Starting phenix.real_space_refine (version: dev) on Mon Feb 27 03:27:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2u_32266/02_2023/7w2u_32266_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 ARG 59": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J GLU 320": "OE1" <-> "OE2" Residue "J GLU 365": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "l PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 68170 Number of models: 1 Model: "" Number of chains: 69 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: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1732 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 192} 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: "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: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 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: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 815 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 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: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1277 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 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: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'DCQ': 1, 'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "I" 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: "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: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} 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: "V" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "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: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 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: "i" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 87 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "j" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 189 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "o" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.514 48.282 173.190 1.00 28.62 S ATOM 3060 SG CYS A 425 46.715 45.130 179.064 1.00 29.21 S ATOM 2738 SG CYS A 385 44.255 44.016 173.287 1.00 28.03 S ATOM 2699 SG CYS A 379 42.176 49.043 177.129 1.00 15.88 S ATOM 3961 SG CYS B 113 36.636 62.941 137.915 1.00 12.72 S ATOM 3980 SG CYS B 116 41.738 60.742 141.822 1.00 1.24 S ATOM 4003 SG CYS B 119 42.864 63.253 136.280 1.00 7.99 S ATOM 4332 SG CYS B 162 40.320 57.523 137.004 1.00 1.34 S ATOM 4030 SG CYS B 123 48.952 65.852 131.641 1.00 0.00 S ATOM 4256 SG CYS B 152 47.264 63.959 125.788 1.00 8.91 S ATOM 4303 SG CYS B 158 45.272 60.286 130.798 1.00 6.38 S ATOM 4282 SG CYS B 155 51.237 60.456 129.309 1.00 4.59 S ATOM 5724 SG CYS C 166 53.729 63.957 121.631 1.00 12.04 S ATOM 4996 SG CYS C 72 54.315 65.104 115.269 1.00 11.21 S ATOM 4990 SG CYS C 71 59.514 63.399 118.244 1.00 5.89 S ATOM 5494 SG CYS C 136 56.301 68.784 120.355 1.00 3.85 S ATOM 14943 SG CYS M 131 40.834 61.244 153.831 1.00 10.37 S ATOM 14922 SG CYS M 128 44.553 56.671 150.842 1.00 9.83 S ATOM 14983 SG CYS M 137 46.653 60.191 155.900 1.00 5.11 S ATOM 15315 SG CYS M 179 44.800 60.701 167.012 1.00 12.75 S ATOM 15669 SG CYS M 226 41.727 63.328 162.613 1.00 16.70 S ATOM 15339 SG CYS M 182 39.243 63.383 168.734 1.00 17.46 S ATOM 15292 SG CYS M 176 39.166 57.931 165.442 1.00 8.15 S ATOM 14540 SG CYS M 78 56.236 56.024 171.090 1.00 20.45 S ATOM 14641 SG CYS M 92 54.562 58.260 173.364 1.00 19.14 S ATOM 14429 SG CYS M 64 50.112 58.092 170.932 1.00 6.42 S ATOM 14515 SG CYS M 75 51.302 56.187 168.002 1.00 12.86 S ATOM 21478 SG CYS O 135 31.370 31.152 181.655 1.00 45.55 S ATOM 21512 SG CYS O 140 31.225 27.973 183.017 1.00 54.28 S ATOM 21792 SG CYS O 176 36.074 32.979 184.008 1.00 54.09 S ATOM 21815 SG CYS O 180 36.144 29.698 185.239 1.00 43.13 S ATOM 28548 SG CYS T 86 29.003 49.961 146.178 1.00 23.84 S ATOM 28726 SG CYS T 111 30.382 53.399 147.008 1.00 23.54 S ATOM 28748 SG CYS T 114 28.466 52.848 143.945 1.00 32.37 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.64 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.64 Time building chain proxies: 29.40, per 1000 atoms: 0.43 Number of scatterers: 68170 At special positions: 0 Unit cell: (220.211, 213.766, 229.879, 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 47 15.00 Mg 1 11.99 O 12233 8.00 N 11230 7.00 C 44148 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.97 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " 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="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " 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="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="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " 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="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " 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 114 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " Number of angles added : 3 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 353 helices and 29 sheets defined 53.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.574A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.679A 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 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 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: 3.678A 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 264 Processing helix chain 'A' and resid 296 through 302 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: 4.396A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 4.021A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 Proline residue: A 434 - end of helix removed outlier: 3.642A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.600A 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 211 removed outlier: 5.836A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 removed outlier: 3.582A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) 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 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 135 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 189 through 194 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: 4.262A 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: 4.350A 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 31 through 39 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' 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 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.043A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' 