (tt0) REVERT: C 1064 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6507 (mttt) REVERT: C 1085 ARG cc_start: 0.4731 (ttt90) cc_final: 0.4280 (tpt170) REVERT: C 1105 THR cc_start: 0.6054 (m) cc_final: 0.5577 (p) REVERT: C 1145 GLN cc_start: 0.7229 (tt0) cc_final: 0.6602 (mt0) REVERT: C 1152 GLN cc_start: 0.6807 (mt0) cc_final: 0.6469 (mt0) REVERT: C 1233 LEU cc_start: 0.7245 (mm) cc_final: 0.6872 (tp) REVERT: C 1244 MET cc_start: 0.5974 (ptp) cc_final: 0.5086 (mmt) REVERT: C 1445 GLU cc_start: 0.7381 (pm20) cc_final: 0.6916 (pt0) REVERT: C 1460 ASP cc_start: 0.7059 (t70) cc_final: 0.6798 (t0) REVERT: C 1480 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.7186 (ttp80) REVERT: D 74 ASP cc_start: 0.7309 (m-30) cc_final: 0.6817 (t0) REVERT: D 77 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6862 (mmtt) REVERT: D 98 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7616 (p) REVERT: D 139 ASP cc_start: 0.7658 (m-30) cc_final: 0.7264 (m-30) REVERT: D 240 HIS cc_start: 0.6803 (m-70) cc_final: 0.6375 (m-70) REVERT: D 284 GLN cc_start: 0.7161 (mt0) cc_final: 0.6903 (mt0) REVERT: D 352 GLN cc_start: 0.7501 (tt0) cc_final: 0.6626 (mt0) REVERT: D 356 GLN cc_start: 0.7035 (mt0) cc_final: 0.6678 (mm-40) REVERT: D 365 GLN cc_start: 0.6657 (mt0) cc_final: 0.5540 (mp10) REVERT: D 433 GLU cc_start: 0.7204 (tt0) cc_final: 0.6856 (mm-30) REVERT: D 506 ARG cc_start: 0.5839 (mtp85) cc_final: 0.5477 (ttt-90) REVERT: D 577 ASP cc_start: 0.6087 (t0) cc_final: 0.5680 (t70) REVERT: D 663 LYS cc_start: 0.6674 (mmmt) cc_final: 0.5751 (mttt) REVERT: D 682 HIS cc_start: 0.6332 (t-90) cc_final: 0.6001 (t-90) REVERT: D 731 LYS cc_start: 0.6851 (ttpt) cc_final: 0.6473 (mttp) REVERT: D 829 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5888 (mm-30) REVERT: D 849 GLU cc_start: 0.7167 (tp30) cc_final: 0.6795 (tp30) REVERT: D 875 MET cc_start: 0.6634 (ptt) cc_final: 0.6307 (ptp) REVERT: D 969 ARG cc_start: 0.6900 (mtp180) cc_final: 0.6097 (mtm-85) REVERT: D 1046 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: D 1062 GLU cc_start: 0.6583 (tt0) cc_final: 0.6310 (tt0) REVERT: D 1064 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6504 (mttt) REVERT: D 1085 ARG cc_start: 0.4774 (ttt90) cc_final: 0.4245 (tpt170) REVERT: D 1105 THR cc_start: 0.6056 (m) cc_final: 0.5579 (p) REVERT: D 1126 ARG cc_start: 0.5436 (mtp-110) cc_final: 0.5144 (mtp-110) REVERT: D 1130 GLU cc_start: 0.6411 (mt-10) cc_final: 0.5745 (mm-30) REVERT: D 1145 GLN cc_start: 0.7272 (tt0) cc_final: 0.6576 (mt0) REVERT: D 1150 MET cc_start: 0.7740 (tpp) cc_final: 0.7190 (mtp) REVERT: D 1152 GLN cc_start: 0.6726 (mt0) cc_final: 0.6397 (mt0) REVERT: D 1233 LEU cc_start: 0.7244 (mm) cc_final: 0.6871 (tp) REVERT: D 1244 MET cc_start: 0.5975 (ptp) cc_final: 0.5086 (mmt) REVERT: D 1445 GLU cc_start: 0.7383 (pm20) cc_final: 0.6916 (pt0) REVERT: D 1460 ASP cc_start: 0.7053 (t70) cc_final: 0.6801 (t0) REVERT: D 1480 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7193 (ttp80) outliers start: 133 outliers final: 61 residues processed: 577 average time/residue: 1.9183 time to fit residues: 1334.8793 Evaluate side-chains 534 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 454 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 324 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 157 optimal weight: 0.0040 chunk 103 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 412 optimal weight: 1.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN B 893 GLN C 514 HIS C 893 GLN D 893 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43668 Z= 0.241 Angle : 0.553 8.001 59372 Z= 0.290 Chirality : 0.041 0.174 6740 Planarity : 0.004 0.048 7504 Dihedral : 8.522 85.152 7056 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 2.68 % Allowed : 15.12 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.12), residues: 5432 helix: 1.85 (0.09), residues: 2996 sheet: -1.03 (0.25), residues: 388 loop : -0.64 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1124 HIS 0.011 0.001 HIS D 514 PHE 0.018 0.002 PHE C1068 TYR 0.016 0.002 TYR B 917 ARG 0.010 0.001 ARG B 594 *********************** 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 575 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 461 time to evaluate : 4.544 Fit side-chains REVERT: A 74 ASP cc_start: 0.7260 (m-30) cc_final: 