Starting phenix.real_space_refine (version: dev) on Mon Feb 27 07:30:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v31_31649/02_2023/7v31_31649_updated.pdb" } resolution = 2.9 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= 0.001 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "L PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 591": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 36": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 63": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "g PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "j TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l ARG 425": "NH1" <-> "NH2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "o TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 141": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 68204 Number of models: 1 Model: "" Number of chains: 71 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} 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: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} 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: 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: 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: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 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: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2586 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'970': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' 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: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: 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: "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: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 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: "j" 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: "l" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 289 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "m" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 95 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "r" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 254 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {' UQ': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 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: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.224 48.244 171.481 1.00 12.97 S ATOM 3060 SG CYS A 425 46.666 45.453 177.373 1.00 15.18 S ATOM 2738 SG CYS A 385 44.121 43.749 171.610 1.00 14.19 S ATOM 2699 SG CYS A 379 41.791 48.584 175.545 1.00 15.13 S ATOM 3961 SG CYS B 113 35.442 63.641 136.707 1.00 13.08 S ATOM 3980 SG CYS B 116 40.571 61.435 140.574 1.00 12.16 S ATOM 4003 SG CYS B 119 41.597 64.312 135.146 1.00 16.83 S ATOM 4332 SG CYS B 162 39.364 58.323 135.774 1.00 15.57 S ATOM 4030 SG CYS B 123 47.522 67.292 130.699 1.00 25.70 S ATOM 4256 SG CYS B 152 46.026 65.378 124.700 1.00 25.70 S ATOM 4303 SG CYS B 158 44.159 61.609 129.617 1.00 25.70 S ATOM 4282 SG CYS B 155 50.229 62.173 128.033 1.00 25.70 S ATOM 5724 SG CYS C 166 52.718 65.726 120.499 1.00 18.38 S ATOM 4996 SG CYS C 72 52.974 67.202 114.146 1.00 9.40 S ATOM 4990 SG CYS C 71 58.316 65.630 117.397 1.00 9.12 S ATOM 5494 SG CYS C 136 54.820 70.914 119.358 1.00 16.70 S ATOM 14949 SG CYS M 131 39.937 61.685 152.616 1.00 10.98 S ATOM 14928 SG CYS M 128 43.590 57.066 149.568 1.00 25.70 S ATOM 14989 SG CYS M 137 45.462 60.607 154.921 1.00 10.76 S ATOM 15321 SG CYS M 179 42.868 60.929 165.640 1.00 15.29 S ATOM 15675 SG CYS M 226 40.598 63.332 161.436 1.00 9.07 S ATOM 15345 SG CYS M 182 38.448 62.992 167.473 1.00 8.69 S ATOM 15298 SG CYS M 176 38.347 58.036 164.134 1.00 8.70 S ATOM 14546 SG CYS M 78 55.564 56.880 169.787 1.00 13.11 S ATOM 14647 SG CYS M 92 53.560 58.880 172.044 1.00 11.11 S ATOM 14435 SG CYS M 64 49.148 58.445 169.662 1.00 6.46 S ATOM 14521 SG CYS M 75 50.352 56.848 167.381 1.00 9.91 S ATOM 21484 SG CYS O 135 31.867 30.084 179.363 1.00 38.02 S ATOM 21518 SG CYS O 140 31.022 26.588 179.960 1.00 41.05 S ATOM 21821 SG CYS O 180 36.233 28.591 182.615 1.00 50.05 S ATOM 28560 SG CYS T 86 28.648 49.938 144.557 1.00 17.88 S ATOM 28738 SG CYS T 111 29.828 53.436 145.725 1.00 17.67 S 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: 28.60, per 1000 atoms: 0.42 Number of scatterers: 68204 At special positions: 0 Unit cell: (206.246, 224.508, 227.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 45 15.00 Mg 1 11.99 O 12229 8.00 N 11239 7.00 C 44179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.05 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 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=2.44 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=2.54 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.56 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 351 helices and 29 sheets defined 52.