Starting phenix.real_space_refine (version: dev) on Mon Feb 27 00:49:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w20_32260/02_2023/7w20_32260_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "M GLU 33": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 217": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 369": "OE1" <-> "OE2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 535": "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 58": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 460": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 63": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "X TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 42": "OE1" <-> "OE2" Residue "u GLU 58": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 124": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 333": "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: 68136 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: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 967 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: 5293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5293 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 657} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 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: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1000 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4797 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "m" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1276 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3624 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1036 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "w" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2586 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 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: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {'970': 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: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 146 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "j" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "l" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 295 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "n" 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: "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: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "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 48.259 48.371 170.226 1.00 26.44 S ATOM 3060 SG CYS A 425 47.554 44.752 176.097 1.00 34.63 S ATOM 2738 SG CYS A 385 45.282 44.041 170.044 1.00 28.82 S ATOM 2699 SG CYS A 379 43.068 48.803 173.867 1.00 22.72 S ATOM 3961 SG CYS B 113 38.194 64.153 135.017 1.00 22.58 S ATOM 3980 SG CYS B 116 43.283 61.997 139.040 1.00 9.12 S ATOM 4003 SG CYS B 119 44.397 64.717 133.516 1.00 12.73 S ATOM 4332 SG CYS B 162 41.962 58.873 134.087 1.00 9.94 S ATOM 4030 SG CYS B 123 50.554 67.767 129.365 1.00 0.00 S ATOM 4256 SG CYS B 152 49.167 65.886 123.403 1.00 9.18 S ATOM 4303 SG CYS B 158 47.080 62.184 128.177 1.00 11.02 S ATOM 4282 SG CYS B 155 53.266 62.543 126.956 1.00 9.13 S ATOM 5724 SG CYS C 166 55.835 66.100 119.403 1.00 10.67 S ATOM 4996 SG CYS C 72 56.564 67.623 113.030 1.00 8.45 S ATOM 4990 SG CYS C 71 61.701 66.221 116.188 1.00 5.95 S ATOM 5494 SG CYS C 136 58.188 71.270 118.370 1.00 16.56 S ATOM 14942 SG CYS M 131 41.930 62.042 151.113 1.00 17.11 S ATOM 14921 SG CYS M 128 45.792 57.488 148.156 1.00 4.60 S ATOM 14982 SG CYS M 137 47.526 61.041 153.508 1.00 18.34 S ATOM 15314 SG CYS M 179 45.512 61.058 164.413 1.00 17.91 S ATOM 15668 SG CYS M 226 42.540 63.662 159.954 1.00 17.22 S ATOM 15338 SG CYS M 182 39.826 63.532 165.978 1.00 18.69 S ATOM 15291 SG CYS M 176 39.892 58.209 162.503 1.00 14.77 S ATOM 14539 SG CYS M 78 57.014 56.752 168.755 1.00 27.80 S ATOM 14640 SG CYS M 92 55.025 58.756 170.861 1.00 9.92 S ATOM 14428 SG CYS M 64 50.734 58.569 168.484 1.00 20.24 S ATOM 14514 SG CYS M 75 51.959 56.650 165.533 1.00 7.36 S ATOM 21474 SG CYS O 135 32.605 30.765 177.588 1.00 40.24 S ATOM 21508 SG CYS O 140 32.510 27.386 178.952 1.00 45.41 S ATOM 21788 SG CYS O 176 36.839 32.436 180.509 1.00 49.72 S ATOM 21811 SG CYS O 180 37.418 29.184 181.472 1.00 54.83 S ATOM 28550 SG CYS T 86 30.779 50.686 142.746 1.00 26.35 S ATOM 28728 SG CYS T 111 31.958 54.135 143.639 1.00 23.34 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.66 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.66 Time building chain proxies: 28.70, per 1000 atoms: 0.42 Number of scatterers: 68136 At special positions: 0 Unit cell: (216.988, 222.359, 227.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 46 15.00 Mg 1 11.99 O 12220 8.00 N 11238 7.00 C 44120 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.31 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: 22.57 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="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " 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="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " 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="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " 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="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 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: 361 helices and 29 sheets defined 52.