Starting phenix.real_space_refine (version: dev) on Mon Feb 27 07:34:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257_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/7w1v_32257/02_2023/7w1v_32257_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1v_32257/02_2023/7w1v_32257_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 175": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M GLU 269": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 648": "OE1" <-> "OE2" Residue "M GLU 716": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q GLU 206": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "Q GLU 406": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 117": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 268": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 111": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 42": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 124": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 189": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Residue "w TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 68209 Number of models: 1 Model: "" Number of chains: 67 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: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1411 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 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: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5284 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 657} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1200 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 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: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 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: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 856 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "f" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4797 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "m" Number of atoms: 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: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 172 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "i" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 246 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "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: "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 48.062 48.353 170.130 1.00 28.18 S ATOM 3060 SG CYS A 425 47.359 44.717 175.988 1.00 31.73 S ATOM 2738 SG CYS A 385 45.129 43.992 169.969 1.00 21.33 S ATOM 2699 SG CYS A 379 42.878 48.842 173.648 1.00 17.29 S ATOM 3960 SG CYS B 113 38.320 63.593 134.674 1.00 7.38 S ATOM 3979 SG CYS B 116 43.418 61.395 138.703 1.00 7.59 S ATOM 4002 SG CYS B 119 44.527 64.137 133.190 1.00 5.86 S ATOM 4331 SG CYS B 162 41.924 58.300 133.793 1.00 0.00 S ATOM 4029 SG CYS B 123 50.754 66.976 128.953 1.00 0.00 S ATOM 4255 SG CYS B 152 49.243 65.080 122.984 1.00 9.36 S ATOM 4302 SG CYS B 158 47.213 61.363 127.774 1.00 11.33 S ATOM 4281 SG CYS B 155 53.308 61.718 126.689 1.00 1.52 S ATOM 5723 SG CYS C 166 56.022 65.103 118.989 1.00 1.94 S ATOM 4995 SG CYS C 72 56.781 66.586 112.657 1.00 7.04 S ATOM 4989 SG CYS C 71 61.939 65.153 115.857 1.00 9.41 S ATOM 5493 SG CYS C 136 58.341 70.244 117.943 1.00 4.58 S ATOM 14945 SG CYS M 131 41.901 61.655 150.765 1.00 6.65 S ATOM 14924 SG CYS M 128 45.701 56.987 147.856 1.00 3.99 S ATOM 14985 SG CYS M 137 47.564 60.543 153.109 1.00 4.01 S ATOM 15317 SG CYS M 179 45.423 61.050 164.112 1.00 12.81 S ATOM 15671 SG CYS M 226 42.433 63.484 159.586 1.00 16.30 S ATOM 15341 SG CYS M 182 39.792 63.468 165.600 1.00 15.54 S ATOM 15294 SG CYS M 176 39.827 58.032 162.198 1.00 0.00 S ATOM 14542 SG CYS M 78 56.990 56.542 168.459 1.00 20.23 S ATOM 14643 SG CYS M 92 54.880 58.562 170.696 1.00 4.16 S ATOM 14431 SG CYS M 64 50.675 58.459 168.301 1.00 12.34 S ATOM 14517 SG CYS M 75 51.877 56.553 165.414 1.00 15.23 S ATOM 21464 SG CYS O 135 32.275 30.944 177.524 1.00 37.41 S ATOM 21498 SG CYS O 140 32.060 27.576 178.748 1.00 49.75 S ATOM 21778 SG CYS O 176 36.528 32.454 180.392 1.00 38.67 S ATOM 21801 SG CYS O 180 37.067 29.319 181.541 1.00 44.84 S ATOM 28536 SG CYS T 86 30.930 50.414 142.465 1.00 17.72 S ATOM 28714 SG CYS T 111 31.893 53.741 143.265 1.00 18.36 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.58 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.58 Time building chain proxies: 28.31, per 1000 atoms: 0.42 Number of scatterers: 68209 At special positions: 0 Unit cell: (215.914, 221.285, 226.656, 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 48 15.00 Mg 1 11.99 O 12230 8.00 N 11235 7.00 C 44184 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=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.53 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="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="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " 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="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " 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="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="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="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " 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=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 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: 358 helices and 29 sheets defined 52.