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 75 removed outlier: 3.994A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.149A 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 120 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: 4.139A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 5.021A 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: 3.899A 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 356 removed outlier: 5.678A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) 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 80 removed outlier: 3.622A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.329A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 73 No H-bonds generated for 'chain 'L' and resid 70 through 73' 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: 3.885A 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: 3.922A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 298 removed outlier: 5.208A pdb=" N TYR M 294 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY M 296 " --> pdb=" O PHE M 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU M 297 " --> pdb=" O ALA M 293 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) 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 385 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 425 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.852A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 468 removed outlier: 3.787A pdb=" N ILE M 465 " --> pdb=" O PRO M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 577 through 579 No H-bonds generated for 'chain 'M' and resid 577 through 579' 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 654 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: 3.751A 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: 3.772A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.422A 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 104 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 44 through 46 No H-bonds generated for 'chain 'P' and resid 44 through 46' Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.669A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 3.720A pdb=" N ASP P 102 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 173 removed outlier: 3.914A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (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: 4.040A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.757A 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 120 through 126 removed outlier: 3.792A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.003A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.768A 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 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.792A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.772A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.557A 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 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 3.634A pdb=" N LEU Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.471A 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 29 Proline residue: S 7 - end of helix 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 Processing helix chain 'T' and resid 67 through 72 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 3 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 47 Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.860A pdb=" N ASN U 83 " --> pdb=" O GLU U 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 79 through 83' 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 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 99 Proline residue: W 73 - end of helix removed outlier: 3.968A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 5.874A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.799A 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 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.879A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.742A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.725A 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 69 through 73 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' 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 128 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.652A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.539A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN d 124 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.781A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 3.927A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 88 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.649A 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: 4.180A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.910A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.987A 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: 3.741A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.597A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.551A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.595A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.740A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.604A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.739A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.350A 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: 3.909A 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: 4.002A 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 223 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: 4.039A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.029A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.488A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.095A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.006A 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 389 through 400 removed outlier: 4.644A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.749A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 5.734A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.473A 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: 3.761A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.405A 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: 4.254A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 46 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 108 Processing helix chain 'm' and resid 124 through 127 Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.198A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 removed outlier: 3.575A pdb=" N ARG m 173 " --> pdb=" O MET m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 