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.597A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.519A pdb=" N VAL A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.468A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.982A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.563A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.488A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.123A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.454A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 5.004A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU F 43 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.942A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.090A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.898A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 3.643A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.913A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 353 No H-bonds generated for 'chain 'J' and resid 350 through 353' Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.486A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 4.348A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.867A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.505A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 384 No H-bonds generated for 'chain 'M' and resid 382 through 384' Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 483 removed outlier: 3.884A pdb=" N GLN M 482 " --> pdb=" O SER M 478 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG M 483 " --> pdb=" O SER M 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 478 through 483' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.620A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.902A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.574A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.760A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.578A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.980A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.634A 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 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.664A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 139 removed outlier: 4.102A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 193 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.925A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 286 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.379A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 310 through 313 Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 4.448A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 Processing helix chain 'Q' and resid 458 through 462 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 30 removed outlier: 3.820A 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 'T' and resid 50 through 55 removed outlier: 3.629A pdb=" N ARG T 54 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 73 removed outlier: 3.683A pdb=" N ALA T 72 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU T 73 " --> pdb=" O ASP T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' 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 48 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 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 removed outlier: 3.513A pdb=" N ARG V 81 " --> pdb=" O SER V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 97 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 130 through 137 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: 4.179A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.751A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) 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 37 Processing helix chain 'Z' and resid 46 through 53 removed outlier: 4.337A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.717A 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 removed outlier: 4.333A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.607A 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 '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 40 Processing helix chain 'd' and resid 42 through 58 removed outlier: 3.610A 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 117 Processing helix chain 'd' and resid 121 through 124 No H-bonds generated for 'chain 'd' and resid 121 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 80 through 95 Processing helix chain 'e' and resid 101 through 107 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 72 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: 3.831A 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 43 Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.237A 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 89 removed outlier: 3.721A pdb=" N GLU h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) 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 45 Proline residue: i 42 - end of helix removed outlier: 3.819A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) 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: 4.311A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.796A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix removed outlier: 3.634A pdb=" N GLN i 144 " --> pdb=" O SER i 140 " (cutoff:3.500A) Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.858A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.341A 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: 3.630A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix removed outlier: 3.723A pdb=" N THR i 271 " --> pdb=" O GLN i 268 " (cutoff:3.500A) Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.098A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU i 296 " --> pdb=" O PHE i 292 " (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 Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.542A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.475A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.541A 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 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 4.172A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix removed outlier: 3.894A pdb=" N CYS k 69 " --> pdb=" O PHE k 66 " (cutoff:3.500A) 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 13 removed outlier: 3.836A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 23 removed outlier: 5.082A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.300A 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: 3.887A 