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.374A 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 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: 3.562A 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: 4.402A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.869A pdb=" N ASP A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 Proline residue: A 434 - end of helix removed outlier: 3.541A 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 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.620A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.211A 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: 4.525A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 39 removed outlier: 4.850A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.576A pdb=" N LEU G 108 " --> pdb=" O PHE G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 108' Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.916A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 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: 4.106A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.784A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 213 through 222 removed outlier: 3.686A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (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: 4.014A 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 335 through 338 Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 353 No H-bonds generated for 'chain 'J' and resid 350 through 353' Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.517A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 4.064A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' 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: 3.786A 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 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' 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: 3.847A 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 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 378 through 380 No H-bonds generated for 'chain 'M' and resid 378 through 380' 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 424 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.759A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 478 through 482 Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 520 through 527 removed outlier: 4.745A pdb=" N ALA M 524 " --> pdb=" O ALA M 520 " (cutoff:3.500A) Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 Processing helix chain 'M' and resid 665 through 674 removed outlier: 4.027A pdb=" N LEU M 674 " --> pdb=" O GLU M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 695 removed outlier: 3.954A pdb=" N TYR M 695 " --> pdb=" O LYS M 692 " (cutoff:3.500A) 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: 3.623A 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: 3.578A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.136A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.945A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) 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 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.645A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.611A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.942A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 120 through 125 Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.814A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.768A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 248 Processing helix chain 'Q' and resid 251 through 262 Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.608A 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 350 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 439 removed outlier: 4.450A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.076A 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 30 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 3.557A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 54 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 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 97 Proline residue: W 73 - end of helix removed outlier: 3.684A pdb=" N ILE W 96 " --> pdb=" O GLU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.451A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.982A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.655A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.790A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 90 removed outlier: 3.951A pdb=" N SER Z 90 " --> pdb=" O TYR Z 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 92 removed outlier: 4.188A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.650A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 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 129 through 149 Processing helix chain 'd' and resid 29 through 40 Processing helix chain 'd' and resid 42 through 57 Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.848A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 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 100 through 107 Processing helix chain 'e' and resid 115 through 132 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: 3.819A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 3.818A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 removed outlier: 3.626A pdb=" N GLU h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.680A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.283A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.803A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.727A 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: 3.877A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.279A 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: 3.672A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix removed outlier: 3.950A pdb=" N ILE i 267 " --> pdb=" O TRP i 264 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN i 268 " --> pdb=" O MET i 265 " (cutoff:3.500A) Processing helix chain 'i' and resid 277 through 300 removed outlier: 3.984A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU i 296 " --> pdb=" O PHE i 292 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 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: 3.656A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.545A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.324A 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 Proline residue: k 60 - end of helix removed outlier: 3.940A pdb=" N PHE k 66 " --> pdb=" O LEU k 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS k 69 " --> pdb=" O PHE k 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA k 72 