Starting phenix.real_space_refine on Tue Apr 16 18:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbl_31881/04_2024/7vbl_31881_updated.pdb" } resolution = 2.6 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= 0.000 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 38 5.49 5 S 293 5.16 5 C 26117 2.51 5 N 6281 2.21 5 O 7413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ARG 50": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "U ARG 58": "NH1" <-> "NH2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 82": "NH1" <-> "NH2" Residue "W ARG 88": "NH1" <-> "NH2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "Y ARG 43": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 72": "NH1" <-> "NH2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a ARG 119": "NH1" <-> "NH2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a ARG 158": "NH1" <-> "NH2" Residue "a ARG 161": "NH1" <-> "NH2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d ARG 43": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d ARG 153": "NH1" <-> "NH2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e ARG 54": "NH1" <-> "NH2" Residue "e ARG 113": "NH1" <-> "NH2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ARG 119": "NH1" <-> "NH2" Residue "e ARG 124": "NH1" <-> "NH2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "e GLU 153": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g ARG 80": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h ARG 32": "NH1" <-> "NH2" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 83": "NH1" <-> "NH2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l ARG 161": "NH1" <-> "NH2" Residue "l ARG 176": "NH1" <-> "NH2" Residue "l TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 425": "NH1" <-> "NH2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m GLU 100": "OE1" <-> "OE2" Residue "n ARG 30": "NH1" <-> "NH2" Residue "n ARG 47": "NH1" <-> "NH2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o ARG 30": "NH1" <-> "NH2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 45": "NH1" <-> "NH2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p ARG 129": "NH1" <-> "NH2" Residue "p ARG 150": "NH1" <-> "NH2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r ARG 142": "NH1" <-> "NH2" Residue "r ARG 278": "NH1" <-> "NH2" Residue "r ARG 340": "NH1" <-> "NH2" Residue "r ARG 432": "NH1" <-> "NH2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "s ARG 281": "NH1" <-> "NH2" Residue "u ARG 47": "NH1" <-> "NH2" Residue "u GLU 58": "OE1" <-> "OE2" Residue "u ARG 72": "NH1" <-> "NH2" Residue "u GLU 84": "OE1" <-> "OE2" Residue "u ARG 98": "NH1" <-> "NH2" Residue "u ARG 119": "NH1" <-> "NH2" Residue "u ARG 135": "NH1" <-> "NH2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u ARG 166": "NH1" <-> "NH2" Residue "v ARG 7": "NH1" <-> "NH2" Residue "v ARG 8": "NH1" <-> "NH2" Residue "v ARG 71": "NH1" <-> "NH2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v ARG 106": "NH1" <-> "NH2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w ARG 180": "NH1" <-> "NH2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 262": "OE1" <-> "OE2" Residue "w GLU 264": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w ARG 289": "NH1" <-> "NH2" Residue "w ARG 326": "NH1" <-> "NH2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40142 Number of models: 1 Model: "" Number of chains: 63 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 691 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 611 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 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: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4797 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "m" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1273 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 45 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: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} 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: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "j" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "l" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 231 Unusual residues: {'CDL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "j" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "k" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "l" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "m" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "s" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 19.11, per 1000 atoms: 0.48 Number of scatterers: 40142 At special positions: 0 Unit cell: (183.151, 190.133, 136.423, 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 293 16.00 P 38 15.00 O 7413 8.00 N 6281 7.00 C 26117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.04 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.04 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.21 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.02 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.12 Conformation dependent library (CDL) restraints added in 6.4 seconds 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 206 helices and 4 sheets defined 63.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1784.80 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.981A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.654A 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 4 No H-bonds generated for 'chain 'S' and resid 2 through 4' Processing helix chain 'S' and resid 6 through 29 removed outlier: 3.661A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 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 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 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 97 Proline residue: W 73 - end of helix 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: 5.856A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.298A 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 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.901A 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 77 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 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' 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: 3.930A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.927A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 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: 3.596A 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 25 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' 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 129 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 