Starting phenix.real_space_refine on Fri Feb 16 02:34:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w32_32270/02_2024/7w32_32270_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 34 5.49 5 Mg 1 5.21 5 S 472 5.16 5 C 43055 2.51 5 N 11120 2.21 5 O 11949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 33": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 660": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O ASP 206": "OD1" <-> "OD2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 194": "OE1" <-> "OE2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 406": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "b TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 148": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d GLU 128": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "d GLU 172": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "m PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 46": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 88": "OE1" <-> "OE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66660 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 673 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 26 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: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2613 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3377 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 27, 'TRANS': 391} Chain breaks: 2 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: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} 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: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1014 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 878 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "c" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1458 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "e" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 886 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 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: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4720 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "m" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 919 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 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: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 998 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 45 Chain: "w" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2579 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 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: "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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "l" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 192 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "m" 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: "r" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 302 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' 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: 35 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 2706 SG CYS A 382 48.595 49.412 174.093 1.00 23.27 S ATOM 3048 SG CYS A 425 47.838 45.975 179.750 1.00 19.98 S ATOM 2726 SG CYS A 385 45.320 45.170 174.110 1.00 31.14 S ATOM 2687 SG CYS A 379 43.362 50.214 178.138 1.00 20.42 S ATOM 3949 SG CYS B 113 38.419 66.552 139.644 1.00 24.00 S ATOM 3968 SG CYS B 116 43.331 63.835 143.452 1.00 8.29 S ATOM 3991 SG CYS B 119 44.571 66.592 137.987 1.00 9.32 S ATOM 4320 SG CYS B 162 41.764 60.899 138.491 1.00 0.00 S ATOM 4018 SG CYS B 123 50.727 69.235 133.602 1.00 4.83 S ATOM 4244 SG CYS B 152 48.955 67.672 127.623 1.00 16.98 S ATOM 4291 SG CYS B 158 46.904 63.978 132.457 1.00 12.15 S ATOM 4270 SG CYS B 155 52.932 63.809 130.982 1.00 6.43 S ATOM 5712 SG CYS C 166 55.337 67.576 123.537 1.00 7.78 S ATOM 4984 SG CYS C 72 56.238 68.795 117.370 1.00 5.88 S ATOM 4978 SG CYS C 71 61.191 67.101 119.955 1.00 4.58 S ATOM 5482 SG CYS C 136 58.177 71.898 122.056 1.00 6.81 S ATOM 14772 SG CYS M 131 42.608 63.741 155.399 1.00 19.23 S ATOM 14751 SG CYS M 128 46.011 59.066 152.246 1.00 9.77 S ATOM 14812 SG CYS M 137 48.233 62.295 157.550 1.00 8.21 S ATOM 15144 SG CYS M 179 46.545 62.270 168.648 1.00 22.87 S ATOM 15498 SG CYS M 226 43.561 65.209 164.365 1.00 12.76 S ATOM 15168 SG CYS M 182 41.185 65.091 170.479 1.00 16.95 S ATOM 15121 SG CYS M 176 40.659 59.822 166.937 1.00 19.20 S ATOM 14369 SG CYS M 78 57.802 56.910 172.515 1.00 25.70 S ATOM 14470 SG CYS M 92 56.016 59.083 174.596 1.00 12.67 S ATOM 14258 SG CYS M 64 51.698 59.254 172.341 1.00 21.64 S ATOM 14344 SG CYS M 75 52.638 57.311 169.331 1.00 3.37 S ATOM 21307 SG CYS O 135 31.615 32.601 181.737 1.00 47.21 S ATOM 21341 SG CYS O 140 31.581 29.364 182.862 1.00 68.28 S ATOM 21621 SG CYS O 176 36.223 34.009 184.512 1.00 60.81 S ATOM 21644 SG CYS O 180 36.636 30.852 185.636 1.00 67.85 S ATOM 28302 SG CYS T 86 30.372 53.379 147.196 1.00 26.24 S ATOM 28480 SG CYS T 111 31.703 56.842 148.166 1.00 28.06 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.63 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.63 Time building chain proxies: 26.50, per 1000 atoms: 0.40 Number of scatterers: 66660 At special positions: 0 Unit cell: (219.137, 219.137, 230.953, 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 472 16.00 P 34 15.00 Mg 1 11.99 O 11949 8.00 N 11120 7.00 C 43055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.32 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 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " 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: 19.54 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " 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="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 28 sheets defined 53.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.72 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 103 removed outlier: 3.614A pdb=" N ASN A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 179 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: 3.630A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 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 334 removed outlier: 4.691A pdb=" N THR A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) 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 400 Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.892A 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 Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.917A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 123 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.065A 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: 4.425A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.953A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'G' and resid 76 through 89 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 135 No H-bonds generated for 'chain 'G' and resid 132 through 135' Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.006A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 66 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.175A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 4.745A pdb=" N HIS J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU J 94 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG J 95 " --> pdb=" O THR J 91 " (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 223 removed outlier: 3.562A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.981A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 345 through 356 removed outlier: 4.768A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.379A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (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 131 through 141 Processing helix chain 'L' and resid 161 