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU k 73 " --> pdb=" O GLU k 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU k 75 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL k 81 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 13 removed outlier: 3.711A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 23 removed outlier: 4.918A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.196A 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: 3.902A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.733A pdb=" N GLY l 178 " --> pdb=" O TYR l 174 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.215A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.409A 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: 4.263A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.758A pdb=" N ALA l 289 " --> pdb=" O THR l 285 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 319 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.070A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.957A 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 388 through 400 removed outlier: 3.945A pdb=" N LYS l 392 " --> pdb=" O PHE l 389 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP l 393 " --> pdb=" O TYR l 390 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU l 394 " --> pdb=" O SER l 391 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.698A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 3.651A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.437A 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: 3.804A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.353A 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 528 No H-bonds generated for 'chain 'l' and resid 526 through 528' Processing helix chain 'l' and resid 530 through 533 No H-bonds generated for 'chain 'l' and resid 530 through 533' Processing helix chain 'l' and resid 536 through 547 removed outlier: 3.876A pdb=" N GLN l 546 " --> pdb=" O LEU l 542 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 removed outlier: 3.711A pdb=" N LEU l 589 " --> pdb=" O LYS l 585 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 removed outlier: 3.578A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.776A pdb=" N ALA m 73 " --> pdb=" O GLY m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 124 through 127 removed outlier: 3.628A pdb=" N ILE m 127 " --> pdb=" O ASP m 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 127' Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.421A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 34 removed outlier: 4.626A pdb=" N ASP n 10 " --> pdb=" O GLN n 6 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.571A pdb=" N SER n 31 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) 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: 3.731A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.361A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.560A pdb=" N SER p 132 " --> pdb=" O LEU p 128 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP p 133 " --> pdb=" O ARG p 129 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.682A 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: 4.189A 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: 4.165A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 60 through 80 Proline residue: r 64 - end of helix removed outlier: 3.793A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.607A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.806A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 169 removed outlier: 3.686A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA r 145 " --> pdb=" O ARG r 142 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR r 153 " --> pdb=" O LEU r 150 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU r 154 " --> pdb=" O PHE r 151 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.153A pdb=" N VAL r 165 " --> pdb=" O VAL r 162 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN r 168 " --> pdb=" O VAL r 165 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.514A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.014A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 250 removed outlier: 3.522A pdb=" N LEU r 238 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU r 250 " --> pdb=" O THR r 247 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 277 removed outlier: 3.919A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA r 258 " --> pdb=" O ASN r 255 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR r 259 " --> pdb=" O TYR r 256 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 3.978A pdb=" N MET r 269 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR r 272 " --> pdb=" O MET r 269 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 4.075A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.517A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 4.072A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY r 397 " --> pdb=" O ILE r 394 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA r 404 " --> pdb=" O MET r 401 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR r 406 " --> pdb=" O THR r 403 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER r 407 " --> pdb=" O ALA r 404 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR r 409 " --> pdb=" O TYR r 406 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.018A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 31 Proline residue: s 12 - end of helix removed outlier: 3.742A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.433A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.869A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.136A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 removed outlier: 3.638A pdb=" N MET s 184 " --> pdb=" O PRO s 180 " (cutoff:3.500A) 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 218 through 242 Processing helix chain 's' and resid 252 through 274 Processing helix chain 's' and resid 282 through 291 Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 