0.6739 (t0) REVERT: A 98 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7603 (p) REVERT: A 139 ASP cc_start: 0.7728 (m-30) cc_final: 0.7335 (m-30) REVERT: A 240 HIS cc_start: 0.6766 (m-70) cc_final: 0.6316 (m-70) REVERT: A 284 GLN cc_start: 0.7085 (mt0) cc_final: 0.6843 (mt0) REVERT: A 352 GLN cc_start: 0.7493 (tt0) cc_final: 0.6639 (mt0) REVERT: A 356 GLN cc_start: 0.7122 (mt0) cc_final: 0.6762 (mm-40) REVERT: A 506 ARG cc_start: 0.5878 (mtp85) cc_final: 0.5609 (ttt-90) REVERT: A 618 HIS cc_start: 0.5669 (t70) cc_final: 0.4604 (m170) REVERT: A 663 LYS cc_start: 0.6502 (mmmt) cc_final: 0.5727 (mttt) REVERT: A 666 GLU cc_start: 0.6335 (pt0) cc_final: 0.6014 (tt0) REVERT: A 682 HIS cc_start: 0.6331 (t-90) cc_final: 0.6001 (t-90) REVERT: A 731 LYS cc_start: 0.6908 (ttpt) cc_final: 0.6515 (mttp) REVERT: A 829 GLU cc_start: 0.6762 (mt-10) cc_final: 0.5972 (mm-30) REVERT: A 849 GLU cc_start: 0.7184 (tp30) cc_final: 0.6797 (tp30) REVERT: A 875 MET cc_start: 0.6646 (ptt) cc_final: 0.6255 (ptp) REVERT: A 969 ARG cc_start: 0.6878 (mtp180) cc_final: 0.6166 (mtm-85) REVERT: A 1039 ASP cc_start: 0.7473 (m-30) cc_final: 0.7194 (m-30) REVERT: A 1046 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: A 1062 GLU cc_start: 0.6597 (tt0) cc_final: 0.6214 (tt0) REVERT: A 1064 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6368 (mttt) REVERT: A 1085 ARG cc_start: 0.4821 (ttt90) cc_final: 0.4314 (tpt170) REVERT: A 1105 THR cc_start: 0.6059 (m) cc_final: 0.5577 (p) REVERT: A 1130 GLU cc_start: 0.6392 (mt-10) cc_final: 0.5758 (mm-30) REVERT: A 1145 GLN cc_start: 0.7266 (tt0) cc_final: 0.6576 (mt0) REVERT: A 1150 MET cc_start: 0.7189 (mmt) cc_final: 0.6959 (mtp) REVERT: A 1152 GLN cc_start: 0.6764 (mt0) cc_final: 0.6455 (mt0) REVERT: A 1233 LEU cc_start: 0.7234 (mm) cc_final: 0.6856 (tp) REVERT: A 1244 MET cc_start: 0.5925 (ptp) cc_final: 0.5065 (mmt) REVERT: A 1445 GLU cc_start: 0.7379 (pm20) cc_final: 0.6941 (pt0) REVERT: A 1480 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7206 (ttp80) REVERT: B 74 ASP cc_start: 0.7263 (m-30) cc_final: 0.6738 (t0) REVERT: B 98 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7600 (p) REVERT: B 139 ASP cc_start: 0.7727 (m-30) cc_final: 0.7334 (m-30) REVERT: B 240 HIS cc_start: 0.6759 (m-70) cc_final: 0.6306 (m-70) REVERT: B 284 GLN cc_start: 0.7087 (mt0) cc_final: 0.6821 (mt0) REVERT: B 352 GLN cc_start: 0.7488 (tt0) cc_final: 0.6613 (mt0) REVERT: B 356 GLN cc_start: 0.7041 (mt0) cc_final: 0.6691 (mm-40) REVERT: B 506 ARG cc_start: 0.5881 (mtp85) cc_final: 0.5610 (ttt-90) REVERT: B 663 LYS cc_start: 0.6573 (mmmt) cc_final: 0.5670 (mmtp) REVERT: B 682 HIS cc_start: 0.6339 (t-90) cc_final: 0.6008 (t-90) REVERT: B 731 LYS cc_start: 0.6932 (ttpt) cc_final: 0.6552 (mttp) REVERT: B 829 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5933 (mm-30) REVERT: B 849 GLU cc_start: 0.7189 (tp30) cc_final: 0.6804 (tp30) REVERT: B 875 MET cc_start: 0.6646 (ptt) cc_final: 0.6256 (ptp) REVERT: B 1005 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5546 (mt-10) REVERT: B 1046 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6500 (mt-10) REVERT: B 1062 GLU cc_start: 0.6600 (tt0) cc_final: 0.6217 (tt0) REVERT: B 1064 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6367 (mttt) REVERT: B 1085 ARG cc_start: 0.4825 (ttt90) cc_final: 0.4306 (tpt170) REVERT: B 1105 THR cc_start: 0.6059 (m) cc_final: 0.5578 (p) REVERT: B 1130 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5750 (mm-30) REVERT: B 1145 GLN cc_start: 0.7271 (tt0) cc_final: 0.6553 (mt0) REVERT: B 1152 GLN cc_start: 0.6818 (mt0) cc_final: 0.6458 (mt0) REVERT: B 1233 LEU cc_start: 0.7233 (mm) cc_final: 0.6852 (tp) REVERT: B 1244 MET cc_start: 0.5875 (ptp) cc_final: 0.4981 (mmt) REVERT: B 1445 GLU cc_start: 0.7388 (pm20) cc_final: 0.6941 (pt0) REVERT: B 1480 ARG cc_start: 0.7595 (ttp-170) cc_final: 0.7196 (ttp80) REVERT: C 74 ASP cc_start: 0.7277 (m-30) cc_final: 0.6752 (t0) REVERT: C 98 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7656 (p) REVERT: C 139 ASP cc_start: 0.7724 (m-30) cc_final: 0.7326 (m-30) REVERT: C 240 HIS cc_start: 0.6712 (m-70) cc_final: 0.6298 (m-70) REVERT: C 284 GLN cc_start: 0.7087 (mt0) cc_final: 0.6824 (mt0) REVERT: C 352 GLN cc_start: 0.7486 (tt0) cc_final: 0.6613 (mt0) REVERT: C 356 GLN cc_start: 0.7038 (mt0) cc_final: 0.6689 (mm-40) REVERT: C 365 GLN cc_start: 0.6598 (mt0) cc_final: 0.5501 (mp10) REVERT: C 506 ARG cc_start: 0.5863 (mtp85) cc_final: 0.5587 (ttt-90) REVERT: C 618 HIS cc_start: 0.5775 (t70) cc_final: 0.4702 (m170) REVERT: C 663 LYS cc_start: 0.6632 (mmmt) cc_final: 0.5696 (mttt) REVERT: C 682 HIS cc_start: 0.6339 (t-90) cc_final: 0.6011 (t-90) REVERT: C 731 LYS cc_start: 0.6954 (ttpt) cc_final: 0.6550 (mttp) REVERT: C 829 GLU cc_start: 0.6767 (mt-10) cc_final: 0.5971 (mm-30) REVERT: C 849 GLU cc_start: 0.7189 (tp30) cc_final: 0.6801 (tp30) REVERT: C 875 MET cc_start: 0.6647 (ptt) cc_final: 0.6256 (ptp) REVERT: C 1046 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: C 1062 GLU cc_start: 0.6600 (tt0) cc_final: 0.6217 (tt0) REVERT: C 1064 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6369 (mttt) REVERT: C 1085 ARG cc_start: 0.4864 (ttt90) cc_final: 0.4361 (tpt170) REVERT: C 1105 THR cc_start: 0.6058 (m) cc_final: 0.5575 (p) REVERT: C 1145 GLN cc_start: 0.7194 (tt0) cc_final: 0.6598 (mt0) REVERT: C 1152 GLN cc_start: 0.6779 (mt0) cc_final: 0.6458 (mt0) REVERT: C 1233 LEU cc_start: 0.7232 (mm) cc_final: 0.6852 (tp) REVERT: C 1244 MET cc_start: 0.5876 (ptp) cc_final: 0.4983 (mmt) REVERT: C 1445 GLU cc_start: 0.7393 (pm20) cc_final: 0.6943 (pt0) REVERT: C 1480 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7197 (ttp80) REVERT: D 74 ASP cc_start: 0.7285 (m-30) cc_final: 0.6803 (t0) REVERT: D 77 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6832 (mmtt) REVERT: D 98 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7594 (p) REVERT: D 139 ASP cc_start: 0.7729 (m-30) cc_final: 0.7336 (m-30) REVERT: D 240 HIS cc_start: 0.6759 (m-70) cc_final: 0.6306 (m-70) REVERT: D 284 GLN cc_start: 0.7087 (mt0) cc_final: 0.6846 (mt0) REVERT: D 352 GLN cc_start: 0.7487 (tt0) cc_final: 0.6617 (mt0) REVERT: D 356 GLN cc_start: 0.7038 (mt0) cc_final: 0.6688 (mm-40) REVERT: D 433 GLU cc_start: 0.7219 (tt0) cc_final: 0.6873 (mm-30) REVERT: D 506 ARG cc_start: 0.5883 (mtp85) cc_final: 0.5612 (ttt-90) REVERT: D 663 LYS cc_start: 0.6574 (mmmt) cc_final: 0.5671 (mmtp) REVERT: D 682 HIS cc_start: 0.6336 (t-90) cc_final: 0.6008 (t-90) REVERT: D 731 LYS cc_start: 0.6954 (ttpt) cc_final: 0.6550 (mttp) REVERT: D 829 GLU cc_start: 0.6743 (mt-10) cc_final: 0.5956 (mm-30) REVERT: D 849 GLU cc_start: 0.7188 (tp30) cc_final: 0.6805 (tp30) REVERT: D 875 MET cc_start: 0.6648 (ptt) cc_final: 0.6256 (ptp) REVERT: D 969 ARG cc_start: 0.6896 (mtp180) cc_final: 0.6088 (mtm-85) REVERT: D 1039 ASP cc_start: 0.7434 (m-30) cc_final: 0.7152 (m-30) REVERT: D 1046 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: D 1062 GLU cc_start: 0.6598 (tt0) cc_final: 0.6218 (tt0) REVERT: D 1064 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6388 (mttt) REVERT: D 1085 ARG cc_start: 0.4826 (ttt90) cc_final: 0.4308 (tpt170) REVERT: D 1105 THR cc_start: 0.6058 (m) cc_final: 0.5574 (p) REVERT: D 1126 ARG cc_start: 0.5447 (mtp-110) cc_final: 0.5153 (mtp-110) REVERT: D 1130 GLU cc_start: 0.6422 (mt-10) cc_final: 0.5783 (mm-30) REVERT: D 1145 GLN cc_start: 0.7253 (tt0) cc_final: 0.6565 (mt0) REVERT: D 1150 MET cc_start: 0.7664 (tpp) cc_final: 0.7195 (mtp) REVERT: D 1152 GLN cc_start: 0.6698 (mt0) cc_final: 0.6383 (mt0) REVERT: D 1233 LEU cc_start: 0.7230 (mm) cc_final: 0.6850 (tp) REVERT: D 1244 MET cc_start: 0.5880 (ptp) cc_final: 0.4977 (mmt) REVERT: D 1445 GLU cc_start: 0.7395 (pm20) cc_final: 0.6945 (pt0) REVERT: D 1480 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7199 (ttp80) outliers start: 114 outliers final: 69 residues processed: 551 average time/residue: 1.9485 time to fit residues: 1289.1317 Evaluate side-chains 524 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 441 time to evaluate : 5.