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.603A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.853A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.518A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 395 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: 3.734A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 478 through 482 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 589 through 591 No H-bonds generated for 'chain 'M' and resid 589 through 591' Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 removed outlier: 3.691A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 651 through 654' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.654A 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 Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.353A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 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 210 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.626A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.792A 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: 3.758A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 4.226A 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 48 removed outlier: 3.867A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.781A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 4.090A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.598A 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: 4.261A 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: 4.558A 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: 4.415A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 454 removed outlier: 4.160A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) 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 removed outlier: 3.871A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.099A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.869A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.425A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.346A 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 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.909A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.806A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG Z 52 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 111 No H-bonds generated for 'chain 'a' and resid 109 through 111' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 65 through 73 removed outlier: 3.540A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) 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 126 through 149 Processing helix chain 'c' and resid 174 through 176 No H-bonds generated for 'chain 'c' and resid 174 through 176' Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.563A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.819A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.759A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.777A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 94 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.172A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.760A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.835A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.598A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.336A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 324 through 334 Proline residue: i 327 - end of helix Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.828A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 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 Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.816A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.692A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.566A 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: 3.937A 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: 3.998A 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: 4.104A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.277A 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: 4.063A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.506A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.630A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (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 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.557A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.616A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.564A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.724A 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 534 Proline residue: l 530 - end of helix removed outlier: 4.257A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 removed outlier: 3.684A pdb=" N MET l 544 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.844A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.270A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 172 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.603A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.823A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 27 through 51 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 118 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: 4.888A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 65 through 73 Processing helix chain 'p' and resid 93 through 97 removed outlier: 4.304A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) 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: 3.784A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (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 17 Proline residue: r 7 - end of helix removed outlier: 4.103A 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: 4.253A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.810A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.521A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.660A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.593A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 170 removed outlier: 4.017A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 204 removed outlier: 4.342A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.075A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 249 removed outlier: 4.526A pdb=" N GLY r 239 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 277 removed outlier: 4.557A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 4.062A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.690A 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: 3.755A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.198A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.962A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.188A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 4.533A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.859A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.630A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.162A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.906A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 48 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 95 through 97 No H-bonds generated for 'chain 'w' and resid 95 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.111A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 251 removed outlier: 4.509A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.965A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.914A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 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: 7.241A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.974A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.312A pdb=" N VAL C 102 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE C 67 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 104 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.581A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.868A 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 229 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 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: 8.379A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.138A 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: 7.960A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.437A 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: 6.747A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.832A 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: 6.708A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.819A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.801A 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: 3.682A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.933A 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 62 through 67 removed outlier: 6.502A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.561A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'w' and resid 84 through 86 2933 hydrogen bonds defined for protein. 8214 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: 22.83 Time building geometry restraints manager: 21.55 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: 27348 1.40 - 1.62: 40057 1.62 - 1.85: 836 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 68321 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.263 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.289 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.633 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+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 68316 not shown) Histogram of bond angle deviations from ideal: 73.58 - 86.00: 76 86.00 - 98.43: 6 98.43 - 110.86: 24218 110.86 - 123.28: 65627 123.28 - 135.71: 2555 Bond angle restraints: 92482 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 107.74 123.68 -15.94 1.95e+00 2.62e-01 6.65e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.87 -14.03 1.91e+00 2.73e-01 5.36e+01 angle pdb=" C11 CDL N 201 " pdb=" CA5 CDL N 201 " pdb=" OA6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.58 -9.25 1.32e+00 5.72e-01 4.90e+01 angle pdb=" O1X NDP J 401 " pdb=" P2B NDP J 401 " pdb=" O3X NDP J 401 " ideal model delta sigma weight residual 117.46 109.48 7.98 1.17e+00 7.36e-01 4.68e+01 angle pdb=" C11 CDL r 503 " pdb=" CA5 CDL r 503 " pdb=" OA6 CDL r 503 " ideal model delta sigma weight residual 111.33 120.36 -9.03 1.32e+00 5.72e-01 4.67e+01 ... (remaining 92477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 39695 35.72 - 71.44: 1633 71.44 - 107.17: 94 107.17 - 142.89: 26 142.89 - 178.61: 12 Dihedral angle restraints: 41460 sinusoidal: 17660 harmonic: 23800 Sorted by residual: dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual 257.59 78.98 178.61 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 105.79 -165.78 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -137.04 51.04 1 1.00e+01 1.00e-02 3.56e+01 ... (remaining 41457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 9176 0.075 - 0.150: 849 0.150 - 0.224: 24 0.224 - 0.299: 6 0.299 - 0.374: 3 Chirality restraints: 10058 Sorted by residual: 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=" CB ILE w 214 " pdb=" CA ILE w 214 " pdb=" CG1 ILE w 214 " pdb=" CG2 ILE w 214 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 10055 not shown) Planarity restraints: 11585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " 0.358 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" C11 UQ s 402 " 0.212 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " 0.579 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " -0.713 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.435 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " 0.046 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C3N NDP J 401 " 0.399 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.080 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.229 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.114 2.00e-02 2.50e+03 2.04e-01 4.15e+02 pdb=" C2N NDP J 401 " 0.119 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.120 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.353 2.00e-02 2.50e+03 ... (remaining 11582 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5370 2.74 - 3.28: 66486 3.28 - 3.82: 114688 3.82 - 4.36: 141835 4.36 - 4.90: 237768 Nonbonded interactions: 566147 Sorted by model distance: nonbonded pdb=" OG1 THR G 75 " pdb=" OE1 GLU G 156 " model vdw 2.200 2.440 nonbonded pdb=" O ASP A 50 " pdb=" NH2 ARG A 59 " model vdw 2.201 2.520 nonbonded pdb=" OG SER M 650 " pdb=" OD1 ASN M 652 " model vdw 2.202 2.440 nonbonded pdb=" O ASP T 46 " pdb=" NH1 ARG T 52 " model vdw 2.204 2.520 nonbonded pdb=" O PHE s 293 " pdb=" OG1 THR s 297 " model vdw 2.206 2.440 ... (remaining 566142 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 through 96 or (resid 97 through 99 and (na \ me N or name CA or name C or name O or name CB )) or resid 100 through 101 or (r \ esid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 t \ hrough 156 or resid 201)) selection = (chain 'X' and (resid 69 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 128 or (resid 129 and (name N o \ r name CA or name C or name O or name CB )) or resid 130 through 131 or (resid 1 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 133 or (res \ id 134 through 136 and (name N or name CA or name C or name O or name CB )) or r \ esid 137 through 149 or (resid 150 through 153 and (name N or name 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.63 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: 1.710 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: 0.080 Extract box with map and model: 8.880 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 151.360 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:15.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.314 68321 Z= 0.429 Angle : 0.770 16.997 92482 Z= 0.387 Chirality : 0.043 0.374 10058 Planarity : 0.008 0.491 11585 Dihedral : 18.232 178.609 26091 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 1.48 % Allowed : 16.63 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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 (0.10), residues: 8065 helix: 1.65 (0.08), residues: 4270 sheet: 0.23 (0.25), residues: 422 loop : -0.36 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 100 HIS 0.007 0.001 HIS v 4 PHE 0.029 0.001 PHE i 292 TYR 0.038 0.001 TYR e 128 ARG 0.016 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1078 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.9457 (ttt) cc_final: 0.9148 (ttt) REVERT: C 188 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7684 (ptpt) REVERT: F 64 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7694 (mptp) REVERT: V 88 LEU cc_start: 0.8920 (tt) cc_final: 0.8631 (tp) REVERT: g 84 MET cc_start: 0.9258 (mmm) cc_final: 0.9046 (mmm) REVERT: k 21 MET cc_start: 0.6677 (tmt) cc_final: 0.6007 (mmt) REVERT: n 30 ARG cc_start: 0.7806 (ttt90) cc_final: 0.7247 (ttp-170) REVERT: o 85 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8633 (tptt) REVERT: o 112 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8266 (ttmt) REVERT: p 57 MET cc_start: 0.5975 (tpp) cc_final: 0.4842 (mtm) REVERT: w 251 GLU cc_start: 0.8041 (pp20) cc_final: 0.7673 (pm20) REVERT: w 300 ASN cc_start: 0.7668 (t0) cc_final: 0.7463 (t0) outliers start: 104 outliers final: 71 residues processed: 1157 average time/residue: 1.4959 time to fit residues: 2245.3669 Evaluate side-chains 1106 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1032 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 182 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 455 LYS Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 80 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 175 ARG Chi-restraints excluded: chain w residue 250 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 673 optimal weight: 0.8980 chunk 604 optimal weight: 0.9990 chunk 335 optimal weight: 0.0870 chunk 206 optimal weight: 0.6980 chunk 407 optimal weight: 10.0000 chunk 322 optimal weight: 0.0980 chunk 624 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 379 optimal weight: 3.9990 chunk 464 optimal weight: 7.9990 chunk 723 optimal weight: 6.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN M 464 GLN M 482 GLN N 116 ASN P 236 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN U 52 ASN U 74 GLN V 129 GLN c 127 ASN d 134 GLN l 23 ASN l 518 GLN ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 73 GLN u 104 GLN v 4 HIS w 127 ASN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 68321 Z= 0.147 Angle : 0.521 10.517 92482 Z= 0.259 Chirality : 0.040 0.172 10058 Planarity : 0.004 0.073 11585 Dihedral : 13.997 177.949 10280 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 2.76 % Allowed : 15.79 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 1.29 (0.10), residues: 8065 helix: 1.81 (0.08), residues: 4276 sheet: 0.31 (0.25), residues: 421 loop : -0.27 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.006 0.001 HIS J 37 PHE 0.029 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.007 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1112 time to evaluate : 5.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7630 (tmmm) REVERT: A 269 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7897 (mtp180) REVERT: C 133 MET cc_start: 0.9492 (ttt) cc_final: 0.9173 (ttt) REVERT: E 68 MET cc_start: 0.8704 (mmp) cc_final: 0.8377 (mmp) REVERT: F 62 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: G 117 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: H 94 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7656 (mmm) REVERT: I 33 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7224 (mppt) REVERT: J 298 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6293 (t80) REVERT: M 94 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8724 (tpp) REVERT: M 555 ILE cc_start: 0.8678 (mm) cc_final: 0.8455 (tt) REVERT: M 558 GLN cc_start: 0.7888 (mp10) cc_final: 0.7497 (mm110) REVERT: P 138 ASN cc_start: 0.9153 (t0) cc_final: 0.8884 (t0) REVERT: T 81 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7745 (p) REVERT: V 88 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8609 (tp) REVERT: X 77 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: X 120 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (mmm) REVERT: Y 74 TRP cc_start: 0.8964 (t-100) cc_final: 0.8584 (t-100) REVERT: Z 19 TYR cc_start: 0.8123 (p90) cc_final: 0.7820 (p90) REVERT: Z 35 LYS cc_start: 0.8569 (mttp) cc_final: 0.8289 (mttp) REVERT: Z 49 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: h 53 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: i 68 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9155 (tpt) REVERT: i 334 THR cc_start: 0.9082 (m) cc_final: 0.8587 (p) REVERT: l 60 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8039 (mt-10) REVERT: l 341 MET cc_start: 0.8286 (mtp) cc_final: 0.8072 (mtt) REVERT: l 495 ILE cc_start: 0.8754 (pp) cc_final: 0.8406 (mp) REVERT: m 57 PHE cc_start: 0.8577 (t80) cc_final: 0.8323 (t80) REVERT: n 30 ARG cc_start: 0.7818 (ttt90) cc_final: 0.7271 (ttp-170) REVERT: o 112 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8221 (ttmt) REVERT: r 114 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: r 344 LEU cc_start: 0.8770 (tp) cc_final: 0.8555 (tt) REVERT: s 134 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8284 (mtt180) REVERT: v 22 MET cc_start: 0.8744 (ttm) cc_final: 0.8417 (ttm) outliers start: 194 outliers final: 62 residues processed: 1211 average time/residue: 1.4757 time to fit residues: 2331.4069 Evaluate side-chains 1117 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1041 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 640 ASP Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 68 MET Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 311 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 402 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 602 optimal weight: 5.9990 chunk 492 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 725 optimal weight: 2.9990 chunk 783 optimal weight: 10.0000 chunk 645 optimal weight: 1.9990 chunk 719 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 581 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN F 25 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN K 90 ASN M 464 GLN M 569 GLN M 669 ASN N 52 ASN O 41 HIS U 74 GLN V 129 GLN X 142 GLN a 90 ASN c 127 ASN c 160 GLN d 134 GLN l 23 ASN l 518 GLN l 534 HIS ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 104 GLN w 142 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 68321 Z= 0.402 Angle : 0.659 12.289 92482 Z= 0.331 Chirality : 0.047 0.210 10058 Planarity : 0.006 0.068 11585 Dihedral : 13.277 179.900 10169 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 3.86 % Allowed : 15.94 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 0.84 (0.09), residues: 8065 helix: 1.43 (0.08), residues: 4280 sheet: 0.25 (0.25), residues: 407 loop : -0.49 (0.11), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP u 86 HIS 0.020 0.002 HIS l 534 PHE 0.031 0.002 PHE l 335 TYR 0.021 0.002 TYR Q 308 ARG 0.007 0.001 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1056 time to evaluate : 5.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7808 (tmmm) REVERT: B 59 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: E 68 MET cc_start: 0.8699 (mmp) cc_final: 0.8345 (mmp) REVERT: F 62 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: G 117 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: I 73 GLN cc_start: 0.7720 (mt0) cc_final: 0.7384 (pp30) REVERT: J 298 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6308 (t80) REVERT: J 324 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7562 (ttm) REVERT: K 109 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7652 (ttp-110) REVERT: M 94 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8613 (tpp) REVERT: M 158 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8122 (ptt90) REVERT: M 555 ILE cc_start: 0.8732 (mm) cc_final: 0.8519 (tt) REVERT: M 558 GLN cc_start: 0.7846 (mp10) cc_final: 0.7497 (mm110) REVERT: N 68 MET cc_start: 0.7895 (ttt) cc_final: 0.7502 (mtp) REVERT: N 136 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: Q 100 GLU cc_start: 0.8041 (pt0) cc_final: 0.7826 (pt0) REVERT: Q 108 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8712 (tttm) REVERT: T 82 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7861 (ttt180) REVERT: U 31 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8567 (mp) REVERT: X 77 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: X 120 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8411 (mmm) REVERT: Y 74 TRP cc_start: 0.8973 (t-100) cc_final: 0.8632 (t-100) REVERT: Z 19 TYR cc_start: 0.8308 (p90) cc_final: 0.8054 (p90) REVERT: Z 34 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: Z 49 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: f 68 GLU cc_start: 0.8955 (tp30) cc_final: 0.8647 (tp30) REVERT: g 14 GLN cc_start: 0.8535 (tt0) cc_final: 0.8089 (tp-100) REVERT: h 53 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: i 334 THR cc_start: 0.9306 (m) cc_final: 0.8900 (p) REVERT: k 8 ILE cc_start: 0.8750 (mm) cc_final: 0.8546 (mt) REVERT: l 267 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8838 (mmt) REVERT: l 486 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8507 (ttm) REVERT: l 495 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8272 (mp) REVERT: m 135 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: o 114 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7965 (mtpm) REVERT: p 9 TYR cc_start: 0.8434 (p90) cc_final: 0.8185 (p90) REVERT: r 103 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8902 (tt0) REVERT: r 114 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: r 294 MET cc_start: 0.9425 (mmp) cc_final: 0.9211 (mmp) REVERT: s 24 GLU cc_start: 0.9105 (tt0) cc_final: 0.8898 (tt0) outliers start: 272 outliers final: 122 residues processed: 1205 average time/residue: 1.4869 time to fit residues: 2330.4289 Evaluate side-chains 1161 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1015 time to evaluate : 5.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 400 ILE Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain M residue 701 SER Chi-restraints excluded: chain N residue 9 ARG Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 437 LYS Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 82 ARG Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain b residue 16 ARG Chi-restraints excluded: chain b residue 91 THR Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 173 THR Chi-restraints excluded: chain i residue 226 THR Chi-restraints excluded: chain i residue 268 GLN Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 495 ILE Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 716 optimal weight: 0.9980 chunk 545 optimal weight: 4.9990 chunk 376 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 chunk 727 optimal weight: 0.8980 chunk 770 optimal weight: 7.9990 chunk 380 optimal weight: 3.9990 chunk 689 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN M 51 GLN M 464 GLN M 669 ASN O 246 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 74 GLN V 129 GLN c 127 ASN d 134 GLN h 21 GLN l 23 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 518 GLN p 12 HIS r 139 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 68321 Z= 0.202 Angle : 0.548 10.724 92482 Z= 0.275 Chirality : 0.041 0.181 10058 Planarity : 0.005 0.066 11585 Dihedral : 12.491 179.126 10165 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 3.48 % Allowed : 17.20 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 8065 helix: 1.64 (0.08), residues: 4269 sheet: 0.26 (0.25), residues: 415 loop : -0.42 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 144 HIS 0.008 0.001 HIS l 534 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1059 time to evaluate : 6.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7773 (tmmm) REVERT: B 59 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: B 65 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: E 68 MET cc_start: 0.8694 (mmp) cc_final: 0.8400 (mmp) REVERT: F 62 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: G 117 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: H 38 ILE cc_start: 0.8689 (mm) cc_final: 0.8463 (mm) REVERT: H 66 LYS cc_start: 0.7439 (mtpp) cc_final: 0.7201 (mttm) REVERT: H 94 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: I 62 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8618 (mt-10) REVERT: J 298 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6092 (t80) REVERT: J 324 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7595 (ttm) REVERT: K 95 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8207 (ptmm) REVERT: M 94 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8678 (tpp) REVERT: M 158 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8004 (ptt90) REVERT: M 473 MET cc_start: 0.9174 (mtp) cc_final: 0.8966 (ttt) REVERT: M 555 ILE cc_start: 0.8781 (mm) cc_final: 0.8548 (tt) REVERT: M 558 GLN cc_start: 0.7835 (mp10) cc_final: 0.7531 (mm110) REVERT: M 640 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: N 136 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: O 202 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: Q 100 GLU cc_start: 0.8073 (pt0) cc_final: 0.7835 (pt0) REVERT: T 81 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7800 (p) REVERT: U 31 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8514 (mp) REVERT: V 16 THR cc_start: 0.4718 (p) cc_final: 0.4305 (t) REVERT: V 88 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8682 (tp) REVERT: X 77 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: X 120 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8477 (mmm) REVERT: Y 74 TRP cc_start: 0.8979 (t-100) cc_final: 0.8606 (t-100) REVERT: Z 19 TYR cc_start: 0.8267 (p90) cc_final: 0.7994 (p90) REVERT: Z 34 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: Z 49 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: a 72 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7864 (ttm110) REVERT: f 68 GLU cc_start: 0.8896 (tp30) cc_final: 0.8639 (tp30) REVERT: h 53 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: i 334 THR cc_start: 0.9313 (m) cc_final: 0.8929 (p) REVERT: l 140 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9153 (tt) REVERT: l 186 MET cc_start: 0.9503 (ttm) cc_final: 0.9247 (mtm) REVERT: l 486 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8519 (ttm) REVERT: l 495 ILE cc_start: 0.8746 (pp) cc_final: 0.8287 (mp) REVERT: m 135 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: p 9 TYR cc_start: 0.8396 (p90) cc_final: 0.8125 (p90) REVERT: p 59 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7902 (ttmm) REVERT: r 114 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: r 378 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: s 24 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: v 22 MET cc_start: 0.8589 (ttm) cc_final: 0.8333 (ttm) REVERT: w 209 VAL cc_start: 0.8960 (t) cc_final: 0.8677 (m) outliers start: 245 outliers final: 116 residues processed: 1193 average time/residue: 1.5160 time to fit residues: 2348.7758 Evaluate side-chains 1168 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1022 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 640 ASP Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain M residue 701 SER Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 35 LYS Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 173 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 223 LYS Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 365 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 641 optimal weight: 2.9990 chunk 437 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 573 optimal weight: 5.9990 chunk 317 optimal weight: 0.7980 chunk 657 optimal weight: 1.9990 chunk 532 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 393 optimal weight: 6.9990 chunk 691 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 GLN M 464 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN V 129 GLN a 90 ASN b 83 HIS c 127 ASN ** c 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 GLN i 91 ASN j 10 ASN l 23 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 136 ASN l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 104 GLN v 65 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 68321 Z= 0.219 Angle : 0.555 11.012 92482 Z= 0.278 Chirality : 0.041 0.184 10058 Planarity : 0.005 0.064 11585 Dihedral : 12.010 178.713 10160 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 3.62 % Allowed : 17.44 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 1.08 (0.09), residues: 8065 helix: 1.65 (0.08), residues: 4278 sheet: 0.25 (0.25), residues: 419 loop : -0.38 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP l 144 HIS 0.010 0.001 HIS l 534 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.014 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1057 time to evaluate : 5.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7791 (tmmm) REVERT: A 329 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7902 (mtpp) REVERT: B 59 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: B 65 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: E 68 MET cc_start: 0.8686 (mmp) cc_final: 0.8339 (mmp) REVERT: F 62 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: G 117 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: H 66 LYS cc_start: 0.7450 (mtpp) cc_final: 0.7213 (mttm) REVERT: H 94 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: I 62 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8603 (mt-10) REVERT: J 97 MET cc_start: 0.9341 (mtt) cc_final: 0.9069 (mtt) REVERT: J 298 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6122 (t80) REVERT: J 324 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7608 (ttm) REVERT: M 94 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8657 (tpp) REVERT: M 158 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8002 (ptt90) REVERT: M 361 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8060 (p) REVERT: M 555 ILE cc_start: 0.8800 (mm) cc_final: 0.8563 (tt) REVERT: M 558 GLN cc_start: 0.7827 (mp10) cc_final: 0.7527 (mm110) REVERT: N 136 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: O 202 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: Q 100 GLU cc_start: 0.8065 (pt0) cc_final: 0.7836 (pt0) REVERT: T 81 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7817 (p) REVERT: T 82 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7817 (ttt180) REVERT: U 31 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8520 (mp) REVERT: V 88 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8701 (tp) REVERT: X 77 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: X 120 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8485 (mmm) REVERT: X 151 LYS cc_start: 0.8388 (tptt) cc_final: 0.7931 (tttm) REVERT: Y 74 TRP cc_start: 0.8983 (t-100) cc_final: 0.8588 (t-100) REVERT: Z 34 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: Z 49 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: a 72 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7867 (ttm110) REVERT: c 165 ASP cc_start: 0.8185 (t0) cc_final: 0.7933 (t0) REVERT: d 83 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8587 (mt) REVERT: f 68 GLU cc_start: 0.8892 (tp30) cc_final: 0.8600 (tp30) REVERT: h 53 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: i 334 THR cc_start: 0.9328 (m) cc_final: 0.8976 (p) REVERT: l 140 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9161 (tt) REVERT: l 150 MET cc_start: 0.9324 (mmm) cc_final: 0.9044 (mmm) REVERT: l 486 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8518 (ttm) REVERT: l 495 ILE cc_start: 0.8752 (pp) cc_final: 0.8374 (mp) REVERT: m 135 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: o 114 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7918 (mtpm) REVERT: p 9 TYR cc_start: 0.8413 (p90) cc_final: 0.8160 (p90) REVERT: p 59 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8004 (tppt) REVERT: r 114 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: s 24 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: v 22 MET cc_start: 0.8586 (ttm) cc_final: 0.8291 (ttm) REVERT: v 53 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8219 (mp) REVERT: w 209 VAL cc_start: 0.8956 (t) cc_final: 0.8698 (m) REVERT: w 297 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8462 (tm) outliers start: 255 outliers final: 131 residues processed: 1208 average time/residue: 1.4782 time to fit residues: 2329.7973 Evaluate side-chains 1185 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1020 time to evaluate : 5.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 82 ARG Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain e residue 136 LEU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 173 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 365 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 259 optimal weight: 0.9980 chunk 693 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 452 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 771 optimal weight: 0.0980 chunk 640 optimal weight: 4.9990 chunk 357 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 255 optimal weight: 0.0970 chunk 404 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN F 25 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 669 ASN O 246 GLN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 74 GLN V 129 GLN c 127 ASN ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 GLN d 149 HIS h 21 GLN j 10 ASN l 23 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN r 251 ASN r 304 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 68321 Z= 0.193 Angle : 0.542 10.735 92482 Z= 0.271 Chirality : 0.041 0.179 10058 Planarity : 0.004 0.064 11585 Dihedral : 11.652 178.802 10160 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 3.51 % Allowed : 17.98 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 1.12 (0.10), residues: 8065 helix: 1.69 (0.08), residues: 4284 sheet: 0.19 (0.25), residues: 431 loop : -0.37 (0.11), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS l 534 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.006 0.000 ARG M 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1053 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7785 (tmmm) REVERT: A 329 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (mtpp) REVERT: B 59 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: B 65 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: C 191 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7328 (ttm110) REVERT: E 68 MET cc_start: 0.8700 (mmp) cc_final: 0.8385 (mmp) REVERT: F 62 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7138 (mt0) REVERT: F 75 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7867 (mptt) REVERT: G 117 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: H 38 ILE cc_start: 0.8659 (mm) cc_final: 0.8392 (mm) REVERT: H 66 LYS cc_start: 0.7450 (mtpp) cc_final: 0.7212 (mttm) REVERT: H 94 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: J 298 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5996 (t80) REVERT: K 109 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7661 (ttp-110) REVERT: M 94 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8670 (tpp) REVERT: M 158 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7979 (ptt90) REVERT: M 361 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7972 (p) REVERT: M 555 ILE cc_start: 0.8790 (mm) cc_final: 0.8562 (tt) REVERT: M 558 GLN cc_start: 0.7856 (mp10) cc_final: 0.7537 (mm110) REVERT: N 136 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: O 202 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: Q 100 GLU cc_start: 0.8068 (pt0) cc_final: 0.7811 (pt0) REVERT: T 81 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7789 (p) REVERT: T 82 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7811 (ttt180) REVERT: U 31 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8495 (mp) REVERT: V 88 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8700 (tp) REVERT: X 77 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: X 120 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8483 (mmm) REVERT: X 151 LYS cc_start: 0.8402 (tptt) cc_final: 0.7938 (tttm) REVERT: Y 74 TRP cc_start: 0.8984 (t-100) cc_final: 0.8614 (t-100) REVERT: Z 34 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: Z 49 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: a 72 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7846 (ttm110) REVERT: c 165 ASP cc_start: 0.8165 (t0) cc_final: 0.7925 (t0) REVERT: d 83 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8568 (mt) REVERT: h 53 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: i 334 THR cc_start: 0.9347 (m) cc_final: 0.8950 (p) REVERT: l 140 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9138 (tt) REVERT: l 150 MET cc_start: 0.9296 (mmm) cc_final: 0.9037 (mmm) REVERT: l 486 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8458 (ttm) REVERT: l 495 ILE cc_start: 0.8685 (pp) cc_final: 0.8331 (mp) REVERT: m 135 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: p 9 TYR cc_start: 0.8408 (p90) cc_final: 0.8160 (p90) REVERT: p 59 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7997 (tppt) REVERT: r 114 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: r 378 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8770 (tt0) REVERT: s 24 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: s 270 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.7674 (t80) REVERT: v 22 MET cc_start: 0.8601 (ttm) cc_final: 0.8318 (ttm) REVERT: w 209 VAL cc_start: 0.8965 (t) cc_final: 0.8714 (m) REVERT: w 223 ASN cc_start: 0.8309 (t0) cc_final: 0.7983 (t0) outliers start: 247 outliers final: 134 residues processed: 1191 average time/residue: 1.5116 time to fit residues: 2344.0091 Evaluate side-chains 1187 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1020 time to evaluate : 5.