Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 04:34:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz8_32222/05_2023/7vz8_32222_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 27 5.49 5 S 283 5.16 5 C 25365 2.51 5 N 6210 2.21 5 O 7134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 42": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "n ARG 30": "NH1" <-> "NH2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 143": "OE1" <-> "OE2" Residue "r GLU 141": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 88": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 189": "OE1" <-> "OE2" Residue "w GLU 197": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39019 Number of models: 1 Model: "" Number of chains: 64 Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 740 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "l" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4782 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 925 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "l" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 146 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "m" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 354 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "S" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "j" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "k" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "l" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "m" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "u" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.62 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.62 Time building chain proxies: 27.26, per 1000 atoms: 0.70 Number of scatterers: 39019 At special positions: 0 Unit cell: (179.507, 192.681, 136.689, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 283 16.00 P 27 15.00 O 7134 8.00 N 6210 7.00 C 25365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=1.86 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.23 Conformation dependent library (CDL) restraints added in 5.8 seconds 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 4 sheets defined 63.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.207A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 33 through 99 Proline residue: W 73 - end of helix removed outlier: 3.741A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.357A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.381A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.699A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.591A pdb=" N ALA Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 46 through 53' Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.659A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.618A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.858A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.848A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.531A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.277A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.909A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.772A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.674A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.317A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix removed outlier: 3.558A pdb=" N SER i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.828A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.942A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.751A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.753A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 56 removed outlier: 4.155A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.801A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.968A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 3.993A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.373A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.756A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.819A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.745A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.607A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 547 Proline residue: l 530 - end of helix removed outlier: 4.081A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.320A pdb=" N SER l 543 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.854A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.193A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 38 removed outlier: 6.424A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.559A pdb=" N GLU n 33 " --> pdb=" O ARG n 29 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR n 36 " --> pdb=" O ASP n 32 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA n 37 " --> pdb=" O GLU n 33 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 48 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 93 through 97 removed outlier: 4.447A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.943A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.206A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.255A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.791A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.405A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.629A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 170 removed outlier: 3.794A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.509A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.123A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 249 removed outlier: 