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.503A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 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: 3.739A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.233A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.984A 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: 3.526A pdb=" N ARG A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.531A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.847A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'E' and resid 25 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.198A 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: 4.372A 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: 5.127A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 104 through 107 No H-bonds generated for 'chain 'G' and resid 104 through 107' 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: 4.025A 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: 4.009A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.761A 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 221 removed outlier: 3.709A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.867A 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 337 No H-bonds generated for 'chain 'J' and resid 335 through 337' Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' 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 'K' and resid 77 through 80 Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.310A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' 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 140 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.756A 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 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: 3.870A 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 391 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: 3.714A 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 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 527 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 673 Processing helix chain 'M' and resid 691 through 695 removed outlier: 3.902A 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: 3.650A 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: 3.695A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.209A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.900A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.584A 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: 3.606A pdb=" N ASN P 164 " --> pdb=" O LYS P 161 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET P 173 " --> pdb=" O ILE P 170 " (cutoff:3.500A) removed outlier: 4.061A 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: 4.177A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.625A 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: 3.844A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.501A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.326A 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: 4.537A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 373 Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 438 removed outlier: 4.410A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 453 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: 3.576A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 54 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 99 Proline residue: W 73 - end of helix removed outlier: 3.729A pdb=" N ILE W 96 " --> pdb=" O GLU W 92 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.479A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.231A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.967A 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 37 Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.585A 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: 3.830A pdb=" N SER Z 90 " --> pdb=" O TYR Z 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 92 removed outlier: 4.324A 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: 3.757A 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 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 40 Processing helix chain 'd' and resid 42 through 58 removed outlier: 3.602A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.572A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN d 124 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 101 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 72 Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.793A 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: 3.756A 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: 3.826A 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 21 Processing helix chain 'i' and resid 26 through 44 Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.208A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.859A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix removed outlier: 3.620A pdb=" N GLN i 144 " --> pdb=" O SER i 140 " (cutoff:3.500A) 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: 3.885A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.307A 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: 3.759A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.606A 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: 3.857A pdb=" N ILE i 267 " --> pdb=" O TRP i 264 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN i 268 " --> pdb=" O MET i 265 " (cutoff:3.500A) Processing helix chain 'i' and resid 277 through 300 removed outlier: 3.947A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) removed outlier: 3.916A 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 24 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.654A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.620A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.244A 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: 4.138A pdb=" N PHE k 66 " --> pdb=" O LEU k 63 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS k 69 " --> pdb=" O PHE k 66 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA k 72 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU k 75 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 