Starting phenix.real_space_refine on Sun Nov 19 10:14:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si3_40497/11_2023/8si3_40497_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si3_40497/11_2023/8si3_40497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si3_40497/11_2023/8si3_40497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si3_40497/11_2023/8si3_40497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si3_40497/11_2023/8si3_40497_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si3_40497/11_2023/8si3_40497_neut_trim_updated.pdb" } resolution = 2.61 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= 0.008 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 240 5.16 5 C 25448 2.51 5 N 6004 2.21 5 O 6872 1.98 5 H 36136 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 74749 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 17962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17962 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 738 Unusual residues: {' CA': 1, 'CLR': 1, 'DU0': 1, 'POV': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 685 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 685 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 633 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 23.85, per 1000 atoms: 0.32 Number of scatterers: 74749 At special positions: 0 Unit cell: (181.77, 181.77, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 240 16.00 P 48 15.00 O 6872 8.00 N 6004 7.00 C 25448 6.00 H 36136 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.08 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.08 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.08 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.08 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 49.45 Conformation dependent library (CDL) restraints added in 5.5 seconds 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 8 sheets defined 53.9% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.28 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 80 through 83 No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 117 through 125 removed outlier: 3.627A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.902A pdb=" N LEU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 213 through 216 No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.544A pdb=" N TYR A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.739A pdb=" N THR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.712A pdb=" N PHE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 390 through 401 removed outlier: 4.120A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.523A pdb=" N THR A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.695A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.887A pdb=" N ILE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.532A pdb=" N LEU A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 648 through 667 Processing helix chain 'A' and resid 677 through 700 removed outlier: 3.580A pdb=" N GLN A 688 " --> pdb=" O ASN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.800A pdb=" N MET A 773 " --> pdb=" O ALA A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.548A pdb=" N PHE A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 removed outlier: 3.836A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 Processing helix chain 'A' and resid 912 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.563A pdb=" N THR A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 982 removed outlier: 4.796A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 999 removed outlier: 3.860A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1030 through 1035 removed outlier: 3.625A pdb=" N LYS A1034 " --> pdb=" O SER A1031 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A1035 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1045 removed outlier: 3.935A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1086 Proline residue: A1074 - end of helix removed outlier: 3.527A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1121 removed outlier: 5.129A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1142 removed outlier: 3.686A pdb=" N VAL A1139 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A1142 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1190 Processing helix chain 'A' and resid 1193 through 1224 removed outlier: 4.089A pdb=" N ASP A1216 " --> pdb=" O LYS A1212 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 80 through 83 No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.627A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.902A pdb=" N LEU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 213 through 216 No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 296 through 305 removed outlier: 3.544A pdb=" N TYR B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.738A pdb=" N THR B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.713A pdb=" N PHE B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 390 through 401 removed outlier: 4.120A pdb=" N ALA B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.523A pdb=" N THR B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 465 through 468 No H-bonds generated for 'chain 'B' and resid 465 through 468' Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.694A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 531 through 539 removed outlier: 3.887A pdb=" N ILE B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.533A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 648 through 667 Processing helix chain 'B' and resid 677 through 700 removed outlier: 3.580A pdb=" N GLN B 688 " --> pdb=" O ASN B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 709 Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 737 through 748 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 768 through 773 removed outlier: 3.800A pdb=" N MET B 773 " --> pdb=" O ALA B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 793 Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.548A pdb=" N PHE B 848 " --> pdb=" O LYS