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: 3.878A pdb=" N GLY l 178 " --> pdb=" O TYR l 174 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.016A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.705A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) 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 272 through 294 removed outlier: 3.577A pdb=" N ALA l 289 " --> pdb=" O THR l 285 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.129A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.935A 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 392 through 400 Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.732A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 3.766A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.487A 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: 3.973A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.464A 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 533 Proline residue: l 530 - end of helix removed outlier: 4.242A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 removed outlier: 3.689A pdb=" N GLN l 546 " --> pdb=" O LEU l 542 " (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 603 removed outlier: 3.879A pdb=" N LEU l 589 " --> pdb=" O LYS l 585 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 removed outlier: 3.536A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.723A pdb=" N ALA m 73 " --> pdb=" O GLY m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 removed outlier: 3.818A pdb=" N ILE m 127 " --> pdb=" O ASP m 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 127' Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.344A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 removed outlier: 3.669A pdb=" N ARG m 173 " --> pdb=" O MET m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 11 removed outlier: 5.031A pdb=" N ASP n 10 " --> pdb=" O GLN n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 34 removed outlier: 5.068A pdb=" N VAL n 17 " --> pdb=" O HIS n 14 " (cutoff:3.500A) Proline residue: n 18 - end of helix 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 removed outlier: 3.763A 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 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 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: 4.510A 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 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 3.601A pdb=" N SER p 132 " --> pdb=" O LEU p 128 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP p 133 " --> pdb=" O ARG p 129 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.786A 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: 4.299A 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: 4.125A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.769A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 110 Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.905A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.530A 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: 4.019A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.573A 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 204 removed outlier: 4.415A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.103A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 250 removed outlier: 5.051A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.534A pdb=" N TYR r 256 " --> pdb=" O LEU r 253 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 253 through 257' Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.237A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.559A pdb=" N VAL r 291 " --> pdb=" O ALA r 287 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.524A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) 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: 3.600A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 448 Proline residue: r 443 - end of helix removed outlier: 3.690A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (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: 3.785A 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: 4.436A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.856A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.000A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 168 Processing helix chain 's' and resid 174 through 192 removed outlier: 3.880A pdb=" N SER s 178 " --> pdb=" O ILE s 175 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TRP s 179 " --> pdb=" O PHE s 176 " (cutoff:3.500A) Proline residue: s 180 - end of helix removed outlier: 3.760A pdb=" N MET s 183 " --> pdb=" O PRO s 180 " (cutoff:3.500A) 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 274 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.567A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 35 removed outlier: 5.071A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 6.314A 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 57 through 77 Processing helix chain 'u' and resid 80 through 91 removed outlier: 3.825A pdb=" N CYS u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 10 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 124 removed outlier: 3.548A pdb=" N LYS v 113 " --> pdb=" O LEU v 109 " (cutoff:3.500A) 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 removed outlier: 3.539A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 192 Processing helix chain 'w' and resid 195 through 197 No H-bonds generated for 'chain 'w' and resid 195 through 197' Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 225 through 228 Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 266 through 273 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: 3.761A 