35 removed outlier: 6.203A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.695A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.666A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 75 through 79 removed outlier: 3.689A pdb=" N ASN o 79 " --> pdb=" O ASN o 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 75 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.358A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.930A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.231A 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: 4.227A 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: 4.232A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 Proline residue: r 74 - end of helix removed outlier: 4.443A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.746A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.701A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.422A 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 142 through 171 removed outlier: 3.840A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.731A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.096A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 249 removed outlier: 4.324A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 277 removed outlier: 3.688A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA r 258 " --> pdb=" O ASN r 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR r 259 " --> pdb=" O TYR r 256 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 3.650A pdb=" N TRP r 267 " --> pdb=" O LEU r 264 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.504A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.651A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.569A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 4.146A 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: 3.832A 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 31 Proline residue: s 12 - end of helix removed outlier: 3.758A 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 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.339A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.724A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.294A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.620A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 192 removed outlier: 5.091A pdb=" N TRP s 179 " --> pdb=" O PHE s 176 " (cutoff:3.500A) Proline residue: s 180 - end of helix Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.693A 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: 4.935A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 80 through 91 Processing helix chain 'u' and resid 102 through 115 Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.721A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 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 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.289A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 251 removed outlier: 5.198A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.932A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.315A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing 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: 6.336A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.228A 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: 5.851A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.298A 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: 6.684A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.333A 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: 6.552A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.555A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.715A 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: 6.195A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.488A 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 365 through 368 removed outlier: 4.675A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.460A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q 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: 6.329A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.675A 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: 6.478A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.043A 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: 6.769A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (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: 6.072A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.270A 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 77 through 79 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AA, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AB, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.564A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.715A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC 2938 hydrogen bonds defined for protein. 8244 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: 23.73 Time building geometry restraints manager: 24.04 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: 27766 1.40 - 1.62: 41130 1.62 - 1.84: 880 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 69856 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.298 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 69851 not shown) Histogram of bond angle deviations from ideal: 73.56 - 85.96: 76 85.96 - 98.35: 2 98.35 - 110.74: 23138 110.74 - 123.14: 68050 123.14 - 135.53: 3167 Bond angle restraints: 94433 Sorted by residual: angle pdb=" C PHE b 123 " pdb=" N PRO b 124 " pdb=" CA PRO b 124 " ideal model delta sigma weight residual 119.87 133.84 -13.97 1.04e+00 9.25e-01 1.81e+02 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 124.52 -16.78 1.95e+00 2.62e-01 7.37e+01 angle pdb=" C SER F 27 " pdb=" N PRO F 28 " pdb=" CA PRO F 28 " ideal model delta sigma weight residual 119.05 127.82 -8.77 1.11e+00 8.12e-01 6.25e+01 angle pdb=" N GLN F 25 " pdb=" CA GLN F 25 " pdb=" C GLN F 25 " ideal model delta sigma weight residual 111.28 119.75 -8.47 1.09e+00 8.42e-01 6.04e+01 angle pdb=" C ARG P 44 " pdb=" N PRO P 45 " pdb=" CA PRO P 45 " ideal model delta sigma weight residual 119.05 127.54 -8.49 1.11e+00 8.12e-01 5.84e+01 ... (remaining 94428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 40310 34.79 - 69.57: 1738 69.57 - 104.36: 124 104.36 - 139.15: 18 139.15 - 173.94: 5 Dihedral angle restraints: 42195 sinusoidal: 18102 harmonic: 24093 Sorted by residual: 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 67.83 -170.24 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.87 -139.87 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -138.10 52.10 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 42192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 9607 0.091 - 0.182: 559 0.182 - 0.273: 17 0.273 - 0.364: 7 0.364 - 0.454: 3 Chirality restraints: 10193 Sorted by residual: chirality pdb=" CA LYS b 121 " pdb=" N LYS b 121 " pdb=" C LYS b 121 " pdb=" CB LYS b 121 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA SER Y 77 " pdb=" N SER Y 77 " pdb=" C SER Y 77 " pdb=" CB SER Y 77 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA PHE s 19 " pdb=" N PHE s 19 " pdb=" C PHE s 19 " pdb=" CB PHE s 19 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 10190 not shown) Planarity restraints: 11766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ J 402 " -0.562 2.00e-02 2.50e+03 4.79e-01 2.87e+03 pdb=" C23 UQ J 402 " 0.704 2.00e-02 2.50e+03 pdb=" C24 UQ J 402 " 0.419 2.00e-02 2.50e+03 pdb=" C25 UQ J 402 " -0.325 2.00e-02 2.50e+03 pdb=" C26 UQ J 402 " -0.236 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.359 2.00e-02 2.50e+03 3.28e-01 1.34e+03 pdb=" C18 UQ s 402 " -0.346 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.386 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.001 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.374 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.304 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C13 UQ J 402 " -0.566 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.229 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.025 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.058 2.00e-02 2.50e+03 ... (remaining 11763 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1584 2.71 - 3.25: 66340 3.25 - 3.80: 114644 3.80 - 4.35: 154201 4.35 - 4.90: 248533 Nonbonded interactions: 585302 Sorted by model distance: nonbonded pdb=" CB ARG P 44 " pdb=" CD PRO P 45 " model vdw 2.156 3.840 nonbonded pdb=" O LEU m 61 " pdb=" OH TYR s 114 " model vdw 2.196 2.440 nonbonded pdb=" OE2 GLU c 85 " pdb=" OG1 THR c 119 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR X 85 " pdb=" NE1 TRP Z 22 " model vdw 2.206 2.520 nonbonded pdb=" OE2 GLU w 47 " pdb=" NZ LYS w 52 " model vdw 2.208 2.520 ... (remaining 585297 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 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 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 47 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44148 2.51 5 N 11230 2.21 5 O 12233 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=0.64 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: 1.320 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: 10.820 Check model and map are aligned: 0.770 Process input model: 157.050 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.480 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 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 : 0.008 0.315 69856 Z= 0.500 Angle : 0.809 17.179 94433 Z= 0.414 Chirality : 0.044 0.454 10193 Planarity : 0.010 0.479 11766 Dihedral : 17.928 173.937 26636 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.03 % 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: 1.10 (0.09), residues: 8173 helix: 1.59 (0.08), residues: 4308 sheet: 0.44 (0.26), residues: 383 loop : -0.26 (0.11), residues: 3482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1020 time to evaluate : 6.316 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 74 outliers final: 54 residues processed: 1077 average time/residue: 1.6747 time to fit residues: 2314.4573 Evaluate side-chains 1040 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 986 time to evaluate : 6.944 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 48 residues processed: 8 average time/residue: 0.8717 time to fit residues: 20.0878 ------------------------------------------------------------------------------- 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: 3.9990 chunk 610 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 325 optimal weight: 4.9990 chunk 630 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 469 optimal weight: 0.7980 chunk 731 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN J 323 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 ASN ** M 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 135 GLN O 41 HIS ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN P 247 GLN S 58 ASN U 83 ASN V 129 GLN W 112 HIS b 13 GLN e 65 ASN e 145 ASN p 139 GLN r 51 ASN ** w 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.0416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 69856 Z= 0.249 Angle : 0.574 14.052 94433 Z= 0.292 Chirality : 0.043 0.202 10193 Planarity : 0.005 0.064 11766 Dihedral : 13.447 169.333 10471 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.12 (0.09), residues: 8173 helix: 1.60 (0.08), residues: 4308 sheet: 0.37 (0.26), residues: 389 loop : -0.23 (0.11), residues: 3476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1004 time to evaluate : 6.570 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 207 outliers final: 107 residues processed: 1121 average time/residue: 1.7129 time to fit residues: 2503.1138 Evaluate side-chains 1099 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 992 time to evaluate : 7.187 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 68 residues processed: 40 average time/residue: 1.1923 time to fit residues: 77.6859 ------------------------------------------------------------------------------- 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: 9.9990 chunk 608 optimal weight: 2.9990 chunk 497 optimal weight: 0.3980 chunk 201 optimal weight: 7.9990 chunk 732 optimal weight: 0.4980 chunk 791 optimal weight: 0.9980 chunk 652 optimal weight: 4.9990 chunk 726 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 587 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN J 323 HIS ** M 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 135 GLN O 41 HIS ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN P 247 GLN S 58 ASN U 83 ASN V 129 GLN W 112 HIS b 13 GLN e 65 ASN e 145 ASN i 232 HIS o 52 ASN o 79 ASN v 43 GLN w 223 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 69856 Z= 0.217 Angle : 0.543 11.301 94433 Z= 0.278 Chirality : 0.042 0.232 10193 Planarity : 0.005 0.073 11766 Dihedral : 12.753 169.530 10471 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.70 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.18 (0.09), residues: 8173 helix: 1.68 (0.08), residues: 4290 sheet: 0.34 (0.26), residues: 376 loop : -0.24 (0.11), residues: 3507 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1016 time