4.021A 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 15 removed outlier: 3.574A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 20 No H-bonds generated for 'chain 'l' and resid 17 through 20' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.211A 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: 3.910A 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: 3.794A pdb=" N GLY l 178 " --> pdb=" O TYR l 174 " (cutoff:3.500A) removed outlier: 3.972A 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: 4.149A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.196A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.710A pdb=" N ALA l 289 " --> pdb=" O THR l 285 " (cutoff:3.500A) removed outlier: 4.486A 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: 4.045A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 3.563A pdb=" N ASP l 393 " --> pdb=" O PHE l 389 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.706A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.642A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN l 470 " --> pdb=" O PHE l 466 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN l 471 " --> pdb=" O ILE l 467 " (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: 3.749A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.187A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 removed outlier: 3.788A 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: 3.517A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 removed outlier: 4.777A pdb=" N GLY m 62 " --> pdb=" O LEU m 58 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.573A 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: 4.170A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.089A 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: 4.696A pdb=" N ASP n 10 " --> pdb=" O GLN n 6 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.574A pdb=" N SER n 31 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.710A 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: 4.430A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.633A pdb=" N SER p 132 " --> pdb=" O LEU p 128 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP p 133 " --> pdb=" O ARG p 129 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.584A 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: 4.139A 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: 4.186A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.801A 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: 3.550A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.647A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 171 removed outlier: 3.678A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA r 145 " --> pdb=" O ARG r 142 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR r 153 " --> pdb=" O LEU r 150 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU r 154 " --> pdb=" O PHE r 151 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.098A pdb=" N VAL r 165 " --> pdb=" O VAL r 162 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN r 168 " --> pdb=" O VAL r 165 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.396A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.063A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.698A 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: 3.515A pdb=" N LEU r 238 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE r 249 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.893A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.171A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 4.080A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.563A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) removed outlier: 3.786A 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: 4.054A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY r 397 " --> pdb=" O ILE r 394 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA r 404 " --> pdb=" O MET r 401 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR r 406 " --> pdb=" O THR r 403 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER r 407 " --> pdb=" O ALA r 404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR r 409 " --> pdb=" O TYR r 406 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 448 Proline residue: r 443 - end of helix removed outlier: 4.128A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.688A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.399A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.764A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.111A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.656A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) 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: 3.532A pdb=" N MET s 184 " --> pdb=" O PRO s 180 " (cutoff:3.500A) Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 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 removed outlier: 3.650A pdb=" N CYS u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 102 through 114 removed outlier: 3.593A 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 82 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.712A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 4.184A pdb=" N GLU w 171 " --> pdb=" O VAL w 168 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA w 172 " --> pdb=" O PHE w 169 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 3.512A pdb=" N VAL w 193 " --> pdb=" O GLU w 189 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 249 Processing helix chain 'w' and resid 260 through 263 No H-bonds generated for 'chain 'w' and resid 260 through 263' Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 321 through 333 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.179A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.256A 