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 helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 6.308A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.118A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.712A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.599A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.643A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 6.453A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 338 through 342 removed outlier: 6.463A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 428 through 432 Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.718A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.447A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.864A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU P 83 " --> pdb=" O SER P 79 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.645A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.792A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.446A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2891 hydrogen bonds defined for protein. 8016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.41 Time building geometry restraints manager: 24.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27495 1.40 - 1.62: 41460 1.62 - 1.84: 849 1.84 - 2.06: 7 2.06 - 2.28: 80 Bond restraints: 69891 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=" CB7 CDL N 201 " pdb=" OB8 CDL N 201 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C18 UQ s 403 " pdb=" C19 UQ s 403 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C17 970 C 303 " pdb=" O16 970 C 303 " ideal model delta sigma weight residual 1.355 1.575 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CA7 CDL l 703 " pdb=" OA8 CDL l 703 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 ... (remaining 69886 not shown) Histogram of bond angle deviations from ideal: 73.46 - 85.67: 76 85.67 - 97.88: 2 97.88 - 110.09: 11939 110.09 - 122.30: 72910 122.30 - 134.50: 9543 Bond angle restraints: 94470 Sorted by residual: angle pdb=" N LEU r 250 " pdb=" CA LEU r 250 " pdb=" C LEU r 250 " ideal model delta sigma weight residual 111.28 122.83 -11.55 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N ASN M 74 " pdb=" CA ASN M 74 " pdb=" C ASN M 74 " ideal model delta sigma weight residual 111.36 122.56 -11.20 1.09e+00 8.42e-01 1.06e+02 angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 129.62 -9.77 1.01e+00 9.80e-01 9.35e+01 angle pdb=" N MET Q 197 " pdb=" CA MET Q 197 " pdb=" C MET Q 197 " ideal model delta sigma weight residual 111.36 121.57 -10.21 1.09e+00 8.42e-01 8.77e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 125.44 -17.70 1.95e+00 2.62e-01 8.20e+01 ... (remaining 94465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 41014 35.22 - 70.44: 1128 70.44 - 105.66: 90 105.66 - 140.88: 10 140.88 - 176.10: 6 Dihedral angle restraints: 42248 sinusoidal: 18156 harmonic: 24092 Sorted by residual: 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 -154.66 68.66 1 1.00e+01 1.00e-02 6.11e+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 300.00 125.82 174.18 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 59.26 -161.67 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 42245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 9923 0.119 - 0.238: 212 0.238 - 0.357: 30 0.357 - 0.476: 15 0.476 - 0.596: 6 Chirality restraints: 10186 Sorted by residual: chirality pdb=" C23 970 C 303 " pdb=" C14 970 C 303 " pdb=" C22 970 C 303 " pdb=" C24 970 C 303 " both_signs ideal model delta sigma weight residual False 2.59 1.99 0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CA GLU M 283 " pdb=" N GLU M 283 " pdb=" C GLU M 283 " pdb=" CB GLU M 283 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" CA SER M 484 " pdb=" N SER M 484 " pdb=" C SER M 484 " pdb=" CB SER M 484 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.64e+00 ... (remaining 10183 not shown) Planarity restraints: 11774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " 0.358 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" C18 UQ s 403 " -0.349 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " -0.389 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " 0.005 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.348 2.00e-02 2.50e+03 3.22e-01 1.29e+03 pdb=" C18 UQ J 402 " 0.326 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.391 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " 0.002 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.371 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 403 " -0.056 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C11 UQ s 403 " 0.037 2.00e-02 2.50e+03 pdb=" C7 UQ s 403 " -0.290 2.00e-02 2.50e+03 pdb=" C8 UQ s 403 " 0.549 2.00e-02 2.50e+03 pdb=" C9 UQ s 403 " -0.241 2.00e-02 2.50e+03 ... (remaining 11771 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 116 2.32 - 2.97: 31703 2.97 - 3.61: 100558 3.61 - 4.26: 168372 4.26 - 4.90: 280499 Nonbonded interactions: 581248 Sorted by model distance: nonbonded pdb=" O SER I 46 " pdb=" ND2 ASN I 52 " model vdw 1.681 2.520 nonbonded pdb=" OD1 ASN d 104 " pdb=" O THR l 73 " model vdw 1.842 3.040 nonbonded pdb=" N SER G 112 " pdb=" O1 8Q1 G 201 " model vdw 1.905 2.496 nonbonded pdb=" O LYS S 34 " pdb=" O TYR u 91 " model vdw 1.917 3.040 nonbonded pdb=" NH2 ARG P 125 " pdb=" OD1 ASP P 201 " model vdw 1.923 2.520 ... (remaining 581243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 69 through 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44179 2.51 5 N 11239 2.21 5 O 12229 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.340 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: 0.060 Extract box with map and