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1274 LYS Chi-restraints excluded: chain B residue 1277 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1274 LYS Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1274 LYS Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 476 optimal weight: 0.0370 chunk 502 optimal weight: 1.9990 chunk 458 optimal weight: 2.9990 chunk 488 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 383 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 441 optimal weight: 4.9990 chunk 462 optimal weight: 0.6980 chunk 486 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN B 893 GLN C 514 HIS C 893 GLN D 893 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43668 Z= 0.175 Angle : 0.510 7.802 59372 Z= 0.267 Chirality : 0.039 0.170 6740 Planarity : 0.004 0.048 7504 Dihedral : 8.177 84.179 7056 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 2.16 % Allowed : 15.90 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.12), residues: 5432 helix: 2.00 (0.09), residues: 3000 sheet: -1.20 (0.24), residues: 376 loop : -0.53 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.010 0.001 HIS B 514 PHE 0.015 0.001 PHE C1068 TYR 0.012 0.001 TYR B 917 ARG 0.012 0.000 ARG C 594 *********************** 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 557 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 465 time to evaluate : 4.855 Fit side-chains REVERT: A 74 ASP cc_start: 0.7268 (m-30) cc_final: 0.6747 (t0) REVERT: A 98 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7636 (p) REVERT: A 139 ASP cc_start: 0.7689 (m-30) cc_final: 0.7332 (m-30) REVERT: A 233 ILE cc_start: 0.7616 (mm) cc_final: 0.7294 (mm) REVERT: A 240 HIS cc_start: 0.6605 (m-70) cc_final: 0.6223 (m90) REVERT: A 284 GLN cc_start: 0.7135 (mt0) cc_final: 0.6929 (mt0) REVERT: A 352 GLN cc_start: 0.7511 (tt0) cc_final: 0.6628 (mt0) REVERT: A 356 GLN cc_start: 0.7154 (mt0) cc_final: 0.6788 (mm-40) REVERT: A 506 ARG cc_start: 0.5880 (mtp85) cc_final: 0.5577 (ttt-90) REVERT: A 595 ARG cc_start: 0.6008 (mtt180) cc_final: 0.5772 (mtt180) REVERT: A 663 LYS cc_start: 0.6477 (mmmt) cc_final: 0.5695 (mttp) REVERT: A 682 HIS cc_start: 0.6350 (t-90) cc_final: 0.6009 (t-90) REVERT: A 731 LYS cc_start: 0.6974 (ttpt) cc_final: 0.6592 (mttp) REVERT: A 829 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6030 (mm-30) REVERT: A 849 GLU cc_start: 0.7181 (tp30) cc_final: 0.6790 (tp30) REVERT: A 870 ARG cc_start: 0.6354 (mtt180) cc_final: 0.5876 (mtt180) REVERT: A 875 MET cc_start: 0.6560 (ptt) cc_final: 0.6220 (ptp) REVERT: A 969 ARG cc_start: 0.6847 (mtp180) cc_final: 0.6107 (mtm-85) REVERT: A 1039 ASP cc_start: 0.7464 (m-30) cc_final: 0.7198 (m-30) REVERT: A 1046 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: A 1062 GLU cc_start: 0.6596 (tt0) cc_final: 0.6292 (tt0) REVERT: A 1064 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6364 (mttt) REVERT: A 1085 ARG cc_start: 0.4947 (ttt90) cc_final: 0.4364 (tpt170) REVERT: A 1105 THR cc_start: 0.6037 (m) cc_final: 0.5560 (p) REVERT: A 1127 GLU cc_start: 0.5871 (mt-10) cc_final: 0.5484 (pt0) REVERT: A 1130 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5769 (mm-30) REVERT: A 1145 GLN cc_start: 0.7191 (tt0) cc_final: 0.6516 (mt0) REVERT: A 1152 GLN cc_start: 0.6799 (mt0) cc_final: 0.6472 (mt0) REVERT: A 1233 LEU cc_start: 0.7128 (mm) cc_final: 0.6732 (tp) REVERT: A 1244 MET cc_start: 0.5822 (ptp) cc_final: 0.4978 (mmt) REVERT: A 1445 GLU cc_start: 0.7363 (pm20) cc_final: 0.6913 (pt0) REVERT: A 1480 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7204 (ttp80) REVERT: B 74 ASP cc_start: 0.7269 (m-30) cc_final: 0.6740 (t0) REVERT: B 98 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7637 (p) REVERT: B 139 ASP cc_start: 0.7691 (m-30) cc_final: 0.7333 (m-30) REVERT: B 233 ILE cc_start: 0.7610 (mm) cc_final: 0.7288 (mm) REVERT: B 240 HIS cc_start: 0.6718 (m-70) cc_final: 0.6251 (m-70) REVERT: B 284 GLN cc_start: 0.7138 (mt0) cc_final: 0.6934 (mt0) REVERT: B 352 GLN cc_start: 0.7492 (tt0) cc_final: 0.6604 (mt0) REVERT: B 356 GLN cc_start: 0.7038 (mt0) cc_final: 0.6674 (mm-40) REVERT: B 506 ARG cc_start: 0.5882 (mtp85) cc_final: 0.5617 (ttt-90) REVERT: B 663 LYS cc_start: 0.6537 (mmmt) cc_final: 0.5642 (mmtp) REVERT: B 682 HIS cc_start: 0.6351 (t-90) cc_final: 0.6008 (t-90) REVERT: B 731 LYS cc_start: 0.6944 (ttpt) cc_final: 0.6461 (mptt) REVERT: B 829 GLU cc_start: 0.6736 (mt-10) cc_final: 0.5986 (mm-30) REVERT: B 849 GLU cc_start: 0.7186 (tp30) cc_final: 0.6799 (tp30) REVERT: B 870 ARG cc_start: 0.6343 (mtt180) cc_final: 0.5857 (mtt180) REVERT: B 875 MET cc_start: 0.6557 (ptt) cc_final: 0.6219 (ptp) REVERT: B 969 ARG cc_start: 0.6908 (mtp180) cc_final: 0.6094 (mtm-85) REVERT: B 1005 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5524 (mt-10) REVERT: B 1039 ASP cc_start: 0.7481 (m-30) cc_final: 0.7223 (m-30) REVERT: B 1046 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: B 1062 GLU cc_start: 0.6598 (tt0) cc_final: 0.6294 (tt0) REVERT: B 1064 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6368 (mttt) REVERT: B 1085 ARG cc_start: 0.4936 (ttt90) cc_final: 0.4402 (tpt170) REVERT: B 1105 THR cc_start: 0.6036 (m) cc_final: 0.5560 (p) REVERT: B 1145 GLN cc_start: 0.7190 (tt0) cc_final: 0.6523 (mt0) REVERT: B 1152 GLN cc_start: 0.6829 (mt0) cc_final: 0.6499 (mt0) REVERT: B 1233 LEU cc_start: 0.7168 (mm) cc_final: 0.6782 (tp) REVERT: B 1244 MET cc_start: 0.5713 (ptp) cc_final: 0.4844 (mmt) REVERT: B 1445 GLU cc_start: 0.7403 (pm20) cc_final: 0.6961 (pt0) REVERT: B 1480 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7190 (ttp80) REVERT: C 74 ASP cc_start: 0.7266 (m-30) cc_final: 0.6744 (t0) REVERT: C 98 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7654 (p) REVERT: C 139 ASP cc_start: 0.7688 (m-30) cc_final: 0.7328 (m-30) REVERT: C 233 ILE cc_start: 0.7612 (mm) cc_final: 0.7299 (mm) REVERT: C 240 HIS cc_start: 0.6677 (m-70) cc_final: 0.6241 (m-70) REVERT: C 284 GLN cc_start: 0.7140 (mt0) cc_final: 0.6937 (mt0) REVERT: C 352 GLN cc_start: 0.7492 (tt0) cc_final: 0.6608 (mt0) REVERT: C 356 GLN cc_start: 0.7032 (mt0) cc_final: 0.6656 (mm-40) REVERT: C 506 ARG cc_start: 0.5880 (mtp85) cc_final: 0.5576 (ttt-90) REVERT: C 663 LYS cc_start: 0.6609 (mmmt) cc_final: 0.5677 (mttt) REVERT: C 682 HIS cc_start: 0.6350 (t-90) cc_final: 0.6009 (t-90) REVERT: C 731 LYS cc_start: 0.6949 (ttpt) cc_final: 0.6461 (mptt) REVERT: C 829 GLU cc_start: 0.6744 (mt-10) cc_final: 0.5991 (mm-30) REVERT: C 849 GLU cc_start: 0.7186 (tp30) cc_final: 0.6794 (tp30) REVERT: C 870 ARG cc_start: 0.6346 (mtt180) cc_final: 0.5864 (mtt180) REVERT: C 875 MET cc_start: 0.6558 (ptt) cc_final: 0.6220 (ptp) REVERT: C 1039 ASP cc_start: 0.7485 (m-30) cc_final: 0.7226 (m-30) REVERT: C 1046 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: C 1062 GLU cc_start: 0.6601 (tt0) cc_final: 0.6296 (tt0) REVERT: C 1064 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6366 (mttt) REVERT: C 1085 ARG cc_start: 0.4955 (ttt90) cc_final: 0.4375 (tpt170) REVERT: C 1105 THR cc_start: 0.6036 (m) cc_final: 0.5559 (p) REVERT: C 1127 GLU cc_start: 0.5830 (mt-10) cc_final: 0.5463 (pt0) REVERT: C 1145 GLN cc_start: 0.7155 (tt0) cc_final: 0.6599 (mt0) REVERT: C 1152 GLN cc_start: 0.6797 (mt0) cc_final: 0.6501 (mt0) REVERT: C 1233 LEU cc_start: 0.7178 (mm) cc_final: 0.6781 (tp) REVERT: C 1244 MET cc_start: 0.5711 (ptp) cc_final: 0.4844 (mmt) REVERT: C 1445 GLU cc_start: 0.7408 (pm20) cc_final: 0.6963 (pt0) REVERT: C 1480 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7194 (ttp80) REVERT: D 74 ASP cc_start: 0.7263 (m-30) cc_final: 0.6737 (t0) REVERT: D 98 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7629 (p) REVERT: D 139 ASP cc_start: 0.7690 (m-30) cc_final: 0.7332 (m-30) REVERT: D 233 ILE cc_start: 0.7597 (mm) cc_final: 0.7281 (mm) REVERT: D 240 HIS cc_start: 0.6752 (m-70) cc_final: 0.6312 (m-70) REVERT: D 284 GLN cc_start: 0.7140 (mt0) cc_final: 0.6935 (mt0) REVERT: D 352 GLN cc_start: 0.7494 (tt0) cc_final: 0.6610 (mt0) REVERT: D 356 GLN cc_start: 0.7035 (mt0) cc_final: 0.6674 (mm-40) REVERT: D 506 ARG cc_start: 0.5882 (mtp85) cc_final: 0.5617 (ttt-90) REVERT: D 595 ARG cc_start: 0.6007 (mtt180) cc_final: 0.5779 (mtt180) REVERT: D 663 LYS cc_start: 0.6538 (mmmt) cc_final: 0.5642 (mmtp) REVERT: D 682 HIS cc_start: 0.6349 (t-90) cc_final: 0.6007 (t-90) REVERT: D 731 LYS cc_start: 0.6944 (ttpt) cc_final: 0.6456 (mptt) REVERT: D 829 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6008 (mm-30) REVERT: D 849 GLU cc_start: 0.7186 (tp30) cc_final: 0.6798 (tp30) REVERT: D 870 ARG cc_start: 0.6344 (mtt180) cc_final: 0.5858 (mtt180) REVERT: D 875 MET cc_start: 0.6560 (ptt) cc_final: 0.6220 (ptp) REVERT: D 969 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6038 (mtm-85) REVERT: D 1039 ASP cc_start: 0.7487 (m-30) cc_final: 0.7227 (m-30) REVERT: D 1046 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: D 1062 GLU cc_start: 0.6598 (tt0) cc_final: 0.6296 (tt0) REVERT: D 1064 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6369 (mttt) REVERT: D 1085 ARG cc_start: 0.4933 (ttt90) cc_final: 0.4401 (tpt170) REVERT: D 1105 THR cc_start: 0.6037 (m) cc_final: 0.5555 (p) REVERT: D 1126 ARG cc_start: 0.5440 (mtp-110) cc_final: 0.5131 (mtp-110) REVERT: D 1127 GLU cc_start: 0.5879 (mt-10) cc_final: 0.5510 (pt0) REVERT: D 1130 GLU cc_start: 0.6368 (mt-10) cc_final: 0.5780 (mm-30) REVERT: D 1145 GLN cc_start: 0.7185 (tt0) cc_final: 0.6551 (mt0) REVERT: D 1150 MET cc_start: 0.7671 (tpp) cc_final: 0.7252 (mtp) REVERT: D 1152 GLN cc_start: 0.6783 (mt0) cc_final: 0.6500 (mt0) REVERT: D 1233 LEU cc_start: 0.7167 (mm) cc_final: 0.6782 (tp) REVERT: D 1244 MET cc_start: 0.5711 (ptp) cc_final: 0.4844 (mmt) REVERT: D 1445 GLU cc_start: 0.7408 (pm20) cc_final: 0.6964 (pt0) REVERT: D 1480 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7200 (ttp80) outliers start: 92 outliers final: 61 residues processed: 540 average time/residue: 1.8889 time to fit residues: 1224.4140 Evaluate side-chains 516 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 442 time to evaluate : 5.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 477 LYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 320 optimal weight: 8.9990 chunk 516 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 245 optimal weight: 0.0270 chunk 359 optimal weight: 0.6980 chunk 541 optimal weight: 6.9990 chunk 498 optimal weight: 0.8980 chunk 431 optimal weight: 0.9980 chunk 44 optimal weight: 0.0670 chunk 333 optimal weight: 0.7980 chunk 264 optimal weight: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN B 448 ASN B 893 GLN C 514 HIS C 893 GLN D 893 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43668 Z= 0.151 Angle : 0.495 8.203 59372 Z= 0.259 Chirality : 0.038 0.167 6740 Planarity : 0.004 0.047 7504 Dihedral : 7.907 83.275 7056 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 1.76 % Allowed : 16.42 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.12), residues: 5432 helix: 2.11 (0.09), residues: 3028 sheet: -1.20 (0.24), residues: 376 loop : -0.46 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.011 0.001 HIS D 514 PHE 0.015 0.001 PHE A1068 TYR 0.011 0.001 TYR A 917 ARG 0.011 0.000 ARG D 594 ********************** 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 538 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 463 time to evaluate : 4.748 Fit side-chains REVERT: A 74 ASP cc_start: 0.7243 (m-30) cc_final: 0.6701 (t0) REVERT: A 98 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7620 (p) REVERT: A 139 ASP cc_start: 0.7744 (m-30) cc_final: 0.7407 (m-30) REVERT: A 233 ILE cc_start: 0.7558 (mm) cc_final: 0.7246 (mm) REVERT: A 240 HIS cc_start: 0.6605 (m-70) cc_final: 0.6204 (m90) REVERT: A 284 GLN cc_start: 0.7160 (mt0) cc_final: 0.6957 (mt0) REVERT: A 352 GLN cc_start: 0.7486 (tt0) cc_final: 0.6626 (mt0) REVERT: A 356 GLN cc_start: 0.7167 (mt0) cc_final: 0.6768 (mm-40) REVERT: A 506 ARG cc_start: 0.5761 (mtp85) cc_final: 0.5439 (ttt-90) REVERT: A 595 ARG cc_start: 0.5991 (mtt180) cc_final: 0.5766 (mtt180) REVERT: A 663 LYS cc_start: 0.6570 (mmmt) cc_final: 0.5623 (mttp) REVERT: A 682 HIS cc_start: 0.6341 (t-90) cc_final: 0.5997 (t-90) REVERT: A 731 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6614 (mttp) REVERT: A 829 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6059 (mm-30) REVERT: A 849 GLU cc_start: 0.7181 (tp30) cc_final: 0.6790 (tp30) REVERT: A 870 ARG cc_start: 0.6275 (mtt180) cc_final: 0.5823 (mtt180) REVERT: A 875 MET cc_start: 0.6563 (ptt) cc_final: 0.6256 (ptp) REVERT: A 969 ARG cc_start: 0.6857 (mtp180) cc_final: 0.6041 (mtm-85) REVERT: A 1039 ASP cc_start: 0.7450 (m-30) cc_final: 0.7186 (m-30) REVERT: A 1046 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6331 (mt-10) REVERT: A 1062 GLU cc_start: 0.6654 (tt0) cc_final: 0.6316 (tt0) REVERT: A 1064 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6292 (mttt) REVERT: A 1085 ARG cc_start: 0.4975 (ttt90) cc_final: 0.4410 (tpt170) REVERT: A 1105 THR cc_start: 0.6054 (m) cc_final: 0.5572 (p) REVERT: A 1127 GLU cc_start: 0.5732 (mt-10) cc_final: 0.5410 (pt0) REVERT: A 1130 GLU cc_start: 0.6239 (mt-10) cc_final: 0.5677 (mm-30) REVERT: A 1145 GLN cc_start: 0.7161 (tt0) cc_final: 0.6537 (mt0) REVERT: A 1152 GLN cc_start: 0.6878 (mt0) cc_final: 0.6568 (mt0) REVERT: A 1233 LEU cc_start: 0.7049 (mm) cc_final: 0.6675 (tp) REVERT: A 1244 MET cc_start: 0.5582 (ptp) cc_final: 0.4866 (mmt) REVERT: A 1445 GLU cc_start: 0.7366 (pm20) cc_final: 0.6937 (mm-30) REVERT: A 1480 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7204 (ttp80) REVERT: B 74 ASP cc_start: 0.7244 (m-30) cc_final: 0.6701 (t0) REVERT: B 98 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7615 (p) REVERT: B 139 ASP cc_start: 0.7744 (m-30) cc_final: 0.7407 (m-30) REVERT: B 233 ILE cc_start: 0.7549 (mm) cc_final: 0.7226 (mm) REVERT: B 240 HIS cc_start: 0.6676 (m-70) cc_final: 0.6255 (m90) REVERT: B 284 GLN cc_start: 0.7167 (mt0) cc_final: 0.6937 (mt0) REVERT: B 352 GLN cc_start: 0.7477 (tt0) cc_final: 0.6571 (mt0) REVERT: B 356 GLN cc_start: 0.7100 (mt0) cc_final: 0.6700 (mm-40) REVERT: B 464 GLU cc_start: 0.5968 (tp30) cc_final: 0.5448 (mm-30) REVERT: B 506 ARG cc_start: 0.5756 (mtp85) cc_final: 0.5439 (ttt-90) REVERT: B 566 ARG cc_start: 0.6114 (mpp-170) cc_final: 0.5796 (mpp-170) REVERT: B 663 LYS cc_start: 0.6634 (mmmt) cc_final: 0.5638 (mmtp) REVERT: B 682 HIS cc_start: 0.6348 (t-90) cc_final: 0.5985 (t-90) REVERT: B 731 LYS cc_start: 0.6987 (ttpt) cc_final: 0.6500 (mptt) REVERT: B 829 GLU cc_start: 0.6776 (mt-10) cc_final: 0.5998 (mm-30) REVERT: B 849 GLU cc_start: 0.7187 (tp30) cc_final: 0.6799 (tp30) REVERT: B 870 ARG cc_start: 0.6273 (mtt180) cc_final: 0.5824 (mtt180) REVERT: B 875 MET cc_start: 0.6562 (ptt) cc_final: 0.6225 (ptp) REVERT: B 969 ARG cc_start: 0.6877 (mtp180) cc_final: 0.6044 (mtm-85) REVERT: B 1005 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5546 (mt-10) REVERT: B 1039 ASP cc_start: 0.7467 (m-30) cc_final: 0.7191 (m-30) REVERT: B 1046 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: B 1062 GLU cc_start: 0.6653 (tt0) cc_final: 0.6315 (tt0) REVERT: B 1064 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6291 (mttt) REVERT: B 1085 ARG cc_start: 0.4997 (ttt90) cc_final: 0.4429 (tpt170) REVERT: B 1105 THR cc_start: 0.6053 (m) cc_final: 0.5574 (p) REVERT: B 1126 ARG cc_start: 0.5423 (mtp-110) cc_final: 0.5203 (mtp-110) REVERT: B 1127 GLU cc_start: 0.5748 (mt-10) cc_final: 0.5437 (pt0) REVERT: B 1145 GLN cc_start: 0.7183 (tt0) cc_final: 0.6546 (mt0) REVERT: B 1152 GLN cc_start: 0.6849 (mt0) cc_final: 0.6550 (mt0) REVERT: B 1233 LEU cc_start: 0.7060 (mm) cc_final: 0.6686 (tp) REVERT: B 1244 MET cc_start: 0.5598 (ptp) cc_final: 0.4837 (mmt) REVERT: B 1445 GLU cc_start: 0.7395 (pm20) cc_final: 0.7010 (pt0) REVERT: B 1460 ASP cc_start: 0.7130 (t70) cc_final: 0.6879 (t0) REVERT: B 1480 ARG cc_start: 0.7575 (ttp-170) cc_final: 0.7187 (ttp80) REVERT: C 74 ASP cc_start: 0.7249 (m-30) cc_final: 0.6705 (t0) REVERT: C 98 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7635 (p) REVERT: C 139 ASP cc_start: 0.7743 (m-30) cc_final: 0.7411 (m-30) REVERT: C 233 ILE cc_start: 0.7539 (mm) cc_final: 0.7240 (mm) REVERT: C 240 HIS cc_start: 0.6578 (m-70) cc_final: 0.6200 (m90) REVERT: C 284 GLN cc_start: 0.7168 (mt0) cc_final: 0.6941 (mt0) REVERT: C 352 GLN cc_start: 0.7476 (tt0) cc_final: 0.6571 (mt0) REVERT: C 356 GLN cc_start: 0.7099 (mt0) cc_final: 0.6699 (mm-40) REVERT: C 506 ARG cc_start: 0.5765 (mtp85) cc_final: 0.5442 (ttt-90) REVERT: C 577 ASP cc_start: 0.6096 (t0) cc_final: 0.5705 (t70) REVERT: C 663 LYS cc_start: 0.6559 (mmmt) cc_final: 0.5642 (mttt) REVERT: C 682 HIS cc_start: 0.6336 (t-90) cc_final: 0.5995 (t-90) REVERT: C 731 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6605 (mttp) REVERT: C 829 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6041 (mm-30) REVERT: C 849 GLU cc_start: 0.7184 (tp30) cc_final: 0.6793 (tp30) REVERT: C 870 ARG cc_start: 0.6274 (mtt180) cc_final: 0.5826 (mtt180) REVERT: C 875 MET cc_start: 0.6563 (ptt) cc_final: 0.6255 (ptp) REVERT: C 1039 ASP cc_start: 0.7471 (m-30) cc_final: 0.7194 (m-30) REVERT: C 1046 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: C 1062 GLU cc_start: 0.6655 (tt0) cc_final: 0.6317 (tt0) REVERT: C 1064 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6293 (mttt) REVERT: C 1085 ARG cc_start: 0.4962 (ttt90) cc_final: 0.4403 (tpt170) REVERT: C 1105 THR cc_start: 0.6018 (m) cc_final: 0.5544 (p) REVERT: C 1127 GLU cc_start: 0.5813 (mt-10) cc_final: 0.5476 (pt0) REVERT: C 1145 GLN cc_start: 0.7118 (tt0) cc_final: 0.6623 (mt0) REVERT: C 1152 GLN cc_start: 0.6796 (mt0) cc_final: 0.6503 (mt0) REVERT: C 1157 MET cc_start: 0.7842 (mmt) cc_final: 0.7594 (mmt) REVERT: C 1233 LEU cc_start: 0.7061 (mm) cc_final: 0.6686 (tp) REVERT: C 1244 MET cc_start: 0.5596 (ptp) cc_final: 0.4838 (mmt) REVERT: C 1445 GLU