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: 6.059A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.273A 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: 6.640A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.257A 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: 3.556A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.561A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.766A 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: 6.247A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.454A 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 366 through 368 removed outlier: 8.585A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.131A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.393A 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: 6.518A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.568A 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: 6.754A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.516A 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: 6.777A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.839A 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: 6.403A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.404A 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: 6.509A 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: 6.591A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 84 through 86 2878 hydrogen bonds defined for protein. 8016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.94 Time building geometry restraints manager: 23.59 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: 27751 1.40 - 1.62: 41183 1.62 - 1.84: 882 1.84 - 2.06: 1 2.06 - 2.28: 80 Bond restraints: 69897 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" 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 1.40e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.292 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 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 69892 not shown) Histogram of bond angle deviations from ideal: 73.58 - 85.98: 76 85.98 - 98.37: 1 98.37 - 110.77: 23778 110.77 - 123.16: 67595 123.16 - 135.55: 3036 Bond angle restraints: 94486 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 107.74 123.78 -16.04 1.95e+00 2.62e-01 6.74e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.80 -13.96 1.91e+00 2.73e-01 5.31e+01 angle pdb=" C VAL N 138 " pdb=" N PRO N 139 " pdb=" CA PRO N 139 " ideal model delta sigma weight residual 119.66 124.83 -5.17 7.20e-01 1.93e+00 5.16e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.52 -9.19 1.32e+00 5.72e-01 4.84e+01 angle pdb=" C51 CDL g 202 " pdb=" CB5 CDL g 202 " pdb=" OB6 CDL g 202 " ideal model delta sigma weight residual 111.33 120.37 -9.04 1.32e+00 5.72e-01 4.67e+01 ... (remaining 94481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 40085 34.73 - 69.46: 2001 69.46 - 104.19: 132 104.19 - 138.92: 14 138.92 - 173.65: 6 Dihedral angle restraints: 42238 sinusoidal: 18147 harmonic: 24091 Sorted by residual: dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -146.05 60.05 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 83.94 173.65 1 2.00e+01 2.50e-03 4.79e+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 71.02 -131.02 1 2.00e+01 2.50e-03 3.98e+01 ... (remaining 42235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 9396 0.077 - 0.154: 768 0.154 - 0.231: 24 0.231 - 0.308: 5 0.308 - 0.385: 3 Chirality restraints: 10196 Sorted by residual: chirality pdb=" CA THR Q 188 " pdb=" N THR Q 188 " pdb=" C THR Q 188 " pdb=" CB THR Q 188 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.70e+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 -2.37 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TYR m 60 " pdb=" N TYR m 60 " pdb=" C TYR m 60 " pdb=" CB TYR m 60 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 10193 not shown) Planarity restraints: 11765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ J 402 " -0.470 2.00e-02 2.50e+03 4.09e-01 2.10e+03 pdb=" C18 UQ J 402 " 0.517 2.00e-02 2.50e+03 pdb=" C19 UQ J 402 " 0.410 2.00e-02 2.50e+03 pdb=" C20 UQ J 402 " -0.031 2.00e-02 2.50e+03 pdb=" C21 UQ J 402 " -0.426 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.395 2.00e-02 2.50e+03 3.54e-01 1.57e+03 pdb=" C18 UQ s 402 " -0.398 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.395 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.002 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.396 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.345 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C13 UQ J 402 " -0.326 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " -0.376 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.003 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " 0.360 2.00e-02 2.50e+03 ... (remaining 11762 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1477 2.69 - 3.24: 65098 3.24 - 3.80: 111702 3.80 - 4.35: 154282 4.35 - 4.90: 250457 Nonbonded interactions: 583016 Sorted by model distance: nonbonded pdb=" O ASP m 129 " pdb=" OG1 THR m 130 " model vdw 2.140 2.440 nonbonded pdb=" O TYR a 74 " pdb=" OG SER e 96 " model vdw 2.195 2.440 nonbonded pdb=" O LEU j 73 " pdb=" OH TYR s 160 " model vdw 2.197 2.440 nonbonded pdb=" O SER s 115 " pdb=" OG SER s 119 " model vdw 2.203 2.440 nonbonded pdb=" O TRP Q 268 " pdb=" OG1 THR Q 272 " model vdw 2.206 2.440 ... (remaining 583011 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 113 or (resid 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 156 o \ r 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 48 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44184 2.51 5 N 11235 2.21 5 O 12230 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=0.58 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.430 Check model and map are aligned: 0.760 