4.479A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.641A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.029A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.926A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.664A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.097A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.835A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.407A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.314A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.845A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.518A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 310 removed outlier: 5.028A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 43 through 48 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 95 through 97 No H-bonds generated for 'chain 'w' and resid 95 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.266A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 249 removed outlier: 4.194A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.900A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 333 Processing sheet with id= A, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'l' and resid 61 through 67 removed outlier: 6.527A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.408A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'w' and resid 84 through 86 2008 hydrogen bonds defined for protein. 5625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.70 Time building geometry restraints manager: 19.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5863 1.31 - 1.44: 10781 1.44 - 1.56: 22358 1.56 - 1.69: 164 1.69 - 1.82: 511 Bond restraints: 39677 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CA7 CDL r 503 " pdb=" OA8 CDL r 503 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL r 503 " pdb=" OB8 CDL r 503 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.618 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" CA7 CDL V 201 " pdb=" OA8 CDL V 201 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.10e-02 8.26e+03 7.95e+01 ... (remaining 39672 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.81: 1158 105.81 - 113.02: 21673 113.02 - 120.23: 14737 120.23 - 127.44: 15511 127.44 - 134.65: 538 Bond angle restraints: 53617 Sorted by residual: angle pdb=" C11 CDL r 503 " pdb=" CA5 CDL r 503 " pdb=" OA6 CDL r 503 " ideal model delta sigma weight residual 111.33 121.81 -10.48 1.32e+00 5.72e-01 6.28e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.92 -9.59 1.32e+00 5.72e-01 5.26e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.90 -9.57 1.32e+00 5.72e-01 5.24e+01 angle pdb=" C51 CDL V 201 " pdb=" CB5 CDL V 201 " pdb=" OB6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.74 -9.41 1.32e+00 5.72e-01 5.07e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.59 -9.26 1.32e+00 5.72e-01 4.90e+01 ... (remaining 53612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.93: 22267 29.93 - 59.86: 1419 59.86 - 89.80: 96 89.80 - 119.73: 8 119.73 - 149.66: 8 Dihedral angle restraints: 23798 sinusoidal: 10172 harmonic: 13626 Sorted by residual: dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.51 -68.51 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.21 -145.21 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" CA ILE a 93 " pdb=" C ILE a 93 " pdb=" N GLY a 94 " pdb=" CA GLY a 94 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 23795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4390 0.046 - 0.091: 1142 0.091 - 0.137: 261 0.137 - 0.182: 24 0.182 - 0.228: 15 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CA THR r 111 " pdb=" N THR r 111 " pdb=" C THR r 111 " pdb=" CB THR r 111 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU l 286 " pdb=" CB LEU l 286 " pdb=" CD1 LEU l 286 " pdb=" CD2 LEU l 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL o 59 " pdb=" N VAL o 59 " pdb=" C VAL o 59 " pdb=" CB VAL o 59 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5829 not shown) Planarity restraints: 6559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 62 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO Q 63 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO Q 63 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO Q 63 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER o 26 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO o 27 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO o 27 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO o 27 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY s 218 " -0.043 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO s 219 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO s 219 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO s 219 " -0.037 5.00e-02 4.00e+02 ... (remaining 6556 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3396 2.74 - 3.28: 38632 3.28 - 3.82: 67738 3.82 - 4.36: 83522 4.36 - 4.90: 137931 Nonbonded interactions: 331219 Sorted by model distance: nonbonded pdb=" O THR l 13 " pdb=" OG1 THR l 16 " model vdw 2.199 2.440 nonbonded pdb=" O ALA g 58 " pdb=" O TRP w 353 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU i 269 " pdb=" O HOH i 501 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR r 153 " pdb=" O HOH r 601 " model vdw 2.217 2.440 nonbonded pdb=" NE2 GLN r 81 " pdb=" O HOH r 602 " model vdw 2.218 2.520 ... (remaining 331214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.62 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 26.680 Check model and map are aligned: 0.910 Set scattering table: 0.330 Process input model: 104.740 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 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 : 0.006 0.223 39677 Z= 0.422 Angle : 0.814 17.383 53617 Z= 0.422 Chirality : 0.043 0.228 5832 Planarity : 0.006 0.105 6559 Dihedral : 18.093 149.659 14974 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.12 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.12), residues: 4582 helix: 1.80 (0.10), residues: 2940 sheet: 1.08 (1.27), residues: 20 loop : -0.46 (0.15), residues: 1622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 691 time to evaluate : 4.643 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 43 residues processed: 734 average time/residue: 1.7803 time to fit residues: 1551.0727 Evaluate side-chains 710 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 667 time to evaluate : 4.231 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.7083 time to fit residues: 10.6100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 4.9990 chunk 343 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 411 optimal weight: 0.0010 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 GLN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 310 ASN k 91 GLN l 351 ASN m 46 ASN p 141 GLN s 171 HIS s 284 GLN w 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 39677 Z= 0.162 Angle : 0.534 9.058 53617 Z= 0.270 Chirality : 0.039 0.182 5832 Planarity : 0.005 0.081 6559 Dihedral : 12.940 152.526 5839 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.13), residues: 4582 helix: 2.04 (0.10), residues: 2939 sheet: 0.46 (1.13), residues: 26 loop : -0.39 (0.16), residues: 1617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 689 time to evaluate : 4.566 Fit side-chains revert: symmetry clash outliers start: 141 outliers final: 68 residues processed: 767 average time/residue: 1.6668 time to fit residues: 1532.2565 Evaluate side-chains 741 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 673 time to evaluate : 4.729 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 47 residues processed: 21 average time/residue: 0.5291 time to fit residues: 24.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 342 optimal weight: 0.9990 chunk 280 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 412 optimal weight: 10.0000 chunk 445 optimal weight: 10.0000 chunk 367 optimal weight: 0.9990 chunk 408 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN d 124 ASN e 132 ASN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 221 HIS k 91 GLN l 205 ASN l 351 ASN m 46 ASN p 62 GLN p 141 GLN r 390 ASN s 287 HIS u 64 ASN w 37 GLN w 127 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 39677 Z= 0.325 Angle : 0.635 11.793 53617 Z= 0.322 Chirality : 0.045 0.208 5832 Planarity : 0.005 0.073 6559 Dihedral : 12.460 153.393 5839 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.85 % Rotamer Outliers : 4.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.57 (0.12), residues: 4582 helix: 1.85 (0.10), residues: 2939 sheet: 1.37 (1.28), residues: 20 loop : -0.45 (0.15), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 682 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 94 residues processed: 778 average time/residue: 1.7397 time to fit residues: 1619.4751 Evaluate side-chains 765 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 671 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 60 residues processed: 34 average time/residue: 0.7333 time to fit residues: 42.1796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 413 optimal weight: 2.9990 chunk 437 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 391 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN m 46 ASN p 66 GLN p 141 GLN r 139 GLN r 390 ASN w 37 GLN w 127 ASN w 239 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 39677 Z= 0.161 Angle : 0.525 9.274 53617 Z= 0.266 Chirality : 0.039 0.183 5832 Planarity : 0.005 0.068 6559 Dihedral : 11.620 159.893 5839 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.13), residues: 4582 helix: 2.07 (0.10), residues: 2950 sheet: 0.61 (1.14), residues: 26 loop : -0.40 (0.16), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 697 time to evaluate : 4.896 Fit side-chains revert: symmetry clash outliers start: 128 outliers final: 69 residues processed: 777 average time/residue: 1.7256 time to fit residues: 1610.2833 Evaluate side-chains 735 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 666 time to evaluate : 4.629 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 52 residues processed: 17 average time/residue: 0.7084 time to fit residues: 23.8167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 373 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 393 optimal weight: 0.0570 chunk 110 optimal weight: 9.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN d 140 GLN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN l 351 ASN p 141 GLN r 390 ASN u 64 ASN w 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 39677 Z= 0.247 Angle : 0.578 9.566 53617 Z= 0.293 Chirality : 0.042 0.200 5832 Planarity : 0.005 0.066 6559 Dihedral : 11.455 160.665 5839 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.96 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.13), residues: 4582 helix: 1.99 (0.10), residues: 2945 sheet: 0.92 (1.15), residues: 25 loop : -0.41 (0.16), residues: 1612 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 681 time to evaluate : 5.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 85 residues processed: 766 average time/residue: 1.7992 time to fit residues: 1655.8204 Evaluate side-chains 767 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 682 time to evaluate : 5.000 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 55 residues processed: 30 average time/residue: 0.8774 time to fit residues: 43.2894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 3.9990 chunk 394 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 257 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 438 optimal weight: 0.0170 chunk 363 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN Y 54 GLN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN l 446 ASN p 141 GLN r 139 GLN r 390 ASN s 287 HIS u 64 ASN w 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39677 Z= 0.173 Angle : 0.531 9.917 53617 Z= 0.269 Chirality : 0.039 0.186 5832 Planarity : 0.005 0.064 6559 Dihedral : 11.047 164.506 5839 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.33 