B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 875 removed outlier: 3.836A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 905 Processing helix chain 'B' and resid 912 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.564A pdb=" N THR B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.796A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.860A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1022 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1030 through 1035 removed outlier: 3.626A pdb=" N LYS B1034 " --> pdb=" O SER B1031 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B1035 " --> pdb=" O LEU B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1045 removed outlier: 3.935A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B1045 " --> pdb=" O TYR B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1086 Proline residue: B1074 - end of helix removed outlier: 3.527A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B1081 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B1085 " --> pdb=" O PHE B1082 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B1086 " --> pdb=" O VAL B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1121 removed outlier: 5.129A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1142 removed outlier: 3.686A pdb=" N VAL B1139 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B1142 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1190 Processing helix chain 'B' and resid 1193 through 1224 removed outlier: 4.089A pdb=" N ASP B1216 " --> pdb=" O LYS B1212 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 117 through 125 removed outlier: 3.627A pdb=" N LEU C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.901A pdb=" N LEU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'C' and resid 213 through 216 No H-bonds generated for 'chain 'C' and resid 213 through 216' Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.544A pdb=" N TYR C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.740A pdb=" N THR C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 removed outlier: 3.713A pdb=" N PHE C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 367 " --> pdb=" O HIS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 390 through 401 removed outlier: 4.120A pdb=" N ALA C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 417 removed outlier: 3.524A pdb=" N THR C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 471 through 478 removed outlier: 3.695A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.887A pdb=" N ILE C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 631 removed outlier: 3.532A pdb=" N LEU C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 648 through 667 Processing helix chain 'C' and resid 677 through 700 removed outlier: 3.581A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 709 Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 731 through 734 No H-bonds generated for 'chain 'C' and resid 731 through 734' Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 768 through 773 removed outlier: 3.800A pdb=" N MET C 773 " --> pdb=" O ALA C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 793 Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.549A pdb=" N PHE C 848 " --> pdb=" O LYS C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 875 removed outlier: 3.836A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 905 Processing helix chain 'C' and resid 912 through 919 Processing helix chain 'C' and resid 923 through 943 removed outlier: 3.564A pdb=" N THR C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 982 removed outlier: 4.796A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 999 removed outlier: 3.860A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1022 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1030 through 1035 removed outlier: 3.625A pdb=" N LYS C1034 " --> pdb=" O SER C1031 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP C1035 " --> pdb=" O LEU C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1045 removed outlier: 3.935A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE C1045 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1086 Proline residue: C1074 - end of helix removed outlier: 3.528A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C1081 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C1085 " --> pdb=" O PHE C1082 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE C1086 " --> pdb=" O VAL C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1121 removed outlier: 5.128A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1142 removed outlier: 3.686A pdb=" N VAL C1139 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C1142 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1190 Processing helix chain 'C' and resid 1193 through 1224 removed outlier: 4.089A pdb=" N ASP C1216 " --> pdb=" O LYS C1212 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 80 through 83 No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'D' and resid 117 through 125 removed outlier: 3.627A pdb=" N LEU D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.902A pdb=" N LEU D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 213 through 216 No H-bonds generated for 'chain 'D' and resid 213 through 216' Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.543A pdb=" N TYR D 303 " --> pdb=" O THR D 299 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.740A pdb=" N THR D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 removed outlier: 3.712A pdb=" N PHE D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 367 " --> pdb=" O HIS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 390 through 401 removed outlier: 4.121A pdb=" N ALA D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.523A pdb=" N THR D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 438 through 449 Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 471 through 478 removed outlier: 3.696A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 496 Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.887A pdb=" N ILE D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 