model: 10.730 Check model and map are aligned: 0.730 Process input model: 153.080 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.470 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:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.306 69891 Z= 0.491 Angle : 0.896 18.053 94470 Z= 0.495 Chirality : 0.053 0.596 10186 Planarity : 0.009 0.329 11774 Dihedral : 15.742 176.099 26691 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.09), residues: 8172 helix: 1.42 (0.08), residues: 4270 sheet: -0.12 (0.24), residues: 437 loop : -0.83 (0.10), residues: 3465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1338 time to evaluate : 6.146 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 1357 average time/residue: 1.6009 time to fit residues: 2810.4327 Evaluate side-chains 1110 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1097 time to evaluate : 6.125 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 6 average time/residue: 1.2518 time to fit residues: 18.5667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 0.8980 chunk 610 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 208 optimal weight: 0.7980 chunk 411 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 chunk 630 optimal weight: 0.0980 chunk 244 optimal weight: 9.9990 chunk 383 optimal weight: 3.9990 chunk 469 optimal weight: 5.9990 chunk 731 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN F 25 GLN F 31 GLN F 93 ASN I 21 GLN J 150 HIS J 154 GLN M 39 GLN M 300 GLN M 459 ASN M 464 GLN M 499 ASN N 12 GLN N 31 ASN N 135 GLN O 41 HIS O 48 ASN O 187 GLN P 51 ASN P 63 GLN P 75 GLN P 77 GLN P 124 ASN Q 182 ASN S 31 ASN T 40 HIS U 11 ASN W 76 GLN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN b 14 GLN c 100 ASN c 160 GLN d 124 ASN ** h 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 206 ASN m 46 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN p 62 GLN r 44 GLN r 103 GLN r 138 ASN r 192 ASN r 255 ASN r 304 GLN r 421 HIS s 99 ASN s 258 ASN u 64 ASN u 77 HIS v 47 ASN v 76 ASN w 322 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 69891 Z= 0.155 Angle : 0.543 14.610 94470 Z= 0.271 Chirality : 0.041 0.259 10186 Planarity : 0.005 0.065 11774 Dihedral : 13.468 175.422 10486 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.32 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8172 helix: 1.53 (0.08), residues: 4289 sheet: 0.03 (0.25), residues: 422 loop : -0.72 (0.10), residues: 3461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1150 time to evaluate : 6.175 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 55 residues processed: 1207 average time/residue: 1.5988 time to fit residues: 2512.2330 Evaluate side-chains 1123 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1068 time to evaluate : 6.149 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 34 residues processed: 24 average time/residue: 0.8489 time to fit residues: 39.9321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 608 optimal weight: 0.9980 chunk 497 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 732 optimal weight: 4.9990 chunk 791 optimal weight: 9.9990 chunk 652 optimal weight: 4.9990 chunk 726 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 587 optimal weight: 7.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN F 25 GLN F 31 GLN F 93 ASN I 51 ASN M 300 GLN M 464 GLN M 499 ASN M 669 ASN N 12 GLN N 135 GLN O 41 HIS O 187 GLN P 51 ASN T 40 HIS U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN b 13 GLN b 14 GLN c 154 GLN l 192 HIS l 206 ASN m 46 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN r 44 GLN r 138 ASN r 255 ASN r 304 GLN s 258 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 69891 Z= 0.217 Angle : 0.548 10.664 94470 Z= 0.274 Chirality : 0.042 0.244 10186 Planarity : 0.005 0.059 11774 Dihedral : 12.731 173.671 10486 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 8172 helix: 1.51 (0.08), residues: 4289 sheet: 0.06 (0.25), residues: 415 loop : -0.68 (0.10), residues: 3468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1108 time to evaluate : 7.681 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 74 residues processed: 1175 average time/residue: 1.6355 time to fit residues: 2503.7920 Evaluate side-chains 1135 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1061 time to evaluate : 6.155 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 44 residues processed: 30 average time/residue: 0.8336 time to fit residues: 47.6356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.8980 chunk 550 optimal weight: 8.9990 chunk 380 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 349 optimal weight: 8.9990 chunk 491 optimal weight: 10.0000 chunk 734 optimal weight: 7.9990 chunk 778 optimal weight: 2.9990 chunk 383 optimal weight: 0.9990 chunk 696 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 59 GLN F 25 GLN F 31 GLN F 93 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN N 12 GLN O 41 HIS O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN b 13 GLN b 14 GLN i 273 ASN l 206 ASN m 46 ASN o 123 GLN r 44 GLN r 138 ASN r 180 HIS r 304 GLN s 258 ASN u 64 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 69891 Z= 0.269 Angle : 0.566 10.978 94470 Z= 0.283 Chirality : 0.043 0.238 10186 Planarity : 0.005 0.059 11774 Dihedral : 12.365 174.220 10486 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 8172 helix: 1.42 (0.08), residues: 4294 sheet: -0.02 (0.25), residues: 425 loop : -0.69 (0.10), residues: 3453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1088 time to evaluate : 6.