cc_start: 0.7415 (pm20) cc_final: 0.7013 (pt0) REVERT: C 1460 ASP cc_start: 0.7129 (t70) cc_final: 0.6881 (t0) REVERT: C 1480 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.7187 (ttp80) REVERT: D 74 ASP cc_start: 0.7243 (m-30) cc_final: 0.6698 (t0) REVERT: D 98 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7625 (p) REVERT: D 139 ASP cc_start: 0.7746 (m-30) cc_final: 0.7406 (m-30) REVERT: D 233 ILE cc_start: 0.7544 (mm) cc_final: 0.7212 (mm) REVERT: D 240 HIS cc_start: 0.6609 (m-70) cc_final: 0.6218 (m90) REVERT: D 284 GLN cc_start: 0.7168 (mt0) cc_final: 0.6939 (mt0) REVERT: D 352 GLN cc_start: 0.7477 (tt0) cc_final: 0.6572 (mt0) REVERT: D 356 GLN cc_start: 0.7097 (mt0) cc_final: 0.6698 (mm-40) REVERT: D 464 GLU cc_start: 0.6010 (tp30) cc_final: 0.5494 (mm-30) REVERT: D 506 ARG cc_start: 0.5758 (mtp85) cc_final: 0.5438 (ttt-90) REVERT: D 566 ARG cc_start: 0.6114 (mpp-170) cc_final: 0.5797 (mpp-170) REVERT: D 595 ARG cc_start: 0.5989 (mtt180) cc_final: 0.5764 (mtt180) REVERT: D 663 LYS cc_start: 0.6635 (mmmt) cc_final: 0.5639 (mmtp) REVERT: D 682 HIS cc_start: 0.6336 (t-90) cc_final: 0.5993 (t-90) REVERT: D 731 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6603 (mttp) REVERT: D 829 GLU cc_start: 0.6777 (mt-10) cc_final: 0.5999 (mm-30) REVERT: D 849 GLU cc_start: 0.7186 (tp30) cc_final: 0.6799 (tp30) REVERT: D 870 ARG cc_start: 0.6273 (mtt180) cc_final: 0.5823 (mtt180) REVERT: D 875 MET cc_start: 0.6563 (ptt) cc_final: 0.6255 (ptp) REVERT: D 969 ARG cc_start: 0.6883 (mtp180) cc_final: 0.6010 (mtm-85) REVERT: D 1039 ASP cc_start: 0.7471 (m-30) cc_final: 0.7193 (m-30) REVERT: D 1046 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6412 (tt0) REVERT: D 1062 GLU cc_start: 0.6653 (tt0) cc_final: 0.6315 (tt0) REVERT: D 1064 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6314 (mttt) REVERT: D 1085 ARG cc_start: 0.4989 (ttt90) cc_final: 0.4420 (tpt170) REVERT: D 1105 THR cc_start: 0.6053 (m) cc_final: 0.5570 (p) REVERT: D 1126 ARG cc_start: 0.5438 (mtp-110) cc_final: 0.5228 (mtp-110) REVERT: D 1127 GLU cc_start: 0.5852 (mt-10) cc_final: 0.5517 (pt0) REVERT: D 1145 GLN cc_start: 0.7170 (tt0) cc_final: 0.6559 (mt0) REVERT: D 1150 MET cc_start: 0.7619 (tpp) cc_final: 0.7201 (mtp) REVERT: D 1152 GLN cc_start: 0.6774 (mt0) cc_final: 0.6492 (mt0) REVERT: D 1157 MET cc_start: 0.7799 (mmt) cc_final: 0.7567 (mmm) REVERT: D 1233 LEU cc_start: 0.7060 (mm) cc_final: 0.6684 (tp) REVERT: D 1244 MET cc_start: 0.5595 (ptp) cc_final: 0.4835 (mmt) REVERT: D 1445 GLU cc_start: 0.7401 (pm20) cc_final: 0.7012 (pt0) REVERT: D 1460 ASP cc_start: 0.7111 (t70) cc_final: 0.6862 (t0) REVERT: D 1480 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7188 (ttp80) outliers start: 75 outliers final: 49 residues processed: 525 average time/residue: 1.9256 time to fit residues: 1213.1260 Evaluate side-chains 511 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 449 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1046 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 1046 GLU Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 1046 GLU Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 342 optimal weight: 2.9990 chunk 459 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 397 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 432 optimal weight: 1.9990 chunk 180 optimal weight: 0.0970 chunk 443 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN B 448 ASN B 893 GLN C 514 HIS C 893 GLN D 893 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111187 restraints weight = 58495.874| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.46 r_work: 0.3176 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43668 Z= 0.287 Angle : 0.591 8.474 59372 Z= 0.307 Chirality : 0.042 0.177 6740 Planarity : 0.005 0.050 7504 Dihedral : 8.405 85.188 7056 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.00 % Allowed : 16.20 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 5432 helix: 1.92 (0.09), residues: 2996 sheet: -1.04 (0.24), residues: 388 loop : -0.59 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1124 HIS 0.011 0.001 HIS D 514 PHE 0.020 0.002 PHE A 604 TYR 0.020 0.002 TYR D 917 ARG 0.011 0.001 ARG B 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18971.96 seconds wall clock time: 340 minutes 21.88 seconds (20421.88 seconds total)