5.572A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.547A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) 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 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.625A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN d 123 " --> pdb=" O SER d 120 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN d 124 " --> pdb=" O TYR d 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 118 through 124' 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 95 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'f' and resid 41 through 73 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 removed outlier: 3.759A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' 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 removed outlier: 4.124A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 88 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 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 112 through 121 Proline residue: i 116 - end of helix Processing helix chain 'i' and resid 124 through 144 removed outlier: 4.130A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.808A 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 151 through 171 removed outlier: 4.091A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.820A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.509A 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 removed outlier: 3.671A pdb=" N ILE i 267 " --> pdb=" O TRP i 264 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN i 268 " --> pdb=" O MET i 265 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 300 removed outlier: 4.729A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.305A 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 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 31 through 34 No H-bonds generated for 'chain 'j' and resid 31 through 34' Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.553A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.526A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.622A 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: 3.815A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.842A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.422A 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: 3.881A 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 192 removed outlier: 3.902A 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 231 through 238 removed outlier: 3.593A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.108A 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 252 through 262 removed outlier: 4.294A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.328A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.601A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.622A 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: 4.004A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (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 387 through 400 removed outlier: 3.956A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE l 395 " --> pdb=" O SER l 391 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.765A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 5.715A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.408A 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 508 removed outlier: 4.235A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.205A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 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 removed outlier: 3.535A pdb=" N THR l 600 " --> pdb=" O MET l 596 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 removed outlier: 3.646A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.227A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 171 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.387A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.717A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.701A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 75 through 79 removed outlier: 3.729A pdb=" N ASN o 79 " --> pdb=" O ASN o 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 75 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.601A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' 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 142 removed outlier: 5.060A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (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: 3.859A 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: 4.193A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.515A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.778A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.571A 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 171 removed outlier: 3.514A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU r 154 " --> pdb=" O PHE r 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.750A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.939A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.086A 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 248 removed outlier: 3.514A pdb=" N TYR r 241 " --> pdb=" O LEU r 238 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.530A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.710A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.546A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.683A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (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: 3.648A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY r 397 " --> pdb=" O ILE r 394 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.753A 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: 3.654A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 455 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.726A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' 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: 4.440A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.711A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.102A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 168 removed outlier: 3.670A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 192 removed outlier: 3.699A pdb=" N SER s 178 " --> pdb=" O ILE s 175 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TRP s 179 " --> pdb=" O PHE s 176 " (cutoff:3.500A) Proline residue: s 180 - end of helix Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.519A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 310 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.961A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) 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 102 through 114 Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 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: 4.346A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.600A 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 251 removed outlier: 5.200A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 4.069A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.293A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 333 Processing helix chain 'w' and resid 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' 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 62 through 67 removed outlier: 6.863A 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: 6.595A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (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 2018 hydrogen bonds defined for protein. 