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.13), residues: 4582 helix: 2.10 (0.10), residues: 2949 sheet: 1.26 (1.15), residues: 24 loop : -0.36 (0.16), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 695 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 75 residues processed: 778 average time/residue: 1.7570 time to fit residues: 1636.5186 Evaluate side-chains 746 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 671 time to evaluate : 4.755 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 57 residues processed: 18 average time/residue: 0.8136 time to fit residues: 27.0332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 0.0060 chunk 49 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 320 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 436 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN Y 54 GLN ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 GLN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN ** l 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN l 446 ASN p 141 GLN r 139 GLN r 390 ASN s 287 HIS u 64 ASN w 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 39677 Z= 0.368 Angle : 0.667 12.560 53617 Z= 0.338 Chirality : 0.046 0.213 5832 Planarity : 0.006 0.064 6559 Dihedral : 11.512 167.789 5839 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.47 (0.12), residues: 4582 helix: 1.78 (0.09), residues: 2934 sheet: 0.88 (1.16), residues: 25 loop : -0.48 (0.15), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 676 time to evaluate : 4.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 83 residues processed: 768 average time/residue: 1.7901 time to fit residues: 1653.3009 Evaluate side-chains 748 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 665 time to evaluate : 4.405 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 58 residues processed: 25 average time/residue: 0.6997 time to fit residues: 31.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 297 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 343 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN p 13 GLN p 141 GLN r 139 GLN r 390 ASN u 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39677 Z= 0.174 Angle : 0.546 10.380 53617 Z= 0.277 Chirality : 0.039 0.186 5832 Planarity : 0.005 0.064 6559 Dihedral : 10.971 174.758 5839 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.46 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.13), residues: 4582 helix: 2.03 (0.10), residues: 2942 sheet: 1.24 (1.15), residues: 24 loop : -0.45 (0.15), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 683 time to evaluate : 5.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 64 residues processed: 756 average time/residue: 1.7903 time to fit residues: 1628.4739 Evaluate side-chains 724 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 660 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 52 residues processed: 12 average time/residue: 0.7607 time to fit residues: 19.3050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 0.4980 chunk 418 optimal weight: 0.9980 chunk 381 optimal weight: 2.9990 chunk 406 optimal weight: 0.0770 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 124 optimal weight: 0.0270 chunk 367 optimal weight: 3.9990 chunk 384 optimal weight: 0.0270 chunk 405 optimal weight: 2.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN Y 54 GLN d 140 GLN g 18 ASN k 91 GLN l 351 ASN l 446 ASN ** l 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 GLN p 62 GLN p 141 GLN r 139 GLN r 293 HIS u 65 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 39677 Z= 0.139 Angle : 0.508 10.465 53617 Z= 0.255 Chirality : 0.038 0.169 5832 Planarity : 0.004 0.063 6559 Dihedral : 10.050 178.049 5839 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.13), residues: 4582 helix: 2.27 (0.10), residues: 2937 sheet: 1.74 (1.21), residues: 22 loop : -0.28 (0.16), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 690 time to evaluate : 4.981 Fit side-chains revert: symmetry clash outliers start: 78 outliers final: 47 residues processed: 752 average time/residue: 1.7506 time to fit residues: 1598.0459 Evaluate side-chains 706 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 659 time to evaluate : 4.219 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 3 average time/residue: 1.2879 time to fit residues: 10.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.9980 chunk 430 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 451 optimal weight: 0.9990 chunk 415 optimal weight: 6.9990 chunk 359 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN c 127 ASN d 140 GLN g 18 ASN k 91 GLN l 2 ASN l 59 GLN l 351 ASN l 405 ASN p 141 GLN s 287 HIS u 64 ASN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 85 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 39677 Z= 0.167 Angle : 0.533 10.974 53617 Z= 0.268 Chirality : 0.039 0.182 5832 Planarity : 0.004 0.062 6559 Dihedral : 9.949 170.315 5839 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.44 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.13), residues: 4582 helix: 2.26 (0.10), residues: 2929 sheet: 1.53 (1.16), residues: 24 loop : -0.25 (0.16), residues: 1629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 681 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 57 residues processed: 736 average time/residue: 1.7731 time to fit residues: 1562.9214 Evaluate side-chains 721 residues out of total 4086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 664 time to evaluate : 4.180 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 48 residues processed: 9 average time/residue: 0.9305 time to fit residues: 17.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 5.9990 chunk 382 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 359 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: