Starting phenix.real_space_refine on Mon Apr 15 17:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drj_7999/04_2024/6drj_7999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drj_7999/04_2024/6drj_7999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drj_7999/04_2024/6drj_7999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drj_7999/04_2024/6drj_7999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drj_7999/04_2024/6drj_7999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6drj_7999/04_2024/6drj_7999_updated.pdb" } resolution = 3.3 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= 0.031 sd= 0.778 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 Ca 4 9.91 5 P 8 5.49 5 S 148 5.16 5 C 22956 2.51 5 N 6328 2.21 5 O 6072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ARG 925": "NH1" <-> "NH2" Residue "A ARG 944": "NH1" <-> "NH2" Residue "A PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1162": "NH1" <-> "NH2" Residue "A ARG 1404": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ARG 515": "NH1" <-> "NH2" Residue "B TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 749": "NH1" <-> "NH2" Residue "B ARG 859": "NH1" <-> "NH2" Residue "B ARG 925": "NH1" <-> "NH2" Residue "B ARG 944": "NH1" <-> "NH2" Residue "B PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1162": "NH1" <-> "NH2" Residue "B ARG 1404": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 430": "NH1" <-> "NH2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 515": "NH1" <-> "NH2" Residue "C TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 749": "NH1" <-> "NH2" Residue "C ARG 859": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1162": "NH1" <-> "NH2" Residue "C ARG 1404": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 430": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D TYR 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 596": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 749": "NH1" <-> "NH2" Residue "D ARG 859": "NH1" <-> "NH2" Residue "D ARG 925": "NH1" <-> "NH2" Residue "D ARG 944": "NH1" <-> "NH2" Residue "D PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1162": "NH1" <-> "NH2" Residue "D ARG 1404": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 8842 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 51, 'TRANS': 1214} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1434 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1150 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 28, 'TYR:plan': 4, 'ASN:plan1': 19, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 12, 'GLU:plan': 71, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 902 Chain: "B" Number of atoms: 8842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 8842 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 51, 'TRANS': 1214} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1434 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1150 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 28, 'TYR:plan': 4, 'ASN:plan1': 19, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 12, 'GLU:plan': 71, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 902 Chain: "C" Number of atoms: 8842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 8842 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 51, 'TRANS': 1214} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1434 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1150 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 28, 'TYR:plan': 4, 'ASN:plan1': 19, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 12, 'GLU:plan': 71, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 902 Chain: "D" Number of atoms: 8842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 8842 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 51, 'TRANS': 1214} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1434 Unresolved non-hydrogen angles: 1799 Unresolved non-hydrogen dihedrals: 1150 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 28, 'TYR:plan': 4, 'ASN:plan1': 19, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 12, 'GLU:plan': 71, 'ASP:plan': 43} Unresolved non-hydrogen planarities: 902 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'APR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'APR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'APR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' CA': 1, 'APR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.31, per 1000 atoms: 0.54 Number of scatterers: 35516 At special positions: 0 Unit cell: (152.508, 151.434, 173.988, 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) Ca 4 19.99 S 148 16.00 P 8 15.00 O 6072 8.00 N 6328 7.00 C 22956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.02 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.02 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.02 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.25 Conformation dependent library (CDL) restraints added in 6.8 seconds 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 12 sheets defined 49.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.72 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.727A pdb=" N LYS A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.657A pdb=" N ALA A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.547A pdb=" N ASN A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 removed outlier: 5.085A pdb=" N SER A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 372 through 387 removed outlier: 4.775A pdb=" N GLN A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.813A pdb=" N ALA A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 4.300A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.946A pdb=" N SER A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.584A pdb=" N GLU A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 507 through 517 removed outlier: 3.765A pdb=" N GLN A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.950A pdb=" N GLU A 542 " --> pdb=" O HIS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 603 removed outlier: 3.866A pdb=" N PHE A 599 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 removed outlier: 4.206A pdb=" N GLU A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN A 617 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 637 Processing helix chain 'A' and resid 648 through 671 removed outlier: 3.802A pdb=" N SER A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.880A pdb=" N ILE A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 702 through 705 No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.698A pdb=" N LEU A 732 " --> pdb=" O HIS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.937A pdb=" N TYR A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 738 through 742' Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.771A pdb=" N ALA A 758 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 806 Processing helix chain 'A' and resid 809 through 832 removed outlier: 3.694A pdb=" N TYR A 814 " --> pdb=" O GLN A 810 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 819 " --> pdb=" O TRP A 815 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 863 removed outlier: 3.619A pdb=" N LEU A 845 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 846 " --> pdb=" O GLU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 877 removed outlier: 3.882A pdb=" N MET A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 901 removed outlier: 4.310A pdb=" N LEU A 901 " --> pdb=" O LEU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 930 removed outlier: 4.183A pdb=" N TYR A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 910 " --> pdb=" O THR A 906 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 927 " --> pdb=" O CYS A 923 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 971 removed outlier: 4.033A pdb=" N ILE A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 942 " --> pdb=" O PRO A 938 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 986 Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 998 through 1001 No H-bonds generated for 'chain 'A' and resid 998 through 1001' Processing helix chain 'A' and resid 1037 through 1052 Processing helix chain 'A' and resid 1054 through 1071 removed outlier: 3.720A pdb=" N LEU A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1091 removed outlier: 3.794A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A1087 " --> pdb=" O TYR A1083 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1113 removed outlier: 3.640A pdb=" N ILE A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1156 removed outlier: 3.821A pdb=" N GLU A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU A1135 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A1150 " --> pdb=" O ASN A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.830A pdb=" N HIS A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A1168 " --> pdb=" O HIS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1377 Processing helix chain 'A' and resid 1383 through 1387 Processing helix chain 'A' and resid 1428 through 1432 Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 4.201A pdb=" N GLU A1461 " --> pdb=" O SER A1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1462 " --> pdb=" O TYR A1458 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A1472 " --> pdb=" O HIS A1468 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR A1473 " --> pdb=" O HIS A1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.726A pdb=" N LYS B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.658A pdb=" N ALA B 197 " --> pdb=" O HIS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.547A pdb=" N ASN B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 removed outlier: 5.086A pdb=" N SER B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 372 through 387 removed outlier: 4.776A pdb=" N GLN B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.813A pdb=" N ALA B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 4.300A pdb=" N GLU B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 434 " --> pdb=" O ARG B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.947A pdb=" N SER B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 Proline residue: B 462 - end of helix Processing helix chain 'B' and resid 473 through 481 removed outlier: 3.584A pdb=" N GLU B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 489 No H-bonds generated for 'chain 'B' and resid 486 through 489' Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 507 through 517 removed outlier: 3.765A pdb=" N GLN B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 3.950A pdb=" N GLU B 542 " --> pdb=" O HIS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 removed outlier: 3.867A pdb=" N PHE B 599 " --> pdb=" O GLY B 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 600 " --> pdb=" O ARG B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 removed outlier: 4.206A pdb=" N GLU B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN B 617 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 637 Processing helix chain 'B' and resid 648 through 671 removed outlier: 3.803A pdb=" N SER B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.880A pdb=" N ILE B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 705 No H-bonds generated for 'chain 'B' and resid 702 through 705' Processing helix chain 'B' and resid 708 through 719 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.699A pdb=" N LEU B 732 " --> pdb=" O HIS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 removed outlier: 3.937A pdb=" N TYR B 742 " --> pdb=" O PHE B 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 738 through 742' Processing helix chain 'B' and resid 749 through 764 removed outlier: 3.771A pdb=" N ALA B 758 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 809 through 832 removed outlier: 3.694A pdb=" N TYR B 814 " --> pdb=" O GLN B 810 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER B 819 " --> pdb=" O TRP B 815 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 863 removed outlier: 3.618A pdb=" N LEU B 845 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 846 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 877 removed outlier: 3.882A pdb=" N MET B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 901 removed outlier: 4.311A pdb=" N LEU B 901 " --> pdb=" O LEU B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 930 removed outlier: 4.182A pdb=" N TYR B 909 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE B 910 " --> pdb=" O THR B 906 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 912 " --> pdb=" O PHE B 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 927 " --> pdb=" O CYS B 923 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 971 removed outlier: 4.033A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 942 " --> pdb=" O PRO B 938 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 945 " --> pdb=" O ILE B 941 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 986 Processing helix chain 'B' and resid 988 through 993 Processing helix chain 'B' and resid 998 through 1001 No H-bonds generated for 'chain 'B' and resid 998 through 1001' Processing helix chain 'B' and resid 1037 through 1052 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.721A pdb=" N LEU B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1091 removed outlier: 3.794A pdb=" N TYR B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B1087 " --> pdb=" O TYR B1083 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B1088 " --> pdb=" O GLU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1113 removed outlier: 3.639A pdb=" N ILE B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B1113 " --> pdb=" O ILE B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1156 removed outlier: 3.821A pdb=" N GLU B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B1135 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B1150 " --> pdb=" O ASN B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1182 removed outlier: 3.830A pdb=" N HIS B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B1168 " --> pdb=" O HIS B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1377 Processing helix chain 'B' and resid 1383 through 1387 Processing helix chain 'B' and resid 1428 through 1432 Processing helix chain 'B' and resid 1457 through 1473 removed outlier: 4.202A pdb=" N GLU B1461 " --> pdb=" O SER B1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B1462 " --> pdb=" O TYR B1458 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR B1472 " --> pdb=" O HIS B1468 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B1473 " --> pdb=" O HIS B1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 127 through 135 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.727A pdb=" N LYS C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.657A pdb=" N ALA C 197 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.547A pdb=" N ASN C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 removed outlier: 5.084A pdb=" N SER C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 372 through 387 removed outlier: 4.775A pdb=" N GLN C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 405 through 418 removed outlier: 3.814A pdb=" N ALA C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 4.300A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 434 " --> pdb=" O ARG C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 448 removed outlier: 3.945A pdb=" N SER C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 469 Proline residue: C 462 - end of helix Processing helix chain 'C' and resid 473 through 481 removed outlier: 3.583A pdb=" N GLU C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 489 No H-bonds generated for 'chain 'C' and resid 486 through 489' Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'C' and resid 507 through 517 removed outlier: 3.765A pdb=" N GLN C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 547 removed outlier: 3.949A pdb=" N GLU C 542 " --> pdb=" O HIS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 603 removed outlier: 3.865A pdb=" N PHE C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 600 " --> pdb=" O ARG C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 617 removed outlier: 4.207A pdb=" N GLU C 616 " --> pdb=" O GLU C 612 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 637 Processing helix chain 'C' and resid 648 through 671 removed outlier: 3.802A pdb=" N SER C 670 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP C 671 " --> pdb=" O GLU C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 removed outlier: 3.880A pdb=" N ILE C 681 " --> pdb=" O GLN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 687 No H-bonds generated for 'chain 'C' and resid 685 through 687' Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 702 through 705 No H-bonds generated for 'chain 'C' and resid 702 through 705' Processing helix chain 'C' and resid 708 through 719 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.699A pdb=" N LEU C 732 " --> pdb=" O HIS C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 removed outlier: 3.937A pdb=" N TYR C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 742' Processing helix chain 'C' and resid 749 through 764 removed outlier: 3.770A pdb=" N ALA C 758 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 806 Processing helix chain 'C' and resid 809 through 832 removed outlier: 3.694A pdb=" N TYR C 814 " --> pdb=" O GLN C 810 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 819 " --> pdb=" O TRP C 815 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 832 " --> pdb=" O ALA C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 863 removed outlier: 3.619A pdb=" N LEU C 845 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 846 " --> pdb=" O GLU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 877 removed outlier: 3.881A pdb=" N MET C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 901 removed outlier: 4.310A pdb=" N LEU C 901 " --> pdb=" O LEU C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 930 removed outlier: 4.183A pdb=" N TYR C 909 " --> pdb=" O ASP C 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 910 " --> pdb=" O THR C 906 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 912 " --> pdb=" O PHE C 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET C 927 " --> pdb=" O CYS C 923 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 929 " --> pdb=" O ARG C 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE C 930 " --> pdb=" O LEU C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 971 removed outlier: 4.033A pdb=" N ILE C 941 " --> pdb=" O GLY C 937 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 942 " --> pdb=" O PRO C 938 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 986 Processing helix chain 'C' and resid 988 through 993 Processing helix chain 'C' and resid 998 through 1001 No H-bonds generated for 'chain 'C' and resid 998 through 1001' Processing helix chain 'C' and resid 1037 through 1052 Processing helix chain 'C' and resid 1054 through 1071 removed outlier: 3.720A pdb=" N LEU C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1091 removed outlier: 3.795A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C1087 " --> pdb=" O TYR C1083 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C1088 " --> pdb=" O GLU C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1113 removed outlier: 3.640A pdb=" N ILE C1106 " --> pdb=" O LEU C1102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C1112 " --> pdb=" O PHE C1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1130 through 1156 removed outlier: 3.821A pdb=" N GLU C1134 " --> pdb=" O GLN C1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C1150 " --> pdb=" O ASN C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1182 removed outlier: 3.830A pdb=" N HIS C1164 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C1168 " --> pdb=" O HIS C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1369 through 1377 Processing helix chain 'C' and resid 1383 through 1387 Processing helix chain 'C' and resid 1428 through 1432 Processing helix chain 'C' and resid 1457 through 1473 removed outlier: 4.201A pdb=" N GLU C1461 " --> pdb=" O SER C1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C1462 " --> pdb=" O TYR C1458 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR C1472 " --> pdb=" O HIS C1468 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C1473 " --> pdb=" O HIS C1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.726A pdb=" N LYS D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.657A pdb=" N ALA D 197 " --> pdb=" O HIS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.547A pdb=" N ASN D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 removed outlier: 5.085A pdb=" N SER D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 362 Processing helix chain 'D' and resid 372 through 387 removed outlier: 4.775A pdb=" N GLN D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.814A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 removed outlier: 4.299A pdb=" N GLU D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 434 " --> pdb=" O ARG D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 448 removed outlier: 3.946A pdb=" N SER D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 481 removed outlier: 3.584A pdb=" N GLU D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 489 No H-bonds generated for 'chain 'D' and resid 486 through 489' Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'D' and resid 507 through 517 removed outlier: 3.765A pdb=" N GLN D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.951A pdb=" N GLU D 542 " --> pdb=" O HIS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 603 removed outlier: 3.867A pdb=" N PHE D 599 " --> pdb=" O GLY D 595 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 600 " --> pdb=" O ARG D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 617 removed outlier: 4.206A pdb=" N GLU D 616 " --> pdb=" O GLU D 612 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN D 617 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 637 Processing helix chain 'D' and resid 648 through 671 removed outlier: 3.802A pdb=" N SER D 670 " --> pdb=" O SER D 666 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP D 671 " --> pdb=" O GLU D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 681 removed outlier: 3.880A pdb=" N ILE D 681 " --> pdb=" O GLN D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 687 No H-bonds generated for 'chain 'D' and resid 685 through 687' Processing helix chain 'D' and resid 692 through 698 Processing helix chain 'D' and resid 702 through 705 No H-bonds generated for 'chain 'D' and resid 702 through 705' Processing helix chain 'D' and resid 708 through 719 Processing helix chain 'D' and resid 728 through 736 removed outlier: 3.698A pdb=" N LEU D 732 " --> pdb=" O HIS D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 742 removed outlier: 3.938A pdb=" N TYR D 742 " --> pdb=" O PHE D 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 738 through 742' Processing helix chain 'D' and resid 749 through 764 removed outlier: 3.771A pdb=" N ALA D 758 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 759 " --> pdb=" O GLN D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 806 Processing helix chain 'D' and resid 809 through 832 removed outlier: 3.694A pdb=" N TYR D 814 " --> pdb=" O GLN D 810 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER D 819 " --> pdb=" O TRP D 815 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 863 removed outlier: 3.619A pdb=" N LEU D 845 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 846 " --> pdb=" O GLU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 877 removed outlier: 3.882A pdb=" N MET D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 901 removed outlier: 4.310A pdb=" N LEU D 901 " --> pdb=" O LEU D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 930 removed outlier: 4.184A pdb=" N TYR D 909 " --> pdb=" O ASP D 905 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE D 910 " --> pdb=" O THR D 906 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 912 " --> pdb=" O PHE D 908 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET D 927 " --> pdb=" O CYS D 923 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 929 " --> pdb=" O ARG D 925 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE D 930 " --> pdb=" O LEU D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 971 removed outlier: 4.033A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 942 " --> pdb=" O PRO D 938 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG D 945 " --> pdb=" O ILE D 941 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 986 Processing helix chain 'D' and resid 988 through 993 Processing helix chain 'D' and resid 998 through 1001 No H-bonds generated for 'chain 'D' and resid 998 through 1001' Processing helix chain 'D' and resid 1037 through 1052 Processing helix chain 'D' and resid 1054 through 1071 removed outlier: 3.720A pdb=" N LEU D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1091 removed outlier: 