80 through 91 Processing helix chain 'u' and resid 102 through 114 removed outlier: 3.693A pdb=" N ASP u 113 " --> pdb=" O GLU u 109 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 123 removed outlier: 3.748A pdb=" N ARG v 114 " --> pdb=" O GLN v 110 " (cutoff:3.500A) Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 50 through 52 No H-bonds generated for 'chain 'w' and resid 50 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 96 No H-bonds generated for 'chain 'w' and resid 93 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 4.033A pdb=" N GLU w 171 " --> pdb=" O VAL w 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA w 172 " --> pdb=" O PHE w 169 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 192 Processing helix chain 'w' and resid 195 through 197 No H-bonds generated for 'chain 'w' and resid 195 through 197' Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 266 through 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 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 321 through 332 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 240 through 244 removed outlier: 7.094A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 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: 5.893A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.255A 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: 6.660A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.330A 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 57 removed outlier: 3.628A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 7.875A pdb=" N PHE J 263 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER J 168 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.778A 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: 6.095A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.419A 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: 4.622A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.149A 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: 8.115A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.369A 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: 6.370A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.517A 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: 6.783A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.790A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (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: 6.200A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= Z, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AA, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.428A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.642A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2887 hydrogen bonds defined for protein. 7983 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: 23.60 Time building geometry restraints manager: 24.70 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: 27753 1.40 - 1.62: 41112 1.62 - 1.84: 879 1.84 - 2.06: 1 2.06 - 2.28: 80 Bond restraints: 69825 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.264 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.290 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.299 0.229 2.00e-02 2.50e+03 1.31e+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 69820 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.96: 76 85.96 - 98.37: 1 98.37 - 110.79: 24333 110.79 - 123.20: 67197 123.20 - 135.62: 2800 Bond angle restraints: 94407 Sorted by residual: angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.93 -16.19 1.95e+00 2.62e-01 6.86e+01 angle pdb=" N ARG P 125 " pdb=" CA ARG P 125 " pdb=" C ARG P 125 " ideal model delta sigma weight residual 111.71 120.80 -9.09 1.15e+00 7.56e-01 6.25e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.98 -14.14 1.91e+00 2.73e-01 5.45e+01 angle pdb=" N ILE l 26 " pdb=" CA ILE l 26 " pdb=" C ILE l 26 " ideal model delta sigma weight residual 113.71 106.74 6.97 9.50e-01 1.11e+00 5.38e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.40 -9.07 1.32e+00 5.72e-01 4.71e+01 ... (remaining 94402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 40238 35.72 - 71.45: 1813 71.45 - 107.17: 115 107.17 - 142.90: 15 142.90 - 178.62: 5 Dihedral angle restraints: 42186 sinusoidal: 18095 harmonic: 24091 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 257.59 78.97 178.62 1 2.00e+01 2.50e-03 4.80e+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 74.96 -134.96 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -136.88 50.88 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 42183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 9792 0.095 - 0.190: 387 0.190 - 0.285: 12 0.285 - 0.380: 2 0.380 - 0.475: 2 Chirality restraints: 10195 Sorted by residual: chirality pdb=" CA TRP u 86 " pdb=" N TRP u 86 " pdb=" C TRP u 86 " pdb=" CB TRP u 86 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C3B NDP J 401 " pdb=" C2B NDP J 401 " pdb=" C4B NDP J 401 " pdb=" O3B NDP J 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA ARG P 125 " pdb=" N ARG P 125 " pdb=" C ARG P 125 " pdb=" CB ARG P 125 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 10192 not shown) Planarity restraints: 11765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.408 2.00e-02 2.50e+03 3.64e-01 1.66e+03 pdb=" C18 UQ J 402 " 0.419 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.398 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.006 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.403 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.333 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C18 UQ s 402 " -0.313 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.381 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.003 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.358 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.318 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C13 UQ J 402 " -0.291 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " -0.370 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.000 