to evaluate : 6.410 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 182 outliers final: 110 residues processed: 1121 average time/residue: 1.6438 time to fit residues: 2383.3024 Evaluate side-chains 1094 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 984 time to evaluate : 6.213 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 73 residues processed: 38 average time/residue: 0.9927 time to fit residues: 63.9189 ------------------------------------------------------------------------------- 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: 0.7980 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 491 optimal weight: 3.9990 chunk 734 optimal weight: 8.9990 chunk 778 optimal weight: 2.9990 chunk 383 optimal weight: 8.9990 chunk 696 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 76 ASN J 323 HIS M 202 ASN ** M 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 135 GLN O 41 HIS ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN Q 162 GLN S 58 ASN T 117 GLN U 83 ASN V 129 GLN W 112 HIS b 13 GLN b 14 GLN e 65 ASN e 145 ASN i 49 ASN o 79 ASN ** w 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 69856 Z= 0.308 Angle : 0.592 12.225 94433 Z= 0.303 Chirality : 0.045 0.209 10193 Planarity : 0.005 0.076 11766 Dihedral : 12.580 169.191 10471 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.38 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.02 (0.09), residues: 8173 helix: 1.51 (0.08), residues: 4306 sheet: 0.37 (0.26), residues: 382 loop : -0.29 (0.11), residues: 3485 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 998 time to evaluate : 6.381 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 203 outliers final: 119 residues processed: 1122 average time/residue: 1.6824 time to fit residues: 2440.2973 Evaluate side-chains 1112 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 993 time to evaluate : 6.251 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 86 residues processed: 34 average time/residue: 0.9753 time to fit residues: 57.9119 ------------------------------------------------------------------------------- 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: 0.9980 chunk 441 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 579 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 664 optimal weight: 10.0000 chunk 537 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 7.9990 chunk 698 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN F 62 GLN F 76 ASN J 323 HIS ** M 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 135 GLN ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN S 58 ASN U 83 ASN V 129 GLN W 112 HIS b 13 GLN e 65 ASN e 145 ASN i 322 GLN l 447 ASN l 534 HIS o 79 ASN w 223 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 69856 Z= 0.294 Angle : 0.586 11.812 94433 Z= 0.301 Chirality : 0.044 0.275 10193 Planarity : 0.005 0.079 11766 Dihedral : 12.315 168.987 10471 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.38 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 0.99 (0.09), residues: 8173 helix: 1.49 (0.08), residues: 4303 sheet: 0.34 (0.26), residues: 382 loop : -0.31 (0.10), residues: 3488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1013 time to evaluate : 6.646 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 209 outliers final: 130 residues processed: 1147 average time/residue: 1.6603 time to fit residues: 2477.7802 Evaluate side-chains 1121 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 991 time to evaluate : 6.316 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 94 residues processed: 37 average time/residue: 1.0236 time to fit residues: 64.1987 ------------------------------------------------------------------------------- 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: 0.7980 chunk 700 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 456 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 778 optimal weight: 0.5980 chunk 646 optimal weight: 5.9990 chunk 360 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 257 optimal weight: 7.9990 chunk 408 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN J 323 HIS M 598 ASN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN N 135 GLN O 41 HIS ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 247 GLN S 58 ASN U 83 ASN V 129 GLN W 112 HIS b 13 GLN b 14 GLN e 65 ASN e 145 ASN i 322 GLN l 447 ASN o 79 ASN v 43 GLN w 223 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 69856 Z= 0.144 Angle : 0.500 11.184 94433 Z= 0.255 Chirality : 0.040 0.193 10193 Planarity : 0.004 0.080 11766 Dihedral : 11.523 170.551 10471 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.32 (0.09), residues: 8173 helix: 1.80 (0.08), residues: 4306 sheet: 0.32 (0.26), residues: 394 loop : -0.18 (0.11), residues: 3473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1043 time to evaluate : 6.351 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 170 outliers final: 96 residues processed: 1164 average time/residue: 1.6510 time to fit residues: 2505.5864 Evaluate side-chains 1103 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1007 time to evaluate : 6.305 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 85 residues processed: 13 average time/residue: 1.0684 time to fit residues: 28.6171 ------------------------------------------------------------------------------- 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: 9.9990 chunk 87 optimal weight: 5.9990 chunk 443 optimal weight: 0.0270 chunk 568 optimal weight: 5.9990 chunk 440 optimal weight: 0.0670 chunk 655 optimal weight: 0.0060 chunk 434 optimal weight: 0.6980 chunk 775 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 chunk 473 optimal weight: 9.9990 chunk 358 optimal weight: 0.0270 overall best weight: 0.1650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN F 76 ASN J 323 HIS ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 688 GLN N 52 ASN N 112 ASN N 135 GLN O 246 GLN P 247 GLN S 58 ASN U 83 ASN V 129 GLN W 112 HIS b 13 GLN b 14 GLN e 65 ASN e 145 ASN f 73 ASN l 323 HIS l 447 ASN v 110 GLN w 223 ASN w 225 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 69856 Z= 0.121 Angle : 0.476 10.830 94433 Z= 0.241 Chirality : 0.039 0.179 10193 Planarity : 0.004 0.078 11766 Dihedral : 10.739 175.733 10471 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.59 (0.09), residues: 8173 helix: 2.00 (0.08), residues: 4299 sheet: 0.44 (0.25), residues: 411 loop : -0.03 (0.11), residues: 3463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1079 time to evaluate : 6.361 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 148 outliers final: 87 residues processed: 1187 average time/residue: 1.6431 time to fit residues: 2544.1503 Evaluate side-chains 1098 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1011 time to evaluate : 6.295 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 76 residues processed: 11 average time/residue: 1.4124 time to fit residues: 29.3006 ------------------------------------------------------------------------------- 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: 0.2980 chunk 463 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 493 optimal weight: 0.3980 chunk 528 optimal weight: 0.7980 chunk 383 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 609 optimal weight: 7.