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 100 residues processed: 1180 average time/residue: 1.6127 time to fit residues: 2484.8548 Evaluate side-chains 1163 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1063 time to evaluate : 6.120 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 63 residues processed: 38 average time/residue: 0.8146 time to fit residues: 57.7316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 2.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 579 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 664 optimal weight: 6.9990 chunk 537 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 397 optimal weight: 0.0060 chunk 698 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN E 95 ASN F 25 GLN F 31 GLN F 93 ASN H 76 GLN L 86 ASN M 202 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 540 ASN N 12 GLN O 87 GLN O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 43 GLN T 74 GLN U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 GLN c 100 ASN l 206 ASN m 46 ASN r 44 GLN r 304 GLN s 258 ASN u 77 HIS v 76 ASN w 149 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 69891 Z= 0.340 Angle : 0.606 12.329 94470 Z= 0.304 Chirality : 0.045 0.245 10186 Planarity : 0.005 0.062 11774 Dihedral : 12.314 175.417 10486 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.93 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 8172 helix: 1.28 (0.08), residues: 4292 sheet: -0.20 (0.24), residues: 429 loop : -0.73 (0.10), residues: 3451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1088 time to evaluate : 6.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 114 residues processed: 1202 average time/residue: 1.6030 time to fit residues: 2526.0496 Evaluate side-chains 1177 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1063 time to evaluate : 6.176 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 79 residues processed: 37 average time/residue: 0.7957 time to fit residues: 55.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 0.6980 chunk 700 optimal weight: 3.9990 chunk 153 optimal weight: 0.0870 chunk 456 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 778 optimal weight: 3.9990 chunk 646 optimal weight: 8.9990 chunk 360 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 408 optimal weight: 0.5980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 93 ASN H 76 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 202 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN N 12 GLN N 91 HIS O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 74 GLN U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN b 14 GLN b 89 HIS l 206 ASN l 405 ASN l 579 ASN m 46 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN r 44 GLN r 81 GLN r 138 ASN r 304 GLN s 258 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 69891 Z= 0.156 Angle : 0.515 12.270 94470 Z= 0.258 Chirality : 0.040 0.182 10186 Planarity : 0.004 0.059 11774 Dihedral : 11.623 175.851 10486 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8172 helix: 1.54 (0.08), residues: 4274 sheet: -0.02 (0.24), residues: 440 loop : -0.65 (0.10), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1129 time to evaluate : 6.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 85 residues processed: 1226 average time/residue: 1.6196 time to fit residues: 2588.3655 Evaluate side-chains 1171 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1086 time to evaluate : 6.159 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 72 residues processed: 13 average time/residue: 0.7828 time to fit residues: 24.8176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 443 optimal weight: 3.9990 chunk 568 optimal weight: 4.9990 chunk 440 optimal weight: 5.9990 chunk 655 optimal weight: 0.9990 chunk 434 optimal weight: 0.9990 chunk 775 optimal weight: 9.9990 chunk 485 optimal weight: 5.9990 chunk 473 optimal weight: 10.0000 chunk 358 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN F 93 ASN H 76 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 202 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 669 ASN N 12 GLN N 135 GLN O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 74 GLN T 117 GLN U 11 ASN V 79 GLN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN b 14 GLN l 206 ASN m 46 ASN o 117 GLN r 44 GLN r 138 ASN r 304 GLN s 258 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 69891 Z= 0.272 Angle : 0.571 12.625 94470 Z= 0.285 Chirality : 0.043 0.185 10186 Planarity : 0.005 0.059 11774 Dihedral : 11.617 175.352 10486 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.94 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 8172 helix: 1.45 (0.08), residues: 4275 sheet: -0.02 (0.25), residues: 427 loop : -0.64 (0.10), residues: 3470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1074 time to evaluate : 6.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 115 residues processed: 1183 average time/residue: 1.6321 time to fit residues: 2525.2644 Evaluate side-chains 1185 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1070 time to evaluate : 6.523 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 85 residues processed: 30 average time/residue: 0.8842 time to fit residues: 49.8001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 463 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 493 optimal weight: 0.6980 chunk 528 optimal weight: 1.9990 chunk 383 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 609 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN H 76 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN N 12 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 74 GLN U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN l 206 ASN m 46 ASN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 117 GLN p 124 GLN r 44 GLN r 103 GLN r 138 ASN r 304 GLN s 258 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 69891 Z= 0.153 Angle : 0.514 12.449 94470 Z= 0.257 Chirality : 0.040 0.170 10186 Planarity : 0.004 0.058 11774 Dihedral : 11.127 176.579 10486 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.37 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 8172 helix: 1.61 (0.08), residues: 4280 sheet: -0.01 (0.24), residues: 434 loop : -0.57 (0.11), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1096 time to evaluate : 6.