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.342 2.00e-02 2.50e+03 ... (remaining 11762 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4546 2.74 - 3.28: 67225 3.28 - 3.82: 118277 3.82 - 4.36: 147044 4.36 - 4.90: 246287 Nonbonded interactions: 583379 Sorted by model distance: nonbonded pdb=" OD2 ASP S 51 " pdb=" OG SER u 22 " model vdw 2.195 2.440 nonbonded pdb=" OE1 GLN F 62 " pdb=" OG SER F 78 " model vdw 2.195 2.440 nonbonded pdb=" O GLU F 92 " pdb=" OG SER F 96 " model vdw 2.199 2.440 nonbonded pdb=" OG SER Y 62 " pdb=" OG1 THR l 371 " model vdw 2.201 2.440 nonbonded pdb=" O TRP Q 268 " pdb=" OG1 THR Q 272 " model vdw 2.208 2.440 ... (remaining 583374 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 and (name N or name CA or name \ C or name O or name CB )) or resid 95 or (resid 96 through 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 46 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44120 2.51 5 N 11238 2.21 5 O 12220 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=0.66 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: 1.260 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: 0.070 Extract box with map and model: 10.920 Check model and map are aligned: 0.770 Process input model: 154.530 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.520 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 0.310 69825 Z= 0.486 Angle : 0.779 17.307 94407 Z= 0.388 Chirality : 0.041 0.475 10195 Planarity : 0.009 0.364 11765 Dihedral : 18.377 178.621 26627 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.01 % 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: 1.20 (0.09), residues: 8173 helix: 1.75 (0.08), residues: 4291 sheet: 0.33 (0.25), residues: 427 loop : -0.31 (0.11), residues: 3455 *********************** 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 1207 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1114 time to evaluate : 6.340 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 93 outliers final: 67 residues processed: 1189 average time/residue: 1.5665 time to fit residues: 2418.9309 Evaluate side-chains 1107 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1040 time to evaluate : 6.230 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 60 residues processed: 7 average time/residue: 1.0035 time to fit residues: 18.4900 ------------------------------------------------------------------------------- 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: 4.9990 chunk 610 optimal weight: 0.9990 chunk 338 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 630 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 383 optimal weight: 0.9990 chunk 469 optimal weight: 0.3980 chunk 731 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS M 464 GLN M 569 GLN M 677 GLN O 48 ASN O 187 GLN P 138 ASN P 236 ASN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 GLN b 13 GLN e 65 ASN h 25 GLN i 147 GLN k 57 ASN l 534 HIS r 180 HIS r 220 HIS s 258 ASN v 54 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 69825 Z= 0.172 Angle : 0.504 10.397 94407 Z= 0.252 Chirality : 0.040 0.171 10195 Planarity : 0.004 0.071 11765 Dihedral : 12.853 179.239 10451 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 8173 helix: 1.77 (0.08), residues: 4292 sheet: 0.21 (0.24), residues: 451 loop : -0.26 (0.11), residues: 3430 *********************** 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 1310 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1080 time to evaluate : 6.458 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 230 outliers final: 111 residues processed: 1225 average time/residue: 1.5753 time to fit residues: 2525.3718 Evaluate side-chains 1154 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1043 time to evaluate : 6.261 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 79 residues processed: 32 average time/residue: 1.1252 time to fit residues: 59.3857 ------------------------------------------------------------------------------- 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: 7.9990 chunk 226 optimal weight: 7.9990 chunk 608 optimal weight: 10.0000 chunk 497 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 732 optimal weight: 3.9990 chunk 791 optimal weight: 8.9990 chunk 652 optimal weight: 5.9990 chunk 726 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 587 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN J 138 ASN J 323 HIS ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 499 ASN M 569 GLN O 187 GLN P 138 ASN P 236 ASN T 123 HIS Z 21 GLN a 170 GLN b 13 GLN b 89 HIS d 124 ASN e 65 ASN h 98 HIS i 147 GLN s 258 ASN u 73 GLN v 47 ASN v 54 GLN v 110 GLN w 149 HIS ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 69825 Z= 0.352 Angle : 0.601 10.855 94407 Z= 0.303 Chirality : 0.045 0.188 10195 Planarity : 0.005 0.067 11765 Dihedral : 12.446 175.106 10451 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 8173 helix: 1.42 (0.08), residues: 4307 sheet: 0.04 (0.24), residues: 455 loop : -0.40 (0.11), residues: 3411 *********************** 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 1359 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1080 time to evaluate : 6.353 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 279 outliers final: 138 residues processed: 1256 average time/residue: 1.6039 time to fit residues: 2631.8767 Evaluate side-chains 1171 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1033 time to evaluate : 6.300 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 109 residues processed: 32 average time/residue: 0.8925 time to fit residues: 53.4525 ------------------------------------------------------------------------------- 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: 2.9990 chunk 550 optimal weight: 5.9990 chunk 380 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 349 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 chunk 734 optimal weight: 4.9990 chunk 778 optimal weight: 7.9990 chunk 383 optimal weight: 5.9990 chunk 696 