631 removed outlier: 3.532A pdb=" N LEU D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 648 through 667 Processing helix chain 'D' and resid 677 through 700 removed outlier: 3.580A pdb=" N GLN D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 709 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 737 through 748 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 773 removed outlier: 3.800A pdb=" N MET D 773 " --> pdb=" O ALA D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 793 Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.549A pdb=" N PHE D 848 " --> pdb=" O LYS D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 875 removed outlier: 3.836A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 905 Processing helix chain 'D' and resid 912 through 919 Processing helix chain 'D' and resid 923 through 943 removed outlier: 3.563A pdb=" N THR D 929 " --> pdb=" O ASN D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.796A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 999 removed outlier: 3.860A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1022 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1030 through 1035 removed outlier: 3.625A pdb=" N LYS D1034 " --> pdb=" O SER D1031 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D1035 " --> pdb=" O LEU D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1045 removed outlier: 3.935A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE D1045 " --> pdb=" O TYR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1086 Proline residue: D1074 - end of helix removed outlier: 3.528A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D1081 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR D1085 " --> pdb=" O PHE D1082 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D1086 " --> pdb=" O VAL D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1121 removed outlier: 5.128A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1142 removed outlier: 3.686A pdb=" N VAL D1139 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D1142 " --> pdb=" O VAL D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1190 Processing helix chain 'D' and resid 1193 through 1224 removed outlier: 4.089A pdb=" N ASP D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 137 through 139 removed outlier: 6.567A pdb=" N VAL A 286 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 289 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 313 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 173 removed outlier: 6.753A pdb=" N CYS A 200 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR A 173 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 202 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS A 244 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA A 205 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE A 246 " --> pdb=" O ALA A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.566A pdb=" N VAL B 286 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE B 289 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 313 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.753A pdb=" N CYS B 200 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR B 173 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 202 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS B 244 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 205 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE B 246 " --> pdb=" O ALA B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 137 through 139 removed outlier: 6.566A pdb=" N VAL C 286 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 289 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 313 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.753A pdb=" N CYS C 200 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR C 173 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE C 202 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS C 244 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA C 205 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE C 246 " --> pdb=" O ALA C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 137 through 139 removed outlier: 6.566A pdb=" N VAL D 286 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE D 289 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 313 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 170 through 173 removed outlier: 6.753A pdb=" N CYS D 200 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR D 173 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 202 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS D 244 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA D 205 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE D 246 " --> pdb=" O ALA D 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 1408 hydrogen bonds defined for protein. 4032 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: 25.64 Time building geometry restraints manager: 52.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 36068 1.01 - 1.23: 345 1.23 - 1.45: 15742 1.45 - 1.66: 22885 1.66 - 1.88: 392 Bond restraints: 75432 Sorted by residual: bond pdb=" C29 POV D1306 " pdb="C210 POV D1306 " ideal model delta sigma weight residual 1.333 1.515 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C29 POV A1305 " pdb="C210 POV A1305 " ideal model delta sigma weight residual 1.333 1.514 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" C29 POV C1306 " pdb="C210 POV C1306 " ideal model delta sigma weight residual 1.333 1.513 -0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C29 POV B1306 " pdb="C210 POV B1306 " ideal model delta sigma weight residual 1.333 1.513 -0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C ASN D 230 " pdb=" N PRO D 231 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 75427 not shown) Histogram of bond angle deviations from ideal: 74.04 - 87.62: 27 87.62 - 101.20: 180 101.20 - 114.78: 93621 114.78 - 128.36: 40651 128.36 - 141.94: 461 Bond angle restraints: 134940 Sorted by residual: angle pdb=" CG2 VAL B 65 " pdb=" CB VAL B 65 " pdb=" HB VAL B 65 " ideal model delta sigma weight residual 108.00 74.04 33.96 3.00e+00 1.11e-01 1.28e+02 angle pdb=" CG1 VAL B 65 " pdb=" CB VAL B 65 " pdb=" HB VAL B 65 " ideal model delta sigma weight residual 108.00 74.06 33.94 3.00e+00 1.11e-01 1.28e+02 angle pdb=" CG1 ILE C 20 " pdb=" CD1 ILE C 20 " pdb="HD11 ILE C 20 " ideal model delta sigma weight residual 109.00 141.94 -32.94 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CA VAL B 65 " pdb=" CB VAL B 65 " pdb=" HB VAL B 65 " ideal model delta sigma weight residual 109.00 76.15 32.85 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CG1 ILE A 20 " pdb=" CD1 ILE A 20 " pdb="HD11 ILE A 20 " ideal model delta sigma weight residual 109.00 141.79 -32.79 3.00e+00 1.11e-01 1.19e+02 ... (remaining 134935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 30268 35.58 - 71.16: 652 71.16 - 106.75: 121 106.75 - 142.33: 42 142.33 - 177.91: 37 Dihedral angle restraints: 31120 sinusoidal: 15412 harmonic: 15708 Sorted by residual: dihedral pdb=" CA GLN B 389 " pdb=" C GLN B 389 " pdb=" N ASP B 390 " pdb=" CA ASP B 390 " ideal model delta harmonic sigma weight residual -180.00 -133.67 -46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA GLN D 389 " pdb=" C GLN D 389 " pdb=" N ASP D 390 " pdb=" CA ASP D 390 " ideal model delta harmonic sigma weight residual -180.00 -133.70 -46.30 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA GLN A 389 " pdb=" C GLN A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta harmonic sigma weight residual -180.00 -133.72 -46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 31117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4009 0.051 - 0.103: 1299 0.103 - 0.154: 306 0.154 - 0.206: 43 0.206 - 0.257: 11 Chirality restraints: 5668 Sorted by residual: chirality pdb=" CB VAL B 65 " pdb=" CA VAL B 65 " pdb=" CG1 VAL B 65 " pdb=" CG2 VAL B 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL C 65 " pdb=" CA VAL C 65 " pdb=" CG1 VAL C 65 " pdb=" CG2 VAL C 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL D 65 " pdb=" CA VAL D 65 " pdb=" CG1 VAL D 65 " pdb=" CG2 VAL D 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 5665 not shown) Planarity restraints: 10568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 271 " -0.082 2.00e-02 2.50e+03 4.42e-01 2.94e+03 pdb=" CG ASN C 271 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 271 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN C 271 " -0.016 2.00e-02 2.50e+03 pdb="HD21 ASN C 271 " -0.720 2.00e-02 2.50e+03 pdb="HD22 ASN C 271 " 0.804 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 271 " -0.084 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN B 271 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 271 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 271 " -0.016 2.00e-02 2.50e+03 pdb="HD21 ASN B 271 " -0.720 2.00e-02 2.50e+03 pdb="HD22 ASN B 271 " 0.803 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 271 " 0.112 2.00e-02 2.50e+03 1.23e-01 2.25e+02 pdb=" CG ASN A 271 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 271 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN A 271 " -0.051 2.00e-02 2.50e+03 pdb="HD21 ASN A 271 " -0.163 2.00e-02 2.50e+03 pdb="HD22 ASN A 271 " 0.199 2.00e-02 2.50e+03 ... (remaining 10565 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3648 2.19 - 2.79: 151880 2.79 - 3.40: 207111 3.40 - 4.00: 277266 4.00 - 4.60: 431208 Nonbonded interactions: 1071113 Sorted by model distance: nonbonded pdb=" O HIS D 27 " pdb=" HE ARG D 28 " model vdw 1.590 1.850 nonbonded pdb=" O HIS B 27 " pdb=" HE ARG B 28 " model vdw 1.591 1.850 nonbonded pdb=" O HIS C 27 " pdb=" HE ARG C 28 " model vdw 1.639 1.850 nonbonded pdb=" O HIS A 27 " pdb=" HE ARG A 28 " model vdw 1.640 1.850 nonbonded pdb=" OE2 GLU A 517 " pdb=" HG1 THR A 529 " model vdw 1.674 1.850 ... (remaining 1071108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 1230 or resid 1301 through 1303 or (resid 1306 a \ nd (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C210 or name C211 or name C212 or name C213 or name C21 \ 4 or name C215 or name C216)) or resid 1307 through 1310 or (resid 1311 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name O11 or name O12 or name O13 or name O1 \ 4 or name O21 or name O22 or name P or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216 or name C217 or name C218)) or re \ sid 1312)) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 th \ rough 1309 or (resid 1310 through 1311 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)) or resid 1312)) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 th \ rough 1309 or (resid 1310 through 1311 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)) or resid 1312)) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 th \ rough 1309 or (resid 1310 through 1311 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)) or resid 1312)) } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.860 Extract box with map and model: 8.710 Check model and map are aligned: 0.830 Set scattering table: 0.530 Process input model: 187.170 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 : 0.009 0.182 39296 Z= 0.588 Angle : 1.182 15.275 52804 Z= 0.615 Chirality : 0.054 0.257 5668 Planarity : 0.006 0.057 6340 Dihedral : 18.763 177.910 15304 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.66 % Favored : 90.70 % Rotamer: Outliers : 0.41 % Allowed : 3.37 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.14 (0.10), residues: 4388 helix: -3.33 (0.07), residues: 2488 sheet: -4.09 (0.24), residues: 216 loop : -3.18 (0.14), residues: 1684 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 805 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 813 average time/residue: 2.7074 time to fit residues: 2671.0895 Evaluate side-chains 455 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 447 time to evaluate : 4.237 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 5.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 209 optimal weight: 0.5980 chunk 256 optimal weight: 10.0000 chunk 399 optimal weight: 0.0570 overall best weight: 2.