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 82 ARG Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 35 LYS Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain h residue 47 ILE Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 173 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 365 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 743 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 563 optimal weight: 2.9990 chunk 436 optimal weight: 8.9990 chunk 649 optimal weight: 5.9990 chunk 430 optimal weight: 2.9990 chunk 768 optimal weight: 10.0000 chunk 480 optimal weight: 1.9990 chunk 468 optimal weight: 10.0000 chunk 354 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN F 25 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 669 ASN U 11 ASN U 74 GLN V 129 GLN c 127 ASN c 160 GLN d 134 GLN h 21 GLN j 10 ASN l 23 ASN l 59 GLN l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 104 GLN w 300 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 68321 Z= 0.356 Angle : 0.630 12.221 92482 Z= 0.315 Chirality : 0.045 0.217 10058 Planarity : 0.005 0.064 11585 Dihedral : 11.872 179.378 10160 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.66 % Rotamer: Outliers : 3.79 % Allowed : 17.84 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 0.83 (0.09), residues: 8065 helix: 1.44 (0.08), residues: 4277 sheet: 0.16 (0.25), residues: 421 loop : -0.52 (0.11), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u 86 HIS 0.011 0.001 HIS l 534 PHE 0.030 0.002 PHE i 292 TYR 0.029 0.002 TYR Z 19 ARG 0.006 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1041 time to evaluate : 5.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7819 (tmmm) REVERT: A 451 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7168 (mm-40) REVERT: B 59 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: B 65 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: E 68 MET cc_start: 0.8649 (mmp) cc_final: 0.8378 (mmp) REVERT: F 25 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: G 117 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: H 66 LYS cc_start: 0.7433 (mtpp) cc_final: 0.7192 (mttm) REVERT: I 73 GLN cc_start: 0.7585 (mt0) cc_final: 0.7276 (pp30) REVERT: J 298 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6084 (t80) REVERT: J 299 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6658 (mmm160) REVERT: K 109 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7637 (ttp-110) REVERT: L 70 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: M 94 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8623 (tpp) REVERT: M 158 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8119 (ptt90) REVERT: M 555 ILE cc_start: 0.8806 (mm) cc_final: 0.8578 (tt) REVERT: M 558 GLN cc_start: 0.7867 (mp10) cc_final: 0.7561 (mm110) REVERT: N 68 MET cc_start: 0.7940 (ttt) cc_final: 0.7505 (mtp) REVERT: N 136 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: O 202 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: Q 100 GLU cc_start: 0.8045 (pt0) cc_final: 0.7775 (pt0) REVERT: Q 258 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9021 (tp) REVERT: T 82 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7878 (ttt180) REVERT: U 31 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8599 (mp) REVERT: V 16 THR cc_start: 0.4922 (OUTLIER) cc_final: 0.4436 (m) REVERT: X 77 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: X 120 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8431 (mmm) REVERT: X 151 LYS cc_start: 0.8394 (tptt) cc_final: 0.7935 (tttm) REVERT: Y 74 TRP cc_start: 0.8929 (t-100) cc_final: 0.8584 (t-100) REVERT: Z 34 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: Z 49 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: b 108 ASP cc_start: 0.7954 (m-30) cc_final: 0.7467 (m-30) REVERT: b 120 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7360 (mmt) REVERT: d 83 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8588 (mt) REVERT: h 53 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: i 334 THR cc_start: 0.9340 (m) cc_final: 0.8994 (p) REVERT: k 21 MET cc_start: 0.6691 (tmm) cc_final: 0.5816 (mmt) REVERT: l 140 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9268 (tt) REVERT: l 150 MET cc_start: 0.9294 (mmm) cc_final: 0.9008 (mmm) REVERT: l 186 MET cc_start: 0.9493 (ttm) cc_final: 0.9235 (mtm) REVERT: l 267 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8817 (mmt) REVERT: l 486 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8582 (ttm) REVERT: l 495 ILE cc_start: 0.8693 (pp) cc_final: 0.8379 (mp) REVERT: m 135 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: o 114 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7962 (mtpm) REVERT: p 9 TYR cc_start: 0.8425 (p90) cc_final: 0.8224 (p90) REVERT: p 59 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7939 (tppt) REVERT: p 144 THR cc_start: 0.7791 (t) cc_final: 0.7411 (m) REVERT: r 103 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8859 (tt0) REVERT: r 114 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: r 427 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8060 (mmtm) REVERT: v 22 MET cc_start: 0.8631 (ttm) cc_final: 0.8389 (ttm) REVERT: v 39 MET cc_start: 0.8311 (tpt) cc_final: 0.8080 (tpt) REVERT: v 105 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: w 51 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7101 (ptp-170) REVERT: w 209 VAL cc_start: 0.9003 (t) cc_final: 0.8752 (m) REVERT: w 223 ASN cc_start: 0.8352 (t0) cc_final: 0.7998 (t0) REVERT: w 251 GLU cc_start: 0.8003 (pp20) cc_final: 0.7749 (pm20) outliers start: 267 outliers final: 154 residues processed: 1196 average time/residue: 1.5131 time to fit residues: 2365.7952 Evaluate side-chains 1201 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1013 time to evaluate : 5.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 82 ARG Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 173 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 281 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 248 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 365 THR Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain r residue 427 LYS Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 475 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 458 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 488 optimal weight: 4.9990 chunk 523 optimal weight: 3.9990 chunk 379 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 603 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 669 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 74 GLN V 129 GLN a 90 ASN c 127 ASN c 160 GLN d 134 GLN i 186 HIS j 10 ASN l 23 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN v 43 GLN w 300 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 68321 Z= 0.221 Angle : 0.570 11.097 92482 Z= 0.285 Chirality : 0.042 0.193 10058 Planarity : 0.005 0.067 11585 Dihedral : 11.597 178.899 10160 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 3.34 % Allowed : 18.59 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.09), residues: 8065 helix: 1.57 (0.08), residues: 4274 sheet: 0.10 (0.25), residues: 431 loop : -0.46 