Process input model: 151.540 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.550 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 0.312 69897 Z= 0.509 Angle : 0.808 17.231 94486 Z= 0.407 Chirality : 0.042 0.385 10196 Planarity : 0.010 0.409 11765 Dihedral : 18.731 173.650 26679 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer Outliers : 1.69 % 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: 1.09 (0.09), residues: 8173 helix: 1.69 (0.08), residues: 4271 sheet: -0.03 (0.24), residues: 440 loop : -0.36 (0.11), residues: 3462 *********************** 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 1263 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1142 time to evaluate : 6.099 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 82 residues processed: 1242 average time/residue: 1.5269 time to fit residues: 2478.1543 Evaluate side-chains 1151 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1069 time to evaluate : 6.008 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 78 residues processed: 7 average time/residue: 0.9174 time to fit residues: 17.7146 ------------------------------------------------------------------------------- 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: 5.9990 chunk 610 optimal weight: 7.9990 chunk 338 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 411 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 630 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 383 optimal weight: 7.9990 chunk 469 optimal weight: 1.9990 chunk 731 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 244 ASN F 93 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN N 116 ASN P 138 ASN T 74 GLN Y 83 HIS a 90 ASN h 25 GLN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 83 ASN k 50 ASN l 351 ASN l 446 ASN l 541 ASN p 66 GLN p 124 GLN s 235 ASN u 65 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 69897 Z= 0.416 Angle : 0.655 13.124 94486 Z= 0.325 Chirality : 0.047 0.306 10196 Planarity : 0.005 0.062 11765 Dihedral : 13.464 177.346 10525 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer Outliers : 5.41 % 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: 0.69 (0.09), residues: 8173 helix: 1.33 (0.08), residues: 4296 sheet: -0.07 (0.24), residues: 436 loop : -0.53 (0.10), residues: 3441 *********************** 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 1446 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1060 time to evaluate : 6.276 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 386 outliers final: 185 residues processed: 1299 average time/residue: 1.5712 time to fit residues: 2687.5877 Evaluate side-chains 1233 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1048 time to evaluate : 6.055 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 129 residues processed: 58 average time/residue: 1.0140 time to fit residues: 94.7357 ------------------------------------------------------------------------------- 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: 1.9990 chunk 226 optimal weight: 8.9990 chunk 608 optimal weight: 3.9990 chunk 497 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 732 optimal weight: 3.9990 chunk 791 optimal weight: 5.9990 chunk 652 optimal weight: 4.9990 chunk 726 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 587 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN N 116 ASN N 135 GLN S 46 ASN T 123 HIS Y 83 HIS a 90 ASN d 55 GLN h 25 GLN i 49 ASN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 446 ASN l 541 ASN p 124 GLN u 16 GLN u 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 69897 Z= 0.216 Angle : 0.540 10.925 94486 Z= 0.271 Chirality : 0.041 0.287 10196 Planarity : 0.004 0.057 11765 Dihedral : 12.591 177.339 10525 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer Outliers : 4.24 % 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: 0.88 (0.09), residues: 8173 helix: 1.51 (0.08), residues: 4299 sheet: -0.06 (0.25), residues: 426 loop : -0.47 (0.11), residues: 3448 *********************** 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 1408 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1105 time to evaluate : 6.117 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 303 outliers final: 181 residues processed: 1298 average time/residue: 1.5500 time to fit residues: 2644.3333 Evaluate side-chains 1225 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1044 time to evaluate : 6.084 Switching outliers to nearest non-outliers outliers start: 181 outliers final: 133 residues processed: 50 average time/residue: 1.0249 time to fit residues: 83.0999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.8980 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 349 optimal weight: 0.9990 chunk 491 optimal weight: 5.9990 chunk 734 optimal weight: 0.5980 chunk 778 optimal weight: 0.0270 chunk 383 optimal weight: 3.9990 chunk 696 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN I 21 GLN I 110 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN M 677 GLN N 116 ASN S 46 ASN a 90 ASN h 25 GLN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 446 ASN p 124 GLN s 157 ASN u 16 GLN u 65 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 69897 Z= 0.156 Angle : 0.504 14.209 94486 Z= 0.251 Chirality : 0.040 0.274 10196 Planarity : 0.004 0.053 11765 Dihedral : 11.828 175.614 10525 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer Outliers : 4.09 % 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: 1.09 (0.09), residues: 8173 helix: 1.69 (0.08), residues: 4293 sheet: 0.01 (0.24), residues: 440 loop : -0.38 (0.11), residues: 3440 *********************** 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 1392 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1100 time to evaluate : 6.074 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 