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN J 323 HIS K 78 HIS ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 498 GLN M 569 GLN M 669 ASN N 31 ASN O 187 GLN P 138 ASN P 236 ASN Z 21 GLN b 13 GLN d 134 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN h 25 GLN i 147 GLN m 86 ASN r 192 ASN r 333 ASN s 258 ASN u 73 GLN v 54 GLN v 110 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 69825 Z= 0.313 Angle : 0.569 10.884 94407 Z= 0.287 Chirality : 0.043 0.187 10195 Planarity : 0.005 0.067 11765 Dihedral : 12.026 175.900 10451 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 8173 helix: 1.36 (0.08), residues: 4296 sheet: 0.01 (0.24), residues: 454 loop : -0.43 (0.11), residues: 3423 *********************** 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 1350 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1065 time to evaluate : 6.307 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 285 outliers final: 159 residues processed: 1253 average time/residue: 1.5774 time to fit residues: 2590.8024 Evaluate side-chains 1194 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1035 time to evaluate : 6.464 Switching outliers to nearest non-outliers outliers start: 159 outliers final: 121 residues processed: 39 average time/residue: 1.0268 time to fit residues: 67.2246 ------------------------------------------------------------------------------- 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: 3.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 579 optimal weight: 7.9990 chunk 321 optimal weight: 10.0000 chunk 664 optimal weight: 7.9990 chunk 537 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 6.9990 chunk 698 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 498 GLN M 569 GLN M 669 ASN N 13 GLN N 31 ASN O 187 GLN P 236 ASN Z 21 GLN b 13 GLN d 134 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN h 25 GLN m 86 ASN p 53 ASN r 333 ASN s 247 HIS s 258 ASN u 73 GLN v 54 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 69825 Z= 0.484 Angle : 0.661 11.107 94407 Z= 0.333 Chirality : 0.048 0.217 10195 Planarity : 0.006 0.068 11765 Dihedral : 12.113 174.114 10451 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.86 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.44 (0.09), residues: 8173 helix: 1.06 (0.08), residues: 4310 sheet: -0.19 (0.24), residues: 446 loop : -0.56 (0.10), residues: 3417 *********************** 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 1353 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1062 time to evaluate : 6.273 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 291 outliers final: 163 residues processed: 1266 average time/residue: 1.5963 time to fit residues: 2650.6217 Evaluate side-chains 1193 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1030 time to evaluate : 6.267 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 130 residues processed: 33 average time/residue: 0.8919 time to fit residues: 53.5817 ------------------------------------------------------------------------------- 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: 0.9980 chunk 700 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 456 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 778 optimal weight: 5.9990 chunk 646 optimal weight: 0.9980 chunk 360 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 chunk 408 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN J 323 HIS K 78 HIS M 453 GLN M 464 GLN M 498 GLN M 669 ASN N 31 ASN O 90 ASN O 187 GLN P 236 ASN Q 131 GLN Z 21 GLN b 13 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 26 GLN k 57 ASN m 86 ASN r 251 ASN r 333 ASN u 73 GLN v 54 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 69825 Z= 0.152 Angle : 0.507 10.620 94407 Z= 0.257 Chirality : 0.040 0.168 10195 Planarity : 0.004 0.061 11765 Dihedral : 11.314 179.666 10451 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.09), residues: 8173 helix: 1.47 (0.08), residues: 4304 sheet: 0.09 (0.24), residues: 449 loop : -0.38 (0.11), residues: 3420 *********************** 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 1342 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1118 time to evaluate : 6.409 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 224 outliers final: 132 residues processed: 1288 average time/residue: 1.6218 time to fit residues: 2774.1721 Evaluate side-chains 1179 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1047 time to evaluate : 6.304 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 115 residues processed: 18 average time/residue: 1.2002 time to fit residues: 39.1542 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 9.9990 chunk 443 optimal weight: 0.4980 chunk 568 optimal weight: 4.9990 chunk 440 optimal weight: 4.9990 chunk 655 optimal weight: 4.9990 chunk 434 optimal weight: 0.4980 chunk 775 optimal weight: 0.5980 chunk 485 optimal weight: 8.9990 chunk 473 optimal weight: 9.9990 chunk 358 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 71 GLN J 323 HIS M 464 GLN M 540 ASN N 31 ASN O 187 GLN P 138 ASN P 236 ASN U 40 ASN Z 21 GLN a 170 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN h 25 GLN i 147 GLN k 57 ASN r 304 GLN u 73 GLN v 50 GLN v 54 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 69825 Z= 0.157 Angle : 0.505 10.623 94407 Z= 0.252 Chirality : 0.040 0.174 10195 Planarity : 0.004 0.053 11765 Dihedral : 10.803 179.713 10451 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 8173 helix: 1.64 (0.08), residues: 4296 sheet: 0.16 (0.24), residues: 449 loop : -0.31 (0.11), residues: 3428 *********************** 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 1297 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1081 time to evaluate : 6.429 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 216 outliers final: 131 residues processed: 1240 average time/residue: 1.6256 time to fit residues: 2644.1872 Evaluate side-chains 1178 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1047 time to evaluate : 6.249 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 113 residues processed: 19 average time/residue: 1.2080 time to fit residues: 40.5722 ------------------------------------------------------------------------------- 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: 0.9990 chunk 309 optimal weight: 0.5980 chunk 463 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 493 optimal weight: 0.0870 chunk 528 optimal weight: 0.6980 chunk 383 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 609 optimal weight: 6.