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.007 0.001 HIS l 534 PHE 0.029 0.001 PHE i 292 TYR 0.028 0.001 TYR Z 19 ARG 0.006 0.000 ARG M 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1031 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7801 (tmmm) REVERT: A 451 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7138 (mm-40) REVERT: B 59 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: B 65 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: E 68 MET cc_start: 0.8668 (mmp) cc_final: 0.8400 (mmp) REVERT: F 73 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7948 (mm-40) REVERT: F 75 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7861 (mptt) REVERT: G 117 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: H 66 LYS cc_start: 0.7417 (mtpp) cc_final: 0.7173 (mttm) REVERT: H 94 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7824 (mmm) REVERT: I 73 GLN cc_start: 0.7579 (mt0) cc_final: 0.7271 (pp30) REVERT: J 298 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6032 (t80) REVERT: J 299 ARG cc_start: 0.6853 (mtp85) cc_final: 0.5896 (tmt90) REVERT: K 109 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7710 (ttp-110) REVERT: M 94 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8674 (tpp) REVERT: M 158 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8730 (ttp-170) REVERT: M 361 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8051 (p) REVERT: M 555 ILE cc_start: 0.8799 (mm) cc_final: 0.8594 (tt) REVERT: M 558 GLN cc_start: 0.7849 (mp10) cc_final: 0.7554 (mm110) REVERT: N 68 MET cc_start: 0.7810 (ttt) cc_final: 0.7474 (mtp) REVERT: N 136 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: O 202 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: Q 100 GLU cc_start: 0.8036 (pt0) cc_final: 0.7774 (pt0) REVERT: Q 258 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8984 (tp) REVERT: T 81 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7841 (p) REVERT: T 82 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7803 (ttt180) REVERT: U 31 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8518 (mp) REVERT: V 16 THR cc_start: 0.4855 (OUTLIER) cc_final: 0.4402 (m) REVERT: X 77 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: X 120 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: X 151 LYS cc_start: 0.8384 (tptt) cc_final: 0.7930 (tttm) REVERT: Y 74 TRP cc_start: 0.8915 (t-100) cc_final: 0.8573 (t-100) REVERT: Z 34 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: Z 49 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: a 72 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7854 (ttm110) REVERT: b 120 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7378 (mmt) REVERT: d 83 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8613 (mt) REVERT: f 63 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8241 (tttp) REVERT: h 53 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: h 88 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7397 (mmtm) REVERT: i 268 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8674 (tm-30) REVERT: i 278 MET cc_start: 0.8521 (mtp) cc_final: 0.8269 (ttm) REVERT: i 334 THR cc_start: 0.9324 (m) cc_final: 0.8928 (p) REVERT: k 21 MET cc_start: 0.6769 (tmm) cc_final: 0.5794 (mmt) REVERT: l 140 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9158 (tt) REVERT: l 149 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9003 (tp) REVERT: l 150 MET cc_start: 0.9276 (mmm) cc_final: 0.9040 (mmm) REVERT: l 186 MET cc_start: 0.9501 (ttm) cc_final: 0.9246 (mtm) REVERT: l 267 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8795 (mmt) REVERT: l 495 ILE cc_start: 0.8657 (pp) cc_final: 0.8352 (mp) REVERT: m 135 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: o 114 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7939 (mtpm) REVERT: p 59 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7956 (tppt) REVERT: p 151 THR cc_start: 0.8445 (m) cc_final: 0.8236 (t) REVERT: r 103 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8855 (tt0) REVERT: r 114 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: v 22 MET cc_start: 0.8649 (ttm) cc_final: 0.8383 (ttm) REVERT: v 101 GLU cc_start: 0.7698 (tp30) cc_final: 0.7285 (mm-30) REVERT: v 105 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: w 51 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7076 (ptp-170) REVERT: w 209 VAL cc_start: 0.9006 (t) cc_final: 0.8762 (m) REVERT: w 223 ASN cc_start: 0.8283 (t0) cc_final: 0.7925 (t0) outliers start: 235 outliers final: 152 residues processed: 1173 average time/residue: 1.4970 time to fit residues: 2291.3544 Evaluate side-chains 1190 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1001 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain J residue 311 GLU Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 515 ILE Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 671 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 83 ASN Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 446 ASP Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 82 ARG Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Y residue 97 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 97 MET Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 173 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 223 LYS Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 169 MET Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 367 LEU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 310 MET Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain v residue 43 GLN Chi-restraints excluded: chain v residue 90 CYS Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 44 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 51 ARG Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 698 optimal weight: 0.0170 chunk 735 optimal weight: 0.9980 chunk 671 optimal weight: 1.9990 chunk 715 optimal weight: 0.0970 chunk 430 optimal weight: 2.9990 chunk 311 optimal weight: 0.9980 chunk 562 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 646 optimal weight: 5.9990 chunk 677 optimal weight: 6.9990 chunk 713 optimal weight: 0.6980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN F 25 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN M 464 GLN M 669 ASN O 69 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 74 GLN V 129 GLN ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN c 127 ASN ** c 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 GLN j 10 ASN l 23 ASN l 59 GLN l 446 ASN l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN s 171 HIS ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 300 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 68321 Z= 0.148 Angle : 0.531 10.817 92482 Z= 0.264 Chirality : 0.040 0.373 10058 Planarity : 0.004 0.072 11585 Dihedral : 11.032 179.609 10160 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 19.77 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.10), residues: 8065 helix: 1.78 (0.08), residues: 4261 sheet: 0.21 (0.25), residues: 429 loop : -0.31 (0.11), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP l 144 HIS 0.006 0.001 HIS l 534 PHE 0.030 0.001 PHE i 292 TYR 0.027 0.001 TYR Z 19 ARG 0.008 0.000 ARG J 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1100 time to evaluate : 6.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7929 (mtp180) REVERT: B 120 GLU cc_start: 0.8967 (tt0) cc_final: 0.8760 (tt0) REVERT: C 65 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8467 (ppp) REVERT: E 68 MET cc_start: 0.8671 (mmp) cc_final: 0.8404 (mmp) REVERT: G 94 ASP cc_start: 0.4871 (p0) cc_final: 0.4115 (p0) REVERT: G 105 MET cc_start: 0.6380 (mmp) cc_final: 0.5819 (mmt) REVERT: G 117 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: H 38 ILE cc_start: 0.8558 (mm) cc_final: 0.8320 (mm) REVERT: H 66 LYS cc_start: 0.7444 (mtpp) cc_final: 0.7196 (mttm