292 outliers final: 156 residues processed: 1301 average time/residue: 1.5299 time to fit residues: 2627.8630 Evaluate side-chains 1210 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1054 time to evaluate : 6.028 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 125 residues processed: 34 average time/residue: 1.0629 time to fit residues: 60.7994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 579 optimal weight: 9.9990 chunk 321 optimal weight: 8.9990 chunk 664 optimal weight: 8.9990 chunk 537 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 698 optimal weight: 0.9990 chunk 196 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN N 116 ASN Q 92 HIS S 46 ASN a 90 ASN d 55 GLN h 25 GLN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 GLN l 446 ASN p 124 GLN s 235 ASN v 76 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 149 HIS w 322 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 69897 Z= 0.354 Angle : 0.603 11.340 94486 Z= 0.301 Chirality : 0.045 0.288 10196 Planarity : 0.005 0.060 11765 Dihedral : 11.956 179.488 10525 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer Outliers : 4.55 % 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: 0.79 (0.09), residues: 8173 helix: 1.43 (0.08), residues: 4304 sheet: -0.01 (0.25), residues: 417 loop : -0.52 (0.11), residues: 3452 *********************** 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 1385 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1060 time to evaluate : 6.144 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 325 outliers final: 192 residues processed: 1272 average time/residue: 1.5474 time to fit residues: 2597.0240 Evaluate side-chains 1215 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1023 time to evaluate : 6.086 Switching outliers to nearest non-outliers outliers start: 192 outliers final: 140 residues processed: 54 average time/residue: 0.9942 time to fit residues: 88.1763 ------------------------------------------------------------------------------- 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: 1.9990 chunk 700 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 456 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 778 optimal weight: 6.9990 chunk 646 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 chunk 257 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN G 115 GLN I 110 GLN J 323 HIS ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN N 116 ASN Q 92 HIS S 46 ASN a 90 ASN d 55 GLN h 25 GLN i 204 ASN l 59 GLN l 446 ASN l 541 ASN p 124 GLN s 235 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 69897 Z= 0.237 Angle : 0.550 14.740 94486 Z= 0.275 Chirality : 0.042 0.286 10196 Planarity : 0.004 0.056 11765 Dihedral : 11.632 176.400 10525 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.09), residues: 8173 helix: 1.51 (0.08), residues: 4301 sheet: -0.07 (0.25), residues: 426 loop : -0.50 (0.11), residues: 3446 *********************** 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 1331 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1053 time to evaluate : 7.315 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 278 outliers final: 176 residues processed: 1248 average time/residue: 1.5823 time to fit residues: 2617.8967 Evaluate side-chains 1213 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1037 time to evaluate : 6.078 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 139 residues processed: 40 average time/residue: 1.1617 time to fit residues: 74.5813 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 1.9990 chunk 443 optimal weight: 0.4980 chunk 568 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 655 optimal weight: 9.9990 chunk 434 optimal weight: 8.9990 chunk 775 optimal weight: 7.9990 chunk 485 optimal weight: 6.9990 chunk 473 optimal weight: 1.9990 chunk 358 optimal weight: 0.0470 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN G 115 GLN I 21 GLN I 110 GLN J 323 HIS ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN N 116 ASN O 144 ASN Q 92 HIS S 46 ASN a 90 ASN c 154 GLN h 25 GLN ** i 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN l 59 GLN l 351 ASN l 446 ASN p 124 GLN s 157 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 69897 Z= 0.182 Angle : 0.522 10.857 94486 Z= 0.261 Chirality : 0.041 0.277 10196 Planarity : 0.004 0.067 11765 Dihedral : 11.155 175.471 10525 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 8173 helix: 1.62 (0.08), residues: 4303 sheet: -0.12 (0.24), residues: 452 loop : -0.42 (0.11), residues: 3418 *********************** 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 1346 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1087 time to evaluate : 6.179 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 259 outliers final: 168 residues processed: 1273 average time/residue: 1.5442 time to fit residues: 2596.3613 Evaluate side-chains 1215 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1047 time to evaluate : 6.046 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 140 residues processed: 30 average time/residue: 1.0251 time to fit residues: 53.3766 ------------------------------------------------------------------------------- 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: 2.9990 chunk 309 optimal weight: 0.4980 chunk 463 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 493 optimal weight: 2.9990 chunk 528 optimal weight: 0.0170 chunk 383 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 609 optimal weight: 4.9990 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN I 110 GLN J 323 HIS ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN N 116 ASN O 144 ASN Q 92 HIS S 46 ASN a 90 ASN c 94 HIS h 25 GLN j 83 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 124 GLN r 304 GLN v 76 ASN ** 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: 0.8764 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 69897 Z= 0.230 Angle : 0.550 14.609 94486 Z= 0.274 Chirality : 0.042 0.277 10196 Planarity : 0.004 0.082 11765 Dihedral : 11.000 175.342 10525 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer Outliers : 3.54 % 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: 0.95 (0.09), residues: 8173 helix: 1.57 (0.08), residues: 4303 sheet: -0.16 (0.24), residues: 446 loop : -0.43 (0.11), residues: 3424 *********************** 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 1302 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1049 time to evaluate : 6.365 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 177 residues processed: 1233 average time/residue: 1.5337 time to fit residues: 2502.8617 Evaluate side-chains 1219 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1042 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 143 residues processed: 36 average time/residue: 1.0537 time to fit residues: 63.6485 ------------------------------------------------------------------------------- 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: 3.9990 chunk 743 optimal weight: 0.7980 chunk 678 optimal weight: 0.8980 chunk 723 optimal weight: 0.9980 chunk 435 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 567 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 653 optimal weight: 6.9990 chunk 683 optimal weight: 4.9990 chunk 720 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 ASN I 21 GLN I 110 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 GLN M 464 GLN M 677 GLN N 116 ASN O 144 ASN Q 92 HIS S 46 ASN a 90 ASN e 115 GLN h 25 GLN ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN p 124 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 69897 Z= 0.187 Angle : 0.530 12.575 94486 Z= 0.264 Chirality : 0.041 0.273 10196 Planarity : 0.004 0.058 11765 Dihedral : 10.707 175.169 10525 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer Outliers : 2.72 % 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: 1.03 (0.09), residues: 8173 helix: 1.64 (0.08), residues: 4300 sheet: -0.10 (0.24), residues: 452 loop : -0.39 (0.11), residues: 3421 *********************** 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 1254 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1060 time to evaluate : 6.302 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 150 residues processed: 1222 average time/residue: 1.5611 time to fit residues: 2534.8464 Evaluate side-chains 1188 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1038 time to evaluate : 6.056 Switching outliers to nearest non-outliers outliers start: 150 outliers final: 139 residues processed: 13 average time/residue: 1.1289 time to fit residues: 29.4302 ------------------------------------------------------------------------------- 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: 5.9990 chunk 764 optimal weight: 5.9990 chunk 466 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 531 optimal weight: 6.9990 chunk 801 optimal weight: 1.9990 chunk 738 optimal weight: 4.9990 chunk 638 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 493 optimal weight: 0.9980 chunk 391 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN N 116 ASN O 144 ASN Q 92 HIS S 46 ASN a 90 ASN h 25 GLN j 83 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 124 GLN s 235 ASN v 76 ASN v 110 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 69897 Z= 0.236 Angle : 0.560 13.629 94486 Z= 0.278 Chirality : 0.042 0.273 10196 Planarity : 0.004 0.057 11765 Dihedral : 10.634 175.296 10525 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer Outliers : 2.55 % 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: 0.94 (0.09), residues: 8173 helix: 1.56 (0.08), residues: 4301 sheet: -0.16 (0.24), residues: 444 loop : -0.43 (0.11), residues: 3428 ********************** 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 1229 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1047 time to evaluate : 6.384 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 157 residues processed: 1204 average time/residue: 1.5305 time to fit residues: 2459.3253 Evaluate side-chains 1193 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1036 time to evaluate : 6.217 Switching outliers to nearest non-outliers outliers start: 157 outliers final: 142 residues processed: 18 average time/residue: 1.1892 time to fit residues: 38.9842 ------------------------------------------------------------------------------- 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: 0.0770 chunk 680 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 588 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 639 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 656 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 GLN ** M 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN N 116 ASN Q 92 HIS S 46 ASN a 90 ASN h 25 GLN j 82 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN p 124 GLN s 235 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106833 restraints weight = 91515.469| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.25 r_work: 0.2978 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 69897 Z= 0.167 Angle : 0.526 13.107 94486 Z= 0.261 Chirality : 0.040 0.263 10196 Planarity : 0.004 0.057 11765 Dihedral : 10.280 174.832 10525 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer Outliers : 2.48 % 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: 1.09 (0.09), residues: 8173 helix: 1.69 (0.08), residues: 4283 sheet: -0.07 (0.24), residues: 452 loop : -0.35 (0.11), residues: 3438 =============================================================================== Job complete usr+sys time: 32351.84 seconds wall clock time: 560 minutes 25.46 seconds (33625.46 seconds total)