3.793A pdb=" N TYR D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D1087 " --> pdb=" O TYR D1083 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1113 removed outlier: 3.640A pdb=" N ILE D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D1113 " --> pdb=" O ILE D1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1156 removed outlier: 3.820A pdb=" N GLU D1134 " --> pdb=" O GLN D1130 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU D1135 " --> pdb=" O THR D1131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D1150 " --> pdb=" O ASN D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1159 through 1182 removed outlier: 3.831A pdb=" N HIS D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D1168 " --> pdb=" O HIS D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1369 through 1377 Processing helix chain 'D' and resid 1383 through 1387 Processing helix chain 'D' and resid 1428 through 1432 Processing helix chain 'D' and resid 1457 through 1473 removed outlier: 4.201A pdb=" N GLU D1461 " --> pdb=" O SER D1457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D1462 " --> pdb=" O TYR D1458 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR D1472 " --> pdb=" O HIS D1468 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR D1473 " --> pdb=" O HIS D1469 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 52 removed outlier: 3.734A pdb=" N ARG A 96 " --> pdb=" O GLU A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.945A pdb=" N HIS A 259 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL A 213 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 145 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 182 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1441 through 1448 removed outlier: 7.265A pdb=" N TRP A1349 " --> pdb=" O GLN A1442 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU A1444 " --> pdb=" O ALA A1347 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA A1347 " --> pdb=" O LEU A1444 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP A1446 " --> pdb=" O PHE A1345 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE A1345 " --> pdb=" O TRP A1446 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A1448 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A1343 " --> pdb=" O GLU A1448 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL A1348 " --> pdb=" O PRO A1330 " (cutoff:3.500A) removed outlier: 15.335A pdb=" N GLU A1350 " --> pdb=" O LEU A1328 " (cutoff:3.500A) removed outlier: 19.961A pdb=" N LEU A1328 " --> pdb=" O GLU A1350 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.734A pdb=" N ARG B 96 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.946A pdb=" N HIS B 259 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL B 213 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 145 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU B 182 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 147 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1441 through 1448 removed outlier: 7.265A pdb=" N TRP B1349 " --> pdb=" O GLN B1442 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU B1444 " --> pdb=" O ALA B1347 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B1347 " --> pdb=" O LEU B1444 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP B1446 " --> pdb=" O PHE B1345 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B1345 " --> pdb=" O TRP B1446 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU B1448 " --> pdb=" O LEU B1343 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU B1343 " --> pdb=" O GLU B1448 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE B1332 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL B1348 " --> pdb=" O PRO B1330 " (cutoff:3.500A) removed outlier: 15.335A pdb=" N GLU B1350 " --> pdb=" O LEU B1328 " (cutoff:3.500A) removed outlier: 19.961A pdb=" N LEU B1328 " --> pdb=" O GLU B1350 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 49 through 52 removed outlier: 3.734A pdb=" N ARG C 96 " --> pdb=" O GLU C 52 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.946A pdb=" N HIS C 259 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL C 213 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU C 145 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU C 182 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 1441 through 1448 removed outlier: 7.265A pdb=" N TRP C1349 " --> pdb=" O GLN C1442 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU C1444 " --> pdb=" O ALA C1347 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C1347 " --> pdb=" O LEU C1444 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP C1446 " --> pdb=" O PHE C1345 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE C1345 " --> pdb=" O TRP C1446 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU C1448 " --> pdb=" O LEU C1343 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU C1343 " --> pdb=" O GLU C1448 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL C1348 " --> pdb=" O PRO C1330 " (cutoff:3.500A) removed outlier: 15.334A pdb=" N GLU C1350 " --> pdb=" O LEU C1328 " (cutoff:3.500A) removed outlier: 19.960A pdb=" N LEU C1328 " --> pdb=" O GLU C1350 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 49 through 52 removed outlier: 3.734A pdb=" N ARG D 96 " --> pdb=" O GLU D 52 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.946A pdb=" N HIS D 259 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL D 213 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU D 145 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU D 182 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 1441 through 1448 removed outlier: 7.265A pdb=" N TRP D1349 " --> pdb=" O GLN D1442 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU D1444 " --> pdb=" O ALA D1347 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA D1347 " --> pdb=" O LEU D1444 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP D1446 " --> pdb=" O PHE D1345 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE D1345 " --> pdb=" O TRP D1446 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D1448 " --> pdb=" O LEU D1343 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D1343 " --> pdb=" O GLU D1448 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE D1332 " --> pdb=" O LEU D1346 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL D1348 " --> pdb=" O PRO D1330 " (cutoff:3.500A) removed outlier: 15.334A pdb=" N GLU D1350 " --> pdb=" O LEU D1328 " (cutoff:3.500A) removed outlier: 19.960A pdb=" N LEU D1328 " --> pdb=" O GLU D1350 " (cutoff:3.500A) 1624 hydrogen bonds defined for protein. 4644 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: 13.68 Time building geometry restraints manager: 14.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5584 1.29 - 1.42: 9660 1.42 - 1.55: 20860 1.55 - 1.68: 28 1.68 - 1.81: 224 Bond restraints: 36356 Sorted by residual: bond pdb=" C PRO A1268 " pdb=" O PRO A1268 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.30e-02 5.92e+03 3.12e+01 bond pdb=" C PRO D1268 " pdb=" O PRO D1268 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C PRO C1268 " pdb=" O PRO C1268 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.30e-02 5.92e+03 3.10e+01 bond pdb=" C PRO B1268 " pdb=" O PRO B1268 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" C ARG B 608 " pdb=" O ARG B 608 " ideal model delta sigma weight residual 1.237 1.176 0.060 1.19e-02 7.06e+03 2.56e+01 ... (remaining 36351 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.74: 1257 106.74 - 114.08: 20656 114.08 - 121.42: 18718 121.42 - 128.77: 8813 128.77 - 136.11: 420 Bond angle restraints: 49864 Sorted by residual: angle pdb=" C GLU C 447 " pdb=" N ILE C 448 " pdb=" CA ILE C 448 " ideal model delta sigma weight residual 121.85 114.50 7.35 1.19e+00 7.06e-01 3.82e+01 angle pdb=" C GLU B 447 " pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta sigma weight residual 121.85 114.51 7.34 1.19e+00 7.06e-01 3.81e+01 angle pdb=" C GLU A 447 " pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 121.85 114.52 7.33 1.19e+00 7.06e-01 3.79e+01 angle pdb=" C GLU D 447 " pdb=" N ILE D 448 " pdb=" CA ILE D 448 " ideal model delta sigma weight residual 121.85 114.53 7.32 1.19e+00 7.06e-01 3.78e+01 angle pdb=" C GLY C 112 " pdb=" N GLN C 113 " pdb=" CA GLN C 113 " ideal model delta sigma weight residual 121.50 112.84 8.66 1.43e+00 4.89e-01 3.67e+01 ... (remaining 