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 177 ASN A 212 ASN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 432 GLN A 500 ASN A 643 GLN A 718 ASN A 752 ASN A 789 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS A1098 ASN ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 177 ASN B 212 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 432 GLN B 500 ASN B 643 GLN B 718 ASN B 752 ASN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS B 968 ASN B1176 GLN C 140 HIS C 177 ASN C 212 ASN ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 432 GLN C 500 ASN C 643 GLN C 718 ASN C 752 ASN ** C 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 HIS C 968 ASN C1098 ASN ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 177 ASN D 212 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 432 GLN D 500 ASN D 643 GLN D 718 ASN D 752 ASN ** D 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS D 968 ASN D1176 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 39296 Z= 0.302 Angle : 0.719 9.274 52804 Z= 0.377 Chirality : 0.046 1.323 5668 Planarity : 0.005 0.047 6340 Dihedral : 22.657 178.558 6628 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.36 % Favored : 91.20 % Rotamer: Outliers : 1.74 % Allowed : 9.63 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.26 (0.11), residues: 4388 helix: -1.49 (0.09), residues: 2572 sheet: -4.47 (0.24), residues: 192 loop : -2.82 (0.14), residues: 1624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 485 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 17 residues processed: 545 average time/residue: 2.4847 time to fit residues: 1674.2677 Evaluate side-chains 429 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 412 time to evaluate : 4.218 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 1.2530 time to fit residues: 12.8698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 400 optimal weight: 5.9990 chunk 432 optimal weight: 7.9990 chunk 356 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 321 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 787 GLN A 789 GLN A 968 ASN A1097 ASN ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN B1098 ASN B1176 GLN C 281 GLN C 787 GLN ** C 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1039 HIS C1097 ASN ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1097 ASN D1098 ASN D1176 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 39296 Z= 0.317 Angle : 0.666 9.920 52804 Z= 0.343 Chirality : 0.046 1.404 5668 Planarity : 0.005 0.054 6340 Dihedral : 21.374 179.033 6628 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.30 % Favored : 91.25 % Rotamer: Outliers : 1.94 % Allowed : 10.96 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -2.36 (0.12), residues: 4388 helix: -0.65 (0.09), residues: 2600 sheet: -3.85 (0.25), residues: 224 loop : -2.68 (0.15), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 416 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 31 residues processed: 472 average time/residue: 2.3213 time to fit residues: 1375.9406 Evaluate side-chains 423 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 392 time to evaluate : 4.261 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 1.2402 time to fit residues: 12.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 401 optimal weight: 0.9980 chunk 425 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 380 optimal weight: 0.7980 chunk 114 optimal weight: 30.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39296 Z= 0.182 Angle : 0.572 10.451 52804 Z= 0.295 Chirality : 0.043 1.440 5668 Planarity : 0.004 0.033 6340 Dihedral : 19.830 179.973 6628 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.41 % Favored : 92.23 % Rotamer: Outliers : 1.63 % Allowed : 11.90 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.50 (0.12), residues: 4388 helix: 0.13 (0.10), residues: 2608 sheet: -3.48 (0.29), residues: 224 loop : -2.53 (0.15), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 402 time to evaluate : 4.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 32 residues processed: 445 average time/residue: 2.2835 time to fit residues: 1294.3812 Evaluate side-chains 410 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 378 time to evaluate : 4.235 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 3.4230 time to fit residues: 29.6470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A1039 HIS ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 HIS B1176 GLN C 358 GLN ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1039 HIS ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 39296 Z= 0.325 Angle : 0.635 10.370 52804 Z= 0.325 Chirality : 0.046 1.435 5668 Planarity : 0.004 0.047 6340 Dihedral : 19.810 177.210 6628 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.11 % Favored : 91.61 % Rotamer: Outliers : 1.99 % Allowed : 12.41 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -1.53 (0.12), residues: 4388 helix: 0.07 (0.10), residues: 2608 sheet: -3.32 (0.30), residues: 224 loop : -2.49 (0.15), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 380 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 37 residues processed: 437 average time/residue: 2.3742 time to fit residues: 1310.9585 Evaluate side-chains 414 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 377 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 1.5337 time to fit residues: 20.5261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 425 optimal weight: 0.8980 chunk 353 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 140 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 GLN ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 39296 Z= 0.295 Angle : 0.601 10.624 52804 Z= 0.308 Chirality : 0.045 1.449 5668 Planarity : 0.004 0.047 6340 Dihedral : 19.251 177.964 6628 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.98 % Favored : 91.75 % Rotamer: Outliers : 2.15 % Allowed : 12.41 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4388 helix: 0.20 (0.10), residues: 2616 sheet: -3.21 (0.31), residues: 224 loop : -2.42 (0.15), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 376 