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS K 78 HIS M 464 GLN N 31 ASN O 187 GLN P 236 ASN V 129 GLN Z 21 GLN b 13 GLN e 65 ASN e 132 ASN h 25 GLN h 82 GLN i 147 GLN k 57 ASN m 175 ASN r 168 GLN r 184 HIS r 192 ASN r 304 GLN u 73 GLN v 54 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 69825 Z= 0.139 Angle : 0.495 11.813 94407 Z= 0.247 Chirality : 0.039 0.170 10195 Planarity : 0.004 0.058 11765 Dihedral : 10.396 178.913 10451 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 8173 helix: 1.74 (0.08), residues: 4282 sheet: 0.21 (0.24), residues: 449 loop : -0.27 (0.11), residues: 3442 *********************** 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 1245 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1079 time to evaluate : 6.368 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 166 outliers final: 120 residues processed: 1215 average time/residue: 1.6237 time to fit residues: 2586.5527 Evaluate side-chains 1181 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1061 time to evaluate : 6.330 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 111 residues processed: 9 average time/residue: 1.1075 time to fit residues: 23.2367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.0470 chunk 743 optimal weight: 5.9990 chunk 678 optimal weight: 0.6980 chunk 723 optimal weight: 5.9990 chunk 435 optimal weight: 0.0470 chunk 314 optimal weight: 7.9990 chunk 567 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 653 optimal weight: 8.9990 chunk 683 optimal weight: 0.8980 chunk 720 optimal weight: 2.9990 overall best weight: 0.9378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN J 323 HIS M 464 GLN N 31 ASN O 187 GLN P 236 ASN V 129 GLN Z 21 GLN e 132 ASN h 25 GLN i 147 GLN k 57 ASN r 184 HIS r 192 ASN u 73 GLN v 54 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 69825 Z= 0.156 Angle : 0.507 12.126 94407 Z= 0.251 Chirality : 0.040 0.174 10195 Planarity : 0.004 0.058 11765 Dihedral : 10.184 179.522 10451 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 8173 helix: 1.76 (0.08), residues: 4280 sheet: 0.22 (0.24), residues: 449 loop : -0.26 (0.11), residues: 3444 *********************** 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 1232 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1077 time to evaluate : 6.336 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 155 outliers final: 116 residues processed: 1212 average time/residue: 1.6449 time to fit residues: 2621.7913 Evaluate side-chains 1173 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1057 time to evaluate : 6.422 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 109 residues processed: 7 average time/residue: 1.0696 time to fit residues: 19.6624 ------------------------------------------------------------------------------- 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: 6.9990 chunk 764 optimal weight: 2.9990 chunk 466 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 chunk 531 optimal weight: 6.9990 chunk 801 optimal weight: 0.9990 chunk 738 optimal weight: 5.9990 chunk 638 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 493 optimal weight: 0.5980 chunk 391 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN J 323 HIS J 341 GLN K 78 HIS M 464 GLN M 499 ASN N 31 ASN O 187 GLN P 138 ASN P 236 ASN V 129 GLN Z 21 GLN e 132 ASN h 25 GLN j 83 ASN k 57 ASN p 53 ASN s 230 ASN s 235 ASN s 258 ASN v 54 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 69825 Z= 0.191 Angle : 0.525 12.696 94407 Z= 0.261 Chirality : 0.041 0.175 10195 Planarity : 0.004 0.060 11765 Dihedral : 10.139 179.132 10451 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8173 helix: 1.71 (0.08), residues: 4292 sheet: 0.22 (0.24), residues: 449 loop : -0.27 (0.11), residues: 3432 ********************** 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 1188 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1054 time to evaluate : 6.391 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 134 outliers final: 118 residues processed: 1173 average time/residue: 1.6825 time to fit residues: 2595.1681 Evaluate side-chains 1161 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1043 time to evaluate : 6.292 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 111 residues processed: 8 average time/residue: 1.0023 time to fit residues: 20.5532 ------------------------------------------------------------------------------- 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: 0.9990 chunk 195 optimal weight: 6.9990 chunk 588 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 639 optimal weight: 0.0970 chunk 267 optimal weight: 0.9990 chunk 656 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS J 341 GLN M 464 GLN M 499 ASN N 31 ASN O 187 GLN P 138 ASN P 236 ASN Z 21 GLN h 25 GLN h 82 GLN j 83 ASN k 57 ASN r 184 HIS r 333 ASN s 258 ASN v 54 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.093670 restraints weight = 91697.355| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.25 r_work: 0.2789 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 69825 Z= 0.201 Angle : 0.533 13.298 94407 Z= 0.265 Chirality : 0.041 0.186 10195 Planarity : 0.004 0.060 11765 Dihedral : 10.106 178.754 10451 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8173 helix: 1.69 (0.08), residues: 4281 sheet: 0.21 (0.24), residues: 449 loop : -0.27 (0.11), residues: 3443 =============================================================================== Job complete usr+sys time: 32264.78 seconds wall clock time: 557 minutes 38.30 seconds (33458.30 seconds total)