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 93 residues processed: 1201 average time/residue: 1.6328 time to fit residues: 2577.7817 Evaluate side-chains 1168 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1075 time to evaluate : 6.140 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 79 residues processed: 15 average time/residue: 0.8376 time to fit residues: 28.3626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.5980 chunk 743 optimal weight: 0.9990 chunk 678 optimal weight: 6.9990 chunk 723 optimal weight: 1.9990 chunk 435 optimal weight: 0.0170 chunk 314 optimal weight: 1.9990 chunk 567 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 653 optimal weight: 5.9990 chunk 683 optimal weight: 0.7980 chunk 720 optimal weight: 0.6980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN H 41 ASN H 76 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN N 12 GLN N 135 GLN O 187 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 74 GLN T 117 GLN U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 206 ASN m 46 ASN o 117 GLN p 124 GLN r 44 GLN r 103 GLN r 138 ASN r 304 GLN s 258 ASN u 64 ASN u 77 HIS v 76 ASN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 69891 Z= 0.141 Angle : 0.506 14.009 94470 Z= 0.251 Chirality : 0.039 0.187 10186 Planarity : 0.004 0.058 11774 Dihedral : 10.547 177.615 10486 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8172 helix: 1.73 (0.08), residues: 4274 sheet: 0.08 (0.24), residues: 441 loop : -0.48 (0.11), residues: 3457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1121 time to evaluate : 6.387 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 117 outliers final: 77 residues processed: 1207 average time/residue: 1.6291 time to fit residues: 2591.2969 Evaluate side-chains 1156 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1079 time to evaluate : 6.196 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 68 residues processed: 10 average time/residue: 0.5608 time to fit residues: 19.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 4.9990 chunk 764 optimal weight: 7.9990 chunk 466 optimal weight: 6.9990 chunk 362 optimal weight: 2.9990 chunk 531 optimal weight: 1.9990 chunk 801 optimal weight: 3.9990 chunk 738 optimal weight: 2.9990 chunk 638 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 493 optimal weight: 3.9990 chunk 391 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 76 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 499 ASN ** M 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 13 GLN N 135 GLN O 153 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 74 GLN T 117 GLN U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 26 GLN l 580 GLN m 46 ASN p 124 GLN r 44 GLN r 304 GLN s 258 ASN u 64 ASN u 77 HIS v 76 ASN w 300 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 69891 Z= 0.236 Angle : 0.564 16.840 94470 Z= 0.279 Chirality : 0.042 0.177 10186 Planarity : 0.005 0.069 11774 Dihedral : 10.733 175.993 10486 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.17 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.09), residues: 8172 helix: 1.60 (0.08), residues: 4287 sheet: 0.01 (0.25), residues: 423 loop : -0.54 (0.11), residues: 3462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1083 time to evaluate : 6.352 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 107 outliers final: 82 residues processed: 1169 average time/residue: 1.6613 time to fit residues: 2563.2274 Evaluate side-chains 1148 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1066 time to evaluate : 6.190 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 72 residues processed: 12 average time/residue: 1.2050 time to fit residues: 29.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 1.9990 chunk 680 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 588 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 177 optimal weight: 0.0470 chunk 639 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 656 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 76 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 499 ASN M 540 ASN ** M 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 13 GLN N 135 GLN O 153 GLN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 HIS T 74 GLN U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 26 GLN ** o 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 124 GLN r 44 GLN r 138 ASN r 304 GLN u 64 ASN u 77 HIS v 76 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.099692 restraints weight = 89204.671| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.30 r_work: 0.2865 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 69891 Z= 0.189 Angle : 0.540 13.708 94470 Z= 0.268 Chirality : 0.041 0.173 10186 Planarity : 0.004 0.076 11774 Dihedral : 10.546 176.692 10486 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.24 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 8172 helix: 1.63 (0.08), residues: 4281 sheet: 0.11 (0.25), residues: 423 loop : -0.52 (0.11), residues: 3468 =============================================================================== Job complete usr+sys time: 32289.37 seconds wall clock time: 559 minutes 30.37 seconds (33570.37 seconds total)