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 51 residues processed: 434 average time/residue: 2.3017 time to fit residues: 1254.0282 Evaluate side-chains 418 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 367 time to evaluate : 4.197 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 38 residues processed: 13 average time/residue: 2.0270 time to fit residues: 39.2062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 358 optimal weight: 8.9990 chunk 237 optimal weight: 20.0000 chunk 424 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1176 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 HIS C1137 HIS ** C1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39296 Z= 0.261 Angle : 0.585 10.430 52804 Z= 0.300 Chirality : 0.044 1.444 5668 Planarity : 0.004 0.045 6340 Dihedral : 18.659 177.995 6628 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.07 % Favored : 91.66 % Rotamer: Outliers : 2.02 % Allowed : 12.72 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.18 (0.12), residues: 4388 helix: 0.34 (0.10), residues: 2620 sheet: -3.12 (0.32), residues: 224 loop : -2.36 (0.15), residues: 1544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 373 time to evaluate : 4.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 47 residues processed: 433 average time/residue: 2.3399 time to fit residues: 1279.5068 Evaluate side-chains 415 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 368 time to evaluate : 4.401 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 43 residues processed: 4 average time/residue: 1.3082 time to fit residues: 13.2600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 10.0000 chunk 169 optimal weight: 0.0570 chunk 253 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C1176 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 GLN ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39296 Z= 0.289 Angle : 0.598 10.577 52804 Z= 0.306 Chirality : 0.045 1.449 5668 Planarity : 0.004 0.048 6340 Dihedral : 18.464 179.433 6628 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.50 % Favored : 91.23 % Rotamer: Outliers : 1.97 % Allowed : 12.82 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.18 (0.13), residues: 4388 helix: 0.31 (0.10), residues: 2644 sheet: -3.03 (0.33), residues: 224 loop : -2.35 (0.15), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 372 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 56 residues processed: 434 average time/residue: 2.2814 time to fit residues: 1254.7592 Evaluate side-chains 419 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 363 time to evaluate : 4.263 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 48 residues processed: 8 average time/residue: 1.0917 time to fit residues: 19.1355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 370 optimal weight: 10.0000 chunk 395 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 357 optimal weight: 8.9990 chunk 373 optimal weight: 6.9990 chunk 393 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39296 Z= 0.215 Angle : 0.566 10.478 52804 Z= 0.290 Chirality : 0.043 1.447 5668 Planarity : 0.004 0.045 6340 Dihedral : 17.833 178.778 6628 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 1.89 % Allowed : 13.20 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.85 (0.13), residues: 4388 helix: 0.60 (0.10), residues: 2616 sheet: -2.90 (0.34), residues: 224 loop : -2.22 (0.15), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 373 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 49 residues processed: 435 average time/residue: 2.3477 time to fit residues: 1291.5543 Evaluate side-chains 426 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 377 time to evaluate : 4.307 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 49 residues processed: 0 time to fit residues: 5.6646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 5.9990 chunk 417 optimal weight: 0.9990 chunk 255 optimal weight: 0.0970 chunk 198 optimal weight: 3.9990 chunk 290 optimal weight: 0.0980 chunk 438 optimal weight: 8.9990 chunk 403 optimal weight: 1.9990 chunk 349 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 HIS ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39296 Z= 0.173 Angle : 0.540 10.516 52804 Z= 0.277 Chirality : 0.042 1.441 5668 Planarity : 0.004 0.047 6340 Dihedral : 16.969 176.998 6628 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.73 % Favored : 92.07 % Rotamer: Outliers : 1.48 % Allowed : 13.61 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.55 (0.13), residues: 4388 helix: 0.87 (0.10), residues: 2604 sheet: -2.84 (0.34), residues: 224 loop : -2.12 (0.15), residues: 1560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 374 time to evaluate : 4.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 46 residues processed: 427 average time/residue: 2.3726 time to fit residues: 1280.6839 Evaluate side-chains 416 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 370 time to evaluate : 4.289 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 46 residues processed: 0 time to fit residues: 5.5991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 321 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 349 optimal weight: 0.6980 chunk 146 optimal weight: 30.0000 chunk 359 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.211814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147623 restraints weight = 113047.773| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.61 r_work: 0.3468 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39296 Z= 0.225 Angle : 0.560 10.488 52804 Z= 0.287 Chirality : 0.043 1.447 5668 Planarity : 0.004 0.037 6340 Dihedral : 16.953 177.590 6628 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.54 % Favored : 92.27 % Rotamer: Outliers : 1.58 % Allowed : 13.71 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.58 (0.13), residues: 4388 helix: 0.81 (0.10), residues: 2604 sheet: -2.81 (0.35), residues: 224 loop : -2.07 (0.15), residues: 1560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22851.41 seconds wall clock time: 394 minutes 3.65 seconds (23643.65 seconds total)