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 688 GLN N 52 ASN N 112 ASN P 75 GLN P 138 ASN P 247 GLN Q 162 GLN S 58 ASN U 83 ASN V 129 GLN W 76 GLN a 189 ASN b 14 GLN c 160 GLN e 65 ASN e 145 ASN e 148 GLN i 322 GLN l 447 ASN p 139 GLN r 184 HIS v 110 GLN w 223 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 69856 Z= 0.258 Angle : 0.567 11.697 94433 Z= 0.288 Chirality : 0.043 0.209 10193 Planarity : 0.005 0.075 11766 Dihedral : 11.088 179.411 10471 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.35 (0.09), residues: 8173 helix: 1.78 (0.08), residues: 4317 sheet: 0.47 (0.26), residues: 406 loop : -0.12 (0.11), residues: 3450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1007 time to evaluate : 6.241 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 147 outliers final: 99 residues processed: 1111 average time/residue: 1.6846 time to fit residues: 2447.9001 Evaluate side-chains 1080 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 981 time to evaluate : 6.308 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 80 residues processed: 20 average time/residue: 0.8874 time to fit residues: 36.2676 ------------------------------------------------------------------------------- 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: 1.9990 chunk 743 optimal weight: 4.9990 chunk 678 optimal weight: 3.9990 chunk 723 optimal weight: 3.9990 chunk 435 optimal weight: 0.4980 chunk 314 optimal weight: 4.9990 chunk 567 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 653 optimal weight: 7.9990 chunk 683 optimal weight: 0.9990 chunk 720 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN F 76 ASN G 115 GLN J 323 HIS M 598 ASN ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 688 GLN N 52 ASN N 112 ASN O 41 HIS P 247 GLN S 58 ASN U 83 ASN V 129 GLN a 189 ASN b 14 GLN e 65 ASN e 145 ASN e 148 GLN i 322 GLN l 136 ASN l 447 ASN o 79 ASN r 184 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 223 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 69856 Z= 0.242 Angle : 0.564 11.701 94433 Z= 0.287 Chirality : 0.043 0.208 10193 Planarity : 0.005 0.075 11766 Dihedral : 11.107 169.351 10471 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.24 (0.09), residues: 8173 helix: 1.69 (0.08), residues: 4299 sheet: 0.40 (0.26), residues: 406 loop : -0.16 (0.11), residues: 3468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 998 time to evaluate : 6.449 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 124 outliers final: 88 residues processed: 1091 average time/residue: 1.7343 time to fit residues: 2459.1637 Evaluate side-chains 1074 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 986 time to evaluate : 6.297 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 78 residues processed: 11 average time/residue: 0.9557 time to fit residues: 24.4107 ------------------------------------------------------------------------------- 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: 7.9990 chunk 764 optimal weight: 8.9990 chunk 466 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 531 optimal weight: 0.5980 chunk 801 optimal weight: 7.9990 chunk 738 optimal weight: 1.9990 chunk 638 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 493 optimal weight: 0.0980 chunk 391 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN J 323 HIS ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 688 GLN N 52 ASN N 112 ASN P 247 GLN S 58 ASN U 83 ASN V 129 GLN a 189 ASN b 14 GLN e 65 ASN e 145 ASN e 148 GLN i 322 GLN l 136 ASN l 447 ASN o 79 ASN r 184 HIS v 43 GLN v 110 GLN w 223 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 69856 Z= 0.264 Angle : 0.581 12.355 94433 Z= 0.295 Chirality : 0.043 0.231 10193 Planarity : 0.005 0.075 11766 Dihedral : 11.154 169.253 10471 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.49 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.16 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4296 sheet: 0.40 (0.26), residues: 404 loop : -0.20 (0.11), residues: 3473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 987 time to evaluate : 6.555 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 106 outliers final: 87 residues processed: 1075 average time/residue: 1.7263 time to fit residues: 2425.2240 Evaluate side-chains 1065 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 978 time to evaluate : 6.290 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 81 residues processed: 7 average time/residue: 1.1382 time to fit residues: 19.9692 ------------------------------------------------------------------------------- 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: 0.7980 chunk 680 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 588 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 639 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 656 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN F 76 ASN J 323 HIS ** M 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 688 GLN N 52 ASN N 112 ASN O 41 HIS P 247 GLN S 58 ASN U 83 ASN V 129 GLN b 14 GLN e 145 ASN i 322 GLN l 136 ASN l 447 ASN r 184 HIS v 110 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102704 restraints weight = 85953.707| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.15 r_work: 0.2989 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 69856 Z= 0.143 Angle : 0.509 12.615 94433 Z= 0.258 Chirality : 0.040 0.229 10193 Planarity : 0.004 0.075 11766 Dihedral : 10.627 170.462 10471 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.90 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: 1.43 (0.09), residues: 8173 helix: 1.86 (0.08), residues: 4300 sheet: 0.38 (0.25), residues: 414 loop : -0.07 (0.11), residues: 3459 =============================================================================== Job complete usr+sys time: 31996.65 seconds wall clock time: 552 minutes 47.16 seconds (33167.16 seconds total)