49859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 20192 17.50 - 35.01: 828 35.01 - 52.51: 228 52.51 - 70.01: 24 70.01 - 87.52: 28 Dihedral angle restraints: 21300 sinusoidal: 6540 harmonic: 14760 Sorted by residual: dihedral pdb=" CA ILE A1053 " pdb=" C ILE A1053 " pdb=" N LEU A1054 " pdb=" CA LEU A1054 " ideal model delta harmonic sigma weight residual -180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N LEU B1054 " pdb=" CA LEU B1054 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ILE C1053 " pdb=" C ILE C1053 " pdb=" N LEU C1054 " pdb=" CA LEU C1054 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 21297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4833 0.076 - 0.153: 890 0.153 - 0.229: 133 0.229 - 0.305: 56 0.305 - 0.382: 8 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA ASN C 607 " pdb=" N ASN C 607 " pdb=" C ASN C 607 " pdb=" CB ASN C 607 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA ASN A 607 " pdb=" N ASN A 607 " pdb=" C ASN A 607 " pdb=" CB ASN A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ASN D 607 " pdb=" N ASN D 607 " pdb=" C ASN D 607 " pdb=" CB ASN D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5917 not shown) Planarity restraints: 6344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 446 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C SER B 446 " -0.065 2.00e-02 2.50e+03 pdb=" O SER B 446 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 447 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 446 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER D 446 " -0.065 2.00e-02 2.50e+03 pdb=" O SER D 446 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU D 447 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 446 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER C 446 " -0.065 2.00e-02 2.50e+03 pdb=" O SER C 446 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU C 447 " 0.022 2.00e-02 2.50e+03 ... (remaining 6341 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 277 2.65 - 3.22: 31299 3.22 - 3.78: 52015 3.78 - 4.34: 63677 4.34 - 4.90: 107400 Nonbonded interactions: 254668 Sorted by model distance: nonbonded pdb=" OE1 GLN B 860 " pdb="CA CA B2002 " model vdw 2.093 2.510 nonbonded pdb=" OE1 GLN D 860 " pdb="CA CA D2002 " model vdw 2.093 2.510 nonbonded pdb=" OE1 GLN C 860 " pdb="CA CA C2002 " model vdw 2.093 2.510 nonbonded pdb=" OE1 GLN A 860 " pdb="CA CA A2002 " model vdw 2.093 2.510 nonbonded pdb=" O GLY A 970 " pdb=" NZ LYS B 912 " model vdw 2.252 2.520 ... (remaining 254663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.080 Check model and map are aligned: 0.520 Set scattering table: 0.340 Process input model: 91.480 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 36356 Z= 0.481 Angle : 1.135 9.755 49864 Z= 0.696 Chirality : 0.065 0.382 5920 Planarity : 0.009 0.127 6344 Dihedral : 11.738 87.515 11696 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Cbeta Deviations : 0.17 % 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: -3.18 (0.10), residues: 5008 helix: -1.69 (0.08), residues: 2484 sheet: -1.87 (0.24), residues: 360 loop : -2.58 (0.11), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 849 HIS 0.013 0.002 HIS D1104 PHE 0.028 0.003 PHE B 395 TYR 0.036 0.003 TYR A1089 ARG 0.011 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 803 time to evaluate : 3.836 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8534 (p90) cc_final: 0.8326 (p90) REVERT: A 284 LEU cc_start: 0.8410 (tp) cc_final: 0.8173 (tt) REVERT: A 404 ASP cc_start: 0.8485 (t70) cc_final: 0.8195 (t0) REVERT: A 481 GLU cc_start: 0.8402 (pp20) cc_final: 0.8194 (pp20) REVERT: A 825 TRP cc_start: 0.8115 (t60) cc_final: 0.7783 (t60) REVERT: A 945 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7727 (mtp85) REVERT: A 947 MET cc_start: 0.7342 (tmm) cc_final: 0.6831 (tmm) REVERT: A 949 ASP cc_start: 0.8100 (t70) cc_final: 0.7884 (m-30) REVERT: A 1043 MET cc_start: 0.8380 (ttm) cc_final: 0.8116 (ttp) REVERT: A 1054 LEU cc_start: 0.8728 (mp) cc_final: 0.8497 (mp) REVERT: A 1153 GLN cc_start: 0.7737 (pp30) cc_final: 0.7406 (pp30) REVERT: B 481 GLU cc_start: 0.8473 (pp20) cc_final: 0.7819 (pp20) REVERT: B 671 TRP cc_start: 0.8702 (t-100) cc_final: 0.8479 (t-100) REVERT: B 719 CYS cc_start: 0.8429 (t) cc_final: 0.8199 (m) REVERT: B 825 TRP cc_start: 0.7730 (t60) cc_final: 0.7498 (t60) REVERT: B 947 MET cc_start: 0.7505 (tmm) cc_final: 0.6807 (tmm) REVERT: B 949 ASP cc_start: 0.8231 (t70) cc_final: 0.7858 (m-30) REVERT: B 998 PHE cc_start: 0.8570 (t80) cc_final: 0.8326 (t80) REVERT: B 1153 GLN cc_start: 0.7841 (pp30) cc_final: 0.7396 (pp30) REVERT: C 106 ILE cc_start: 0.9075 (pt) cc_final: 0.8856 (mt) REVERT: C 284 LEU cc_start: 0.8571 (tp) cc_final: 0.8361 (tt) REVERT: C 404 ASP cc_start: 0.8424 (t70) cc_final: 0.8053 (t0) REVERT: C 481 GLU cc_start: 0.8499 (pp20) cc_final: 0.8033 (pp20) REVERT: C 719 CYS cc_start: 0.8513 (t) cc_final: 0.8240 (m) REVERT: C 825 TRP cc_start: 0.7952 (t60) cc_final: 0.7480 (t60) REVERT: C 856 GLU cc_start: 0.8234 (tp30) cc_final: 0.7694 (tm-30) REVERT: C 886 ASP cc_start: 0.3609 (m-30) cc_final: 0.3329 (m-30) REVERT: C 926 LEU cc_start: 0.8443 (tm) cc_final: 0.8177 (tp) REVERT: C 947 MET cc_start: 0.7405 (tmm) cc_final: 0.6702 (tmm) REVERT: C 949 ASP cc_start: 0.8268 (t70) cc_final: 0.7829 (m-30) REVERT: C 1140 GLU cc_start: 0.8314 (pp20) cc_final: 0.7628 (pp20) REVERT: C 1146 ASN cc_start: 0.8906 (t0) cc_final: 0.8685 (t0) REVERT: C 1153 GLN cc_start: 0.7860 (pp30) cc_final: 0.7463 (pp30) REVERT: D 284 LEU cc_start: 0.8697 (tp) cc_final: 0.8463 (tt) REVERT: D 352 MET cc_start: 0.8154 (mtp) cc_final: 0.7899 (ttm) REVERT: D 404 ASP cc_start: 0.8341 (t70) cc_final: 0.7989 (t0) REVERT: D 464 MET cc_start: 0.8998 (tpt) cc_final: 0.8708 (tpt) REVERT: D 481 GLU cc_start: 0.8426 (pp20) cc_final: 0.7931 (pp20) REVERT: D 825 TRP cc_start: 0.8003 (t60) cc_final: 0.7491 (t60) REVERT: D 856 GLU cc_start: 0.8082 (tp30) cc_final: 0.7743 (tm-30) REVERT: D 886 ASP cc_start: 0.3605 (m-30) cc_final: 0.3318 (m-30) REVERT: D 926 LEU cc_start: 0.8508 (tm) cc_final: 0.8146 (tp) REVERT: D 947 MET cc_start: 0.7400 (tmm) cc_final: 0.6711 (tmm) REVERT: D 949 ASP cc_start: 0.8297 (t70) cc_final: 0.7813 (m-30) REVERT: D 1140 GLU cc_start: 0.8369 (pp20) cc_final: 0.7758 (pp20) outliers start: 4 outliers final: 4 residues processed: 807 average time/residue: 0.4811 time to fit residues: 622.8219 Evaluate side-chains 451 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 447 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain D residue 991 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 240 optimal weight: 30.0000 chunk 294 optimal weight: 2.9990 chunk 457 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 231 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS A 975 ASN A1104 HIS B 137 GLN B 224 HIS B 231 HIS B 259 HIS B 816 ASN B 863 HIS B 975 ASN C 224 HIS C 231 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS C 975 ASN C1104 HIS C1164 HIS D 137 GLN D 224 HIS D 231 HIS D 256 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS D 482 ASN D 975 ASN D1104 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36356 Z= 0.327 Angle : 0.627 7.977 49864 Z= 0.331 Chirality : 0.042 0.198 5920 Planarity : 0.005 0.052 6344 Dihedral : 6.996 72.472 5564 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.30 % Allowed : 11.57 % Favored : 84.13 % 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: -1.54 (0.11), residues: 5008 helix: 0.02 (0.10), residues: 2452 sheet: -1.47 (0.25), residues: 392 loop : -2.16 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 43 HIS 0.009 0.002 HIS D 390 PHE 0.019 0.002 PHE A 893 TYR 0.019 0.002 TYR D1089 ARG 0.007 0.001 ARG B1162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 444 time to evaluate : 4.062 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8772 (p90) cc_final: 0.8398 (p90) REVERT: A 404 ASP cc_start: 0.8499 (t70) cc_final: 0.8228 (t0) REVERT: A 481 GLU cc_start: 0.8580 (pp20) cc_final: 0.7993 (pp20) REVERT: A 945 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7749 (mtp85) REVERT: A 947 MET cc_start: 0.7288 (tmm) cc_final: 0.6968 (tmm) REVERT: A 1140 GLU cc_start: 0.8242 (pp20) cc_final: 0.7682 (pp20) REVERT: B 481 GLU cc_start: 0.8407 (pp20) cc_final: 0.7868 (pp20) REVERT: B 825 TRP cc_start: 0.7983 (t60) cc_final: 0.7640 (t60) REVERT: B 886 ASP cc_start: 0.4037 (m-30) cc_final: 0.3783 (m-30) REVERT: B 947 MET cc_start: 0.7339 (tmm) cc_final: 0.6822 (tmm) REVERT: B 949 ASP cc_start: 0.8302 (t70) cc_final: 0.8046 (m-30) REVERT: B 1026 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7178 (ppp) REVERT: B 1140 GLU cc_start: 0.8409 (pp20) cc_final: 0.7810 (pp20) REVERT: C 404 ASP cc_start: 0.8522 (t70) cc_final: 0.8240 (t0) REVERT: C 481 GLU cc_start: 0.8414 (pp20) cc_final: 0.7909 (pp20) REVERT: C 658 GLU cc_start: 0.7745 (tt0) cc_final: 0.7518 (tt0) REVERT: C 825 TRP cc_start: 0.8089 (t60) cc_final: 0.7485 (t60) REVERT: C 947 MET cc_start: 0.7407 (tmm) cc_final: 0.6816 (tmm) REVERT: C 949 ASP cc_start: 0.8298 (t70) cc_final: 0.8091 (m-30) REVERT: C 1026 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7089 (ppp) REVERT: C 1140 GLU cc_start: 0.8382 (pp20) cc_final: 0.7928 (pp20) REVERT: D 388 MET cc_start: 0.8431 (ptp) cc_final: 0.8046 (ptp) REVERT: D 404 ASP cc_start: 0.8508 (t70) cc_final: 0.8208 (t0) REVERT: D 481 GLU cc_start: 0.8445 (pp20) cc_final: 0.7888 (pp20) REVERT: D 825 TRP cc_start: 0.8037 (t60) cc_final: 0.7529 (t60) REVERT: D 915 LEU cc_start: 0.8920 (mp) cc_final: 0.8689 (mp) REVERT: D 947 MET cc_start: 0.7277 (tmm) cc_final: 0.6775 (tmm) REVERT: D 949 ASP cc_start: 0.8330 (t70) cc_final: 0.7997 (m-30) REVERT: D 1140 GLU cc_start: 0.8387 (pp20) cc_final: 0.7967 (pp20) outliers start: 122 outliers final: 66 residues processed: 525 average time/residue: 0.4275 time to fit residues: 386.1344 Evaluate side-chains 441 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 373 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1099 PHE Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1099 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 380 optimal weight: 0.0980 chunk 311 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 458 optimal weight: 0.7980 chunk 495 optimal weight: 50.0000 chunk 408 optimal weight: 0.8980 chunk 454 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 367 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36356 Z= 0.135 Angle : 0.511 7.580 49864 Z= 0.266 Chirality : 0.039 0.163 5920 Planarity : 0.004 0.049 6344 Dihedral : 6.347 67.086 5564 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.03 % Allowed : 14.07 % Favored : 82.90 % 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: 5008 helix: 0.70 (0.10), residues: 2448 sheet: -0.62 (0.26), residues: 360 loop : -2.06 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 43 HIS 0.019 0.001 HIS A 224 PHE 0.019 0.001 PHE C 550 TYR 0.015 0.001 TYR D1089 ARG 0.003 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 431 time to evaluate : 4.000 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8741 (p90) cc_final: 0.8423 (p90) REVERT: A 404 ASP cc_start: 0.8477 (t70) cc_final: 0.8196 (t0) REVERT: A 481 GLU cc_start: 0.8554 (pp20) cc_final: 0.8026 (pp20) REVERT: A 947 MET cc_start: 0.7134 (tmm) cc_final: 0.6780 (tmm) REVERT: A 1140 GLU cc_start: 0.8168 (pp20) cc_final: 0.7721 (pp20) REVERT: B 481 GLU cc_start: 0.8275 (pp20) cc_final: 0.7788 (pp20) REVERT: B 727 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.7909 (Cg_endo) REVERT: B 825 TRP cc_start: 0.7948 (t60) cc_final: 0.7326 (t60) REVERT: B 947 MET cc_start: 0.7359 (tmm) cc_final: 0.7038 (tmm) REVERT: B 1140 GLU cc_start: 0.8188 (pp20) cc_final: 0.7673 (pp20) REVERT: C 404 ASP cc_start: 0.8441 (t70) cc_final: 0.8151 (t0) REVERT: C 481 GLU cc_start: 0.8344 (pp20) cc_final: 0.7911 (pp20) REVERT: C 825 TRP cc_start: 0.8051 (t60) cc_final: 0.7471 (t60) REVERT: C 947 MET cc_start: 0.7199 (tmm) cc_final: 0.6648 (tmm) REVERT: C 1140 GLU cc_start: 0.8216 (pp20) cc_final: 0.7802 (pp20) REVERT: C 1153 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 388 MET cc_start: 0.8265 (ptp) cc_final: 0.7933 (ptp) REVERT: D 404 ASP cc_start: 0.8471 (t70) cc_final: 0.8163 (t0) REVERT: D 481 GLU cc_start: 0.8346 (pp20) cc_final: 0.7874 (pp20) REVERT: D 825 TRP cc_start: 0.7999 (t60) cc_final: 0.7472 (t60) REVERT: D 947 MET cc_start: 0.7268 (tmm) cc_final: 0.6727 (tmm) REVERT: D 949 ASP cc_start: 0.8240 (t70) cc_final: 0.8009 (m-30) REVERT: D 1140 GLU cc_start: 0.8225 (pp20) cc_final: 0.7842 (pp20) outliers start: 86 outliers final: 52 residues processed: 485 average time/residue: 0.4148 time to fit residues: 348.3628 Evaluate side-chains 432 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 380 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1099 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 307 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 chunk 487 optimal weight: 20.0000 chunk 240 optimal weight: 40.0000 chunk 436 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN C 224 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN D 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 36356 Z= 0.462 Angle : 0.641 6.415 49864 Z= 0.335 Chirality : 0.044 0.177 5920 Planarity : 0.005 0.047 6344 Dihedral : 6.675 72.513 5564 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.83 % Allowed : 14.56 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5008 helix: 0.54 (0.10), residues: 2484 sheet: -0.65 (0.26), residues: 364 loop : -2.07 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 43 HIS 0.028 0.002 HIS A 224 PHE 0.019 0.002 PHE D 550 TYR 0.017 0.002 TYR D1089 ARG 0.005 0.001 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 361 time to evaluate : 3.964 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8831 (p90) cc_final: 0.8278 (p90) REVERT: A 388 MET cc_start: 0.7931 (ptp) cc_final: 0.7610 (ptp) REVERT: A 481 GLU cc_start: 0.8607 (pp20) cc_final: 0.7900 (pp20) REVERT: A 657 TYR cc_start: 0.8847 (m-80) cc_final: 0.8604 (m-80) REVERT: A 1052 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7439 (p0) REVERT: A 1140 GLU cc_start: 0.8434 (pp20) cc_final: 0.7937 (pp20) REVERT: B 388 MET cc_start: 0.8056 (ptp) cc_final: 0.7825 (ptp) REVERT: B 481 GLU cc_start: 0.8486 (pp20) cc_final: 0.7898 (pp20) REVERT: B 825 TRP cc_start: 0.8116 (t60) cc_final: 0.7518 (t60) REVERT: B 892 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8082 (mm) REVERT: B 947 MET cc_start: 0.7316 (tmm) cc_final: 0.6937 (tmm) REVERT: B 1140 GLU cc_start: 0.8428 (pp20) cc_final: 0.7979 (pp20) REVERT: C 388 MET cc_start: 0.7981 (ptp) cc_final: 0.7691 (ptp) REVERT: C 481 GLU cc_start: 0.8426 (pp20) cc_final: 0.7832 (pp20) REVERT: C 657 TYR cc_start: 0.8879 (m-10) cc_final: 0.8668 (m-80) REVERT: C 1026 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7168 (ppp) REVERT: C 1140 GLU cc_start: 0.8423 (pp20) cc_final: 0.7967 (pp20) REVERT: C 1153 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8084 (tm-30) REVERT: D 352 MET cc_start: 0.7607 (mtp) cc_final: 0.7348 (ttm) REVERT: D 388 MET cc_start: 0.8320 (ptp) cc_final: 0.7964 (ptp) REVERT: D 481 GLU cc_start: 0.8413 (pp20) cc_final: 0.7792 (pp20) REVERT: D 657 TYR cc_start: 0.8845 (m-80) cc_final: 0.8635 (m-80) REVERT: D 947 MET cc_start: 0.7273 (tmm) cc_final: 0.6699 (tmm) REVERT: D 949 ASP cc_start: 0.8332 (t70) cc_final: 0.8050 (m-30) REVERT: D 1026 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7147 (ppp) REVERT: D 1140 GLU cc_start: 0.8436 (pp20) cc_final: 0.7956 (pp20) outliers start: 137 outliers final: 100 residues processed: 456 average time/residue: 0.4147 time to fit residues: 328.6942 Evaluate side-chains 456 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 352 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 942 ILE Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 862 TYR Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1099 PHE Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 913 VAL Chi-restraints excluded: chain D residue 942 ILE Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1026 MET Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1099 PHE Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 362 optimal weight: 40.0000 chunk 201 optimal weight: 8.9990 chunk 415 optimal weight: 2.9990 chunk 336 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 437 optimal weight: 3.9990 chunk 122 optimal weight: 0.0570 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 341 HIS A 411 GLN B 816 ASN C 341 HIS C 411 GLN D 341 HIS D 411 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36356 Z= 0.168 Angle : 0.505 6.822 49864 Z= 0.262 Chirality : 0.039 0.143 5920 Planarity : 0.004 0.045 6344 Dihedral : 6.159 68.660 5564 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.63 % Allowed : 16.96 % Favored : 79.41 % 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: -0.48 (0.12), residues: 5008 helix: 1.00 (0.11), residues: 2464 sheet: -0.30 (0.27), residues: 364 loop : -1.94 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 841 HIS 0.009 0.001 HIS A 224 PHE 0.020 0.001 PHE D 550 TYR 0.014 0.001 TYR B1089 ARG 0.003 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 383 time to evaluate : 4.653 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8803 (p90) cc_final: 0.8298 (p90) REVERT: A 388 MET cc_start: 0.7879 (ptp) cc_final: 0.7457 (ptp) REVERT: A 481 GLU cc_start: 0.8563 (pp20) cc_final: 0.7942 (pp20) REVERT: A 947 MET cc_start: 0.7197 (tmm) cc_final: 0.6869 (ttt) REVERT: A 1052 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7267 (p0) REVERT: A 1140 GLU cc_start: 0.8228 (pp20) cc_final: 0.7757 (pp20) REVERT: B 388 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7432 (ptp) REVERT: B 481 GLU cc_start: 0.8396 (pp20) cc_final: 0.7924 (pp20) REVERT: B 825 TRP cc_start: 0.7918 (t60) cc_final: 0.7360 (t60) REVERT: B 892 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8066 (mm) REVERT: B 1026 MET cc_start: 0.7931 (ppp) cc_final: 0.7533 (ppp) REVERT: B 1140 GLU cc_start: 0.8233 (pp20) cc_final: 0.7842 (pp20) REVERT: C 388 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7466 (ptp) REVERT: C 481 GLU cc_start: 0.8362 (pp20) cc_final: 0.7860 (pp20) REVERT: C 816 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8051 (m-40) REVERT: C 1140 GLU cc_start: 0.8238 (pp20) cc_final: 0.7773 (pp20) REVERT: C 1153 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8147 (tm-30) REVERT: D 388 MET cc_start: 0.8203 (ptp) cc_final: 0.7888 (ptp) REVERT: D 481 GLU cc_start: 0.8354 (pp20) cc_final: 0.7840 (pp20) REVERT: D 1140 GLU cc_start: 0.8264 (pp20) cc_final: 0.7794 (pp20) outliers start: 103 outliers final: 79 residues processed: 448 average time/residue: 0.4047 time to fit residues: 320.5121 Evaluate side-chains 440 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 356 time to evaluate : 4.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 816 ASN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 1.9990 chunk 438 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 286 optimal weight: 0.1980 chunk 120 optimal weight: 40.0000 chunk 487 optimal weight: 0.7980 chunk 404 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 816 ASN D 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36356 Z= 0.138 Angle : 0.485 8.175 49864 Z= 0.249 Chirality : 0.038 0.173 5920 Planarity : 0.004 0.048 6344 Dihedral : 5.824 66.188 5564 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.49 % Allowed : 17.45 % Favored : 79.06 % 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: -0.16 (0.12), residues: 5008 helix: 1.36 (0.11), residues: 2452 sheet: 0.07 (0.28), residues: 360 loop : -1.94 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 43 HIS 0.006 0.001 HIS D 224 PHE 0.020 0.001 PHE D1007 TYR 0.013 0.001 TYR B1089 ARG 0.002 0.000 ARG D 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 380 time to evaluate : 4.061 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8793 (p90) cc_final: 0.8283 (p90) REVERT: A 388 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7358 (ptp) REVERT: A 481 GLU cc_start: 0.8528 (pp20) cc_final: 0.7979 (pp20) REVERT: A 947 MET cc_start: 0.7142 (tmm) cc_final: 0.6840 (ttt) REVERT: A 1007 PHE cc_start: 0.7940 (t80) cc_final: 0.7722 (t80) REVERT: A 1052 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7304 (p0) REVERT: A 1140 GLU cc_start: 0.8128 (pp20) cc_final: 0.7655 (pp20) REVERT: B 388 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7420 (ptp) REVERT: B 481 GLU cc_start: 0.8363 (pp20) cc_final: 0.7909 (pp20) REVERT: B 727 PRO cc_start: 0.8436 (Cg_exo) cc_final: 0.8120 (Cg_endo) REVERT: B 825 TRP cc_start: 0.7843 (t60) cc_final: 0.7282 (t60) REVERT: B 892 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 1026 MET cc_start: 0.8066 (ppp) cc_final: 0.7625 (ppp) REVERT: B 1140 GLU cc_start: 0.8184 (pp20) cc_final: 0.7794 (pp20) REVERT: C 388 MET cc_start: 0.7901 (ptp) cc_final: 0.7455 (ptp) REVERT: C 481 GLU cc_start: 0.8341 (pp20) cc_final: 0.7889 (pp20) REVERT: C 1140 GLU cc_start: 0.8168 (pp20) cc_final: 0.7723 (pp20) REVERT: C 1153 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 388 MET cc_start: 0.8064 (ptp) cc_final: 0.7753 (ptp) REVERT: D 481 GLU cc_start: 0.8324 (pp20) cc_final: 0.7794 (pp20) REVERT: D 1140 GLU cc_start: 0.8200 (pp20) cc_final: 0.7758 (pp20) outliers start: 99 outliers final: 73 residues processed: 444 average time/residue: 0.4455 time to fit residues: 349.7139 Evaluate side-chains 437 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 360 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 224 HIS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1050 PHE Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 410 optimal weight: 0.7980 chunk 272 optimal weight: 0.8980 chunk 485 optimal weight: 0.9990 chunk 304 optimal weight: 0.3980 chunk 296 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 HIS B 816 ASN C 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 36356 Z= 0.156 Angle : 0.499 9.756 49864 Z= 0.250 Chirality : 0.039 0.151 5920 Planarity : 0.004 0.044 6344 Dihedral : 5.601 65.052 5562 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.21 % Allowed : 18.19 % Favored : 78.60 % 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: 0.01 (0.12), residues: 5008 helix: 1.51 (0.11), residues: 2456 sheet: 0.25 (0.28), residues: 360 loop : -1.89 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 43 HIS 0.016 0.001 HIS D 224 PHE 0.020 0.001 PHE C1007 TYR 0.013 0.001 TYR D1089 ARG 0.003 0.000 ARG D 945 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 371 time to evaluate : 4.099 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8830 (p90) cc_final: 0.8395 (p90) REVERT: A 163 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8228 (ttmm) REVERT: A 388 MET cc_start: 0.7872 (ptp) cc_final: 0.7280 (ptp) REVERT: A 481 GLU cc_start: 0.8510 (pp20) cc_final: 0.7936 (pp20) REVERT: A 658 GLU cc_start: 0.7667 (tt0) cc_final: 0.7445 (tt0) REVERT: A 947 MET cc_start: 0.7120 (tmm) cc_final: 0.6826 (ttt) REVERT: A 1052 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7317 (p0) REVERT: A 1140 GLU cc_start: 0.8141 (pp20) cc_final: 0.7680 (pp20) REVERT: B 388 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7525 (ptp) REVERT: B 481 GLU cc_start: 0.8368 (pp20) cc_final: 0.7911 (pp20) REVERT: B 727 PRO cc_start: 0.8300 (Cg_exo) cc_final: 0.8007 (Cg_endo) REVERT: B 892 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8124 (mm) REVERT: B 1026 MET cc_start: 0.7996 (ppp) cc_final: 0.7620 (ppp) REVERT: B 1140 GLU cc_start: 0.8194 (pp20) cc_final: 0.7805 (pp20) REVERT: C 388 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7502 (ptp) REVERT: C 481 GLU cc_start: 0.8342 (pp20) cc_final: 0.7868 (pp20) REVERT: C 1140 GLU cc_start: 0.8174 (pp20) cc_final: 0.7742 (pp20) REVERT: D 388 MET cc_start: 0.8003 (ptp) cc_final: 0.7710 (ptp) REVERT: D 1140 GLU cc_start: 0.8204 (pp20) cc_final: 0.7768 (pp20) outliers start: 91 outliers final: 77 residues processed: 429 average time/residue: 0.4135 time to fit residues: 313.0125 Evaluate side-chains 444 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 362 time to evaluate : 4.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1050 PHE Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 146 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 308 optimal weight: 0.4980 chunk 330 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 381 optimal weight: 9.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 36356 Z= 0.135 Angle : 0.488 9.229 49864 Z= 0.244 Chirality : 0.038 0.145 5920 Planarity : 0.004 0.043 6344 Dihedral : 5.390 63.215 5562 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.39 % Allowed : 17.98 % Favored : 78.63 % 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: 0.14 (0.12), residues: 5008 helix: 1.64 (0.11), residues: 2452 sheet: 0.37 (0.29), residues: 360 loop : -1.87 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 43 HIS 0.020 0.001 HIS B 224 PHE 0.019 0.001 PHE D 550 TYR 0.012 0.001 TYR D1089 ARG 0.002 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 379 time to evaluate : 3.821 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8763 (p90) cc_final: 0.8305 (p90) REVERT: A 163 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: A 388 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7378 (ptp) REVERT: A 481 GLU cc_start: 0.8495 (pp20) cc_final: 0.7967 (pp20) REVERT: A 947 MET cc_start: 0.7125 (tmm) cc_final: 0.6820 (ttt) REVERT: A 1052 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7316 (p0) REVERT: A 1140 GLU cc_start: 0.8089 (pp20) cc_final: 0.7752 (pp20) REVERT: B 134 MET cc_start: 0.8833 (tpt) cc_final: 0.8547 (tpt) REVERT: B 388 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7518 (ptp) REVERT: B 481 GLU cc_start: 0.8356 (pp20) cc_final: 0.7939 (pp20) REVERT: B 727 PRO cc_start: 0.8200 (Cg_exo) cc_final: 0.7903 (Cg_endo) REVERT: B 892 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8120 (mm) REVERT: B 1140 GLU cc_start: 0.8156 (pp20) cc_final: 0.7780 (pp20) REVERT: C 388 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7490 (ptp) REVERT: C 481 GLU cc_start: 0.8325 (pp20) cc_final: 0.7862 (pp20) REVERT: C 1140 GLU cc_start: 0.8144 (pp20) cc_final: 0.7725 (pp20) REVERT: D 134 MET cc_start: 0.8851 (tpt) cc_final: 0.8457 (tpt) REVERT: D 388 MET cc_start: 0.7951 (ptp) cc_final: 0.7706 (ptp) REVERT: D 1140 GLU cc_start: 0.8169 (pp20) cc_final: 0.7744 (pp20) outliers start: 96 outliers final: 78 residues processed: 438 average time/residue: 0.3995 time to fit residues: 309.8174 Evaluate side-chains 451 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 367 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 8.9990 chunk 465 optimal weight: 5.9990 chunk 424 optimal weight: 0.7980 chunk 452 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 355 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 409 optimal weight: 0.7980 chunk 428 optimal weight: 5.9990 chunk 451 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1104 HIS C 411 GLN D 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36356 Z= 0.276 Angle : 0.550 9.922 49864 Z= 0.278 Chirality : 0.041 0.160 5920 Planarity : 0.004 0.043 6344 Dihedral : 5.539 64.575 5562 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.46 % Allowed : 18.65 % Favored : 77.89 % 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: 0.00 (0.12), residues: 5008 helix: 1.41 (0.11), residues: 2496 sheet: 0.31 (0.29), residues: 360 loop : -1.83 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 43 HIS 0.006 0.001 HIS B 656 PHE 0.027 0.001 PHE D1007 TYR 0.015 0.001 TYR B1089 ARG 0.003 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 361 time to evaluate : 4.084 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8792 (p90) cc_final: 0.8186 (p90) REVERT: A 388 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7673 (ptp) REVERT: A 481 GLU cc_start: 0.8563 (pp20) cc_final: 0.7960 (pp20) REVERT: A 1140 GLU cc_start: 0.8272 (pp20) cc_final: 0.7813 (pp20) REVERT: B 134 MET cc_start: 0.8874 (tpt) cc_final: 0.8571 (tpt) REVERT: B 727 PRO cc_start: 0.8271 (Cg_exo) cc_final: 0.7978 (Cg_endo) REVERT: B 892 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8046 (mm) REVERT: B 1140 GLU cc_start: 0.8279 (pp20) cc_final: 0.7883 (pp20) REVERT: C 388 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7815 (ptp) REVERT: C 481 GLU cc_start: 0.8418 (pp20) cc_final: 0.7840 (pp20) REVERT: C 1140 GLU cc_start: 0.8278 (pp20) cc_final: 0.7811 (pp20) REVERT: D 134 MET cc_start: 0.8825 (tpt) cc_final: 0.8404 (tpt) REVERT: D 388 MET cc_start: 0.8096 (ptp) cc_final: 0.7816 (ptp) REVERT: D 1140 GLU cc_start: 0.8298 (pp20) cc_final: 0.7822 (pp20) outliers start: 98 outliers final: 86 residues processed: 424 average time/residue: 0.4018 time to fit residues: 301.3720 Evaluate side-chains 443 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 354 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 862 TYR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 1050 PHE Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 4.9990 chunk 478 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 502 optimal weight: 50.0000 chunk 462 optimal weight: 9.9990 chunk 399 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 308 optimal weight: 0.0000 chunk 245 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 HIS C 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 36356 Z= 0.164 Angle : 0.505 9.044 49864 Z= 0.253 Chirality : 0.039 0.149 5920 Planarity : 0.004 0.043 6344 Dihedral : 5.275 62.591 5560 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 18.86 % Favored : 78.00 % 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: 0.16 (0.12), residues: 5008 helix: 1.62 (0.11), residues: 2460 sheet: 0.37 (0.29), residues: 360 loop : -1.80 (0.12), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 43 HIS 0.004 0.001 HIS A 257 PHE 0.022 0.001 PHE D 550 TYR 0.013 0.001 TYR B1089 ARG 0.002 0.000 ARG D 945 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10016 Ramachandran restraints generated. 5008 Oldfield, 0 Emsley, 5008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 369 time to evaluate : 4.283 Fit side-chains TARDY: cannot create tardy model for: "MET A1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C1183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D1183 " (corrupted residue). Skipping it. REVERT: A 118 TYR cc_start: 0.8790 (p90) cc_final: 0.8316 (p90) REVERT: A 388 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7429 (ptp) REVERT: A 481 GLU cc_start: 0.8542 (pp20) cc_final: 0.7962 (pp20) REVERT: A 1140 GLU cc_start: 0.8165 (pp20) cc_final: 0.7825 (pp20) REVERT: B 134 MET cc_start: 0.8822 (tpt) cc_final: 0.8516 (tpt) REVERT: B 481 GLU cc_start: 0.8386 (pp20) cc_final: 0.7935 (pp20) REVERT: B 892 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8047 (mm) REVERT: B 1140 GLU cc_start: 0.8185 (pp20) cc_final: 0.7806 (pp20) REVERT: C 388 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7739 (ptp) REVERT: C 481 GLU cc_start: 0.8375 (pp20) cc_final: 0.7817 (pp20) REVERT: C 1050 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 1140 GLU cc_start: 0.8179 (pp20) cc_final: 0.7856 (pp20) REVERT: D 388 MET cc_start: 0.8056 (ptp) cc_final: 0.7769 (ptp) REVERT: D 1140 GLU cc_start: 0.8194 (pp20) cc_final: 0.7860 (pp20) outliers start: 89 outliers final: 75 residues processed: 421 average time/residue: 0.4131 time to fit residues: 307.6796 Evaluate side-chains 443 residues out of total 4484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 364 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1050 PHE Chi-restraints excluded: chain A residue 1052 ASN Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain A residue 1065 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1052 ASN Chi-restraints excluded: chain B residue 1057 ASN Chi-restraints excluded: chain B residue 1065 TYR Chi-restraints excluded: chain B residue 1257 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 703 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1065 TYR Chi-restraints excluded: chain C residue 1257 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 485 CYS Chi-restraints excluded: chain D residue 497 CYS Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 850 LEU Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1065 TYR Chi-restraints excluded: chain D residue 1257 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 5.9990 chunk 425 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 400 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 411 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 73 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 GLN A 969 GLN D 605 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117821 restraints weight = 66590.930| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.26 r_work: 0.3424 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36356 Z= 0.124 Angle : 0.491 9.546 49864 Z= 0.243 Chirality : 0.038 0.161 5920 Planarity : 0.004 0.043 6344 Dihedral : 4.882 58.997 5556 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.29 % Allowed : 20.06 % Favored : 77.64 % 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: 0.33 (0.12), residues: 5008 helix: 1.78 (0.11), residues: 2452 sheet: 0.49 (0.29), residues: 360 loop : -1.75 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 43 HIS 0.002 0.000 HIS C 257 PHE 0.028 0.001 PHE D1007 TYR 0.024 0.001 TYR A 847 ARG 0.002 0.000 ARG D 945 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7627.10 seconds wall clock time: 138 minutes 48.75 seconds (8328.75 seconds total)