5649 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: 14.21 Time building geometry restraints manager: 15.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6033 1.32 - 1.46: 13563 1.46 - 1.60: 20512 1.60 - 1.74: 75 1.74 - 1.88: 530 Bond restraints: 40713 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CA7 CDL u 201 " pdb=" OA8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL a 201 " pdb=" OB8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL l 702 " pdb=" OA8 CDL l 702 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 ... (remaining 40708 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.42: 1129 105.42 - 113.06: 22386 113.06 - 120.70: 18942 120.70 - 128.34: 12025 128.34 - 135.98: 426 Bond angle restraints: 54908 Sorted by residual: angle pdb=" N ILE s 10 " pdb=" CA ILE s 10 " pdb=" C ILE s 10 " ideal model delta sigma weight residual 110.72 122.90 -12.18 1.01e+00 9.80e-01 1.45e+02 angle pdb=" N ILE r 441 " pdb=" CA ILE r 441 " pdb=" C ILE r 441 " ideal model delta sigma weight residual 110.62 121.36 -10.74 1.02e+00 9.61e-01 1.11e+02 angle pdb=" N ILE r 5 " pdb=" CA ILE r 5 " pdb=" C ILE r 5 " ideal model delta sigma weight residual 110.72 121.20 -10.48 1.01e+00 9.80e-01 1.08e+02 angle pdb=" C ALA X 71 " pdb=" N PRO X 72 " pdb=" CA PRO X 72 " ideal model delta sigma weight residual 119.66 126.72 -7.06 7.20e-01 1.93e+00 9.63e+01 angle pdb=" N ILE i 277 " pdb=" CA ILE i 277 " pdb=" C ILE i 277 " ideal model delta sigma weight residual 110.62 120.06 -9.44 1.02e+00 9.61e-01 8.56e+01 ... (remaining 54903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 23828 35.25 - 70.50: 896 70.50 - 105.76: 62 105.76 - 141.01: 23 141.01 - 176.26: 8 Dihedral angle restraints: 24817 sinusoidal: 10958 harmonic: 13859 Sorted by residual: dihedral pdb=" CA LYS b 121 " pdb=" C LYS b 121 " pdb=" N GLU b 122 " pdb=" CA GLU b 122 " ideal model delta harmonic sigma weight residual 180.00 146.27 33.73 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -144.05 58.05 1 1.00e+01 1.00e-02 4.52e+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 77.17 -137.16 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 24814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5650 0.120 - 0.239: 248 0.239 - 0.359: 24 0.359 - 0.478: 7 0.478 - 0.598: 4 Chirality restraints: 5933 Sorted by residual: chirality pdb=" CA TYR s 282 " pdb=" N TYR s 282 " pdb=" C TYR s 282 " pdb=" CB TYR s 282 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CA PHE r 151 " pdb=" N PHE r 151 " pdb=" C PHE r 151 " pdb=" CB PHE r 151 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA HIS r 422 " pdb=" N HIS r 422 " pdb=" C HIS r 422 " pdb=" CB HIS r 422 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 5930 not shown) Planarity restraints: 6671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.358 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" C18 UQ s 402 " -0.349 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.389 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.004 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.056 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C11 UQ s 402 " 0.037 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.290 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.549 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.110 2.00e-02 2.50e+03 1.82e-01 4.14e+02 pdb=" C13 UQ s 402 " 0.034 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.334 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.067 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.191 2.00e-02 2.50e+03 ... (remaining 6668 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 110 2.35 - 2.98: 20257 2.98 - 3.62: 60828 3.62 - 4.26: 101843 4.26 - 4.90: 162679 Nonbonded interactions: 345717 Sorted by model distance: nonbonded pdb=" OE2 GLU a 97 " pdb=" CD ARG d 60 " model vdw 1.707 3.440 nonbonded pdb=" OE2 GLU m 77 " pdb=" O HOH m 301 " model vdw 1.996 2.440 nonbonded pdb=" O TYR l 27 " pdb=" ND2 ASN l 115 " model vdw 2.046 2.520 nonbonded pdb=" OE2 GLU i 269 " pdb=" O HOH i 501 " model vdw 2.074 2.440 nonbonded pdb=" O PRO j 36 " pdb=" O HOH j 301 " model vdw 2.081 2.440 ... (remaining 345712 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=0.50 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: 12.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 33.180 Check model and map are aligned: 0.630 Set scattering table: 0.320 Process input model: 96.260 Find NCS groups from input model: 1.200 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 0.227 40713 Z= 0.609 Angle : 1.075 17.216 54908 Z= 0.630 Chirality : 0.062 0.598 5933 Planarity : 0.008 0.329 6671 Dihedral : 17.803 176.260 15837 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 0.98 % Allowed : 3.22 % Favored : 95.81 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.80 % 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: -0.18 (0.12), residues: 4667 helix: 0.49 (0.09), residues: 2962 sheet: -2.04 (0.86), residues: 25 loop : -1.08 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 86 HIS 0.018 0.002 HIS l 534 PHE 0.042 0.002 PHE s 270 TYR 0.026 0.002 TYR m 4 ARG 0.009 0.001 ARG W 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 893 time to evaluate : 5.679 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 56 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7491 (mmmt) REVERT: U 16 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7372 (mm-30) REVERT: U 38 TYR cc_start: 0.7669 (m-80) cc_final: 0.7426 (m-80) REVERT: V 140 LYS cc_start: 0.8027 (tttt) cc_final: 0.7517 (mmtm) REVERT: Y 90 SER cc_start: 0.8360 (m) cc_final: 0.7976 (p) REVERT: a 95 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7870 (mt-10) REVERT: c 36 MET cc_start: 0.7349 (mmp) cc_final: 0.6793 (mtt) REVERT: f 70 LYS cc_start: 0.8480 (mttt) cc_final: 0.8192 (mttm) REVERT: h 71 LYS cc_start: 0.8764 (mttt) cc_final: 0.8503 (mttm) REVERT: i 14 MET cc_start: 0.8907 (mtp) cc_final: 0.8636 (mtp) REVERT: i 34 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8283 (mm-30) REVERT: i 69 MET cc_start: 0.8556 (mtp) cc_final: 0.8317 (mtp) REVERT: i 202 ILE cc_start: 0.9046 (mt) cc_final: 0.8841 (mm) REVERT: i 321 LYS cc_start: 0.7376 (tppt) cc_final: 0.7157 (mmmm) REVERT: n 31 SER cc_start: 0.8558 (t) cc_final: 0.8352 (m) REVERT: o 31 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7889 (ttpp) REVERT: o 111 LYS cc_start: 0.8133 (mttt) cc_final: 0.7869 (mttp) REVERT: p 13 GLN cc_start: 0.7642 (tm-30) cc_final: 0.6729 (mp10) REVERT: p 65 ARG cc_start: 0.7323 (ttt90) cc_final: 0.7097 (mtp-110) REVERT: p 66 GLN cc_start: 0.7383 (mt0) cc_final: 0.7172 (mt0) REVERT: p 124 GLN cc_start: 0.7977 (mt0) cc_final: 0.7680 (mt0) REVERT: r 22 MET cc_start: 0.8825 (mmm) cc_final: 0.8594 (mmp) REVERT: r 78 MET cc_start: 0.9107 (mtt) cc_final: 0.8889 (mtp) REVERT: r 401 MET cc_start: 0.8247 (ttp) cc_final: 0.7677 (tpp) REVERT: w 293 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7507 (ttp80) outliers start: 40 outliers final: 7 residues processed: 909 average time/residue: 1.9452 time to fit residues: 2077.5158 Evaluate side-chains 679 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 671 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain d residue 62 TYR Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 0.2980 chunk 347 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 358 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 415 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 38 GLN S 27 HIS S 31 ASN S 61 HIS U 11 ASN V 129 GLN W 61 GLN W 85 GLN Y 39 HIS Y 54 GLN Y 57 GLN a 132 ASN b 83 HIS c 84 GLN c 160 GLN c 183 HIS d 56 HIS d 91 GLN d 107 GLN d 159 GLN e 74 HIS e 86 ASN f 61 GLN g 18 ASN g 99 HIS h 21 GLN i 47 ASN i 83 GLN i 91 ASN i 172 GLN i 174 GLN i 273 ASN j 28 ASN k 92 ASN l 2 ASN l 165 ASN l 226 GLN l 446 ASN l 524 ASN l 579 ASN m 46 ASN p 26 HIS p 108 HIS p 139 GLN p 141 GLN r 43 ASN r 51 ASN r 83 HIS r 139 GLN r 399 ASN r 421 HIS r 440 HIS s 171 HIS s 230 ASN s 287 HIS u 16 GLN v 61 HIS v 92 HIS w 107 GLN w 127 ASN w 142 GLN w 176 GLN w 186 HIS w 235 GLN w 239 ASN w 286 GLN w 292 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40713 Z= 0.171 Angle : 0.583 12.857 54908 Z= 0.295 Chirality : 0.040 0.194 5933 Planarity : 0.005 0.048 6671 Dihedral : 17.347 156.018 6650 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 9.17 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.04 (0.12), residues: 4667 helix: 1.48 (0.09), residues: 2967 sheet: -1.29 (0.92), residues: 25 loop : -0.68 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS l 534 PHE 0.030 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.009 0.000 ARG d 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9334 Ramachandran restraints generated. 4667 Oldfield, 0 Emsley, 4667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 706 time to evaluate : 4.612 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 56 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7382 (mmmt) REVERT: U 16 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7273 (mm-30) REVERT: V 120 LEU cc_start: 0.8380 (tp) cc_final: 0.7834 (mt) REVERT: W 93 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: X 151 LYS cc_start: 0.8492 (tppp) cc_final: 0.8046 (tptm) REVERT: Y 90 SER cc_start: 0.8384 (m) cc_final: 0.7988 (p) REVERT: a 72 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: a 95 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8050 (mt-10) REVERT: c 36 MET cc_start: 0.7129 (mmp) cc_final: 0.6738 (mtt) REVERT: d 6 ASP cc_start: 0.8457 (t0) cc_final: 0.8221 (t0) REVERT: d 78 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: e 54 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5175 (mmt90) REVERT: e 116 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: f 70 LYS cc_start: 0.8490 (mttt) cc_final: 0.8234 (mttm) REVERT: h 53 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: h 55 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: i 34 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8254 (mm-30) REVERT: i 69 MET cc_start: 0.8476 (mtp) cc_final: 0.8258 (mtp) REVERT: i 278 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7387 (tpt) REVERT: j 19 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8398 (mm) REVERT: k 1 MET cc_start: 0.6302 (mtp) cc_final: 0.5819 (ttp) REVERT: k 10 MET cc_start: 0.8248 (tpt) cc_final: 0.7818 (tpt) REVERT: o 31 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7918 (ttpp) REVERT: o 111 LYS cc_start: 0.8050 (mttt) cc_final: 0.7766 (mttp) REVERT: p 13 GLN cc_start: 0.7767 (tm-30) cc_final: 0.6857 (mp10) REVERT: p 59 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7123 (tttp) REVERT: p 65 ARG cc_start: 0.7371 (ttt90) cc_final: 0.7133 (mtp-110) REVERT: p 135 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7480 (ttp-170) REVERT: r 22 MET cc_start: 0.8814 (mmm) cc_final: 0.8570 (mmp) REVERT: s 258 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (t0) REVERT: u 19 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7496 (ptpt) REVERT: u 84 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: w 72 ARG cc_start: 0.7192 (ttp-170) cc_final: 0.6952 (ttp80) REVERT: w 293 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7441 (ttp80) outliers start: 93 outliers final: 29 residues processed: 744 average time/residue: 1.9529 time to fit residues: 1718.4274 Evaluate side-chains 713 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 669 time to evaluate : 4.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 56 LYS Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 44 LYS Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 185 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain e residue 54 ARG Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 115 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 417 SER Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 58 SER Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 256 TYR Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 19 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain v residue 70 LYS Chi-restraints excluded: chain v residue 94 ASP Chi-restraints excluded: chain w residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 450 optimal weight: 0.0870 chunk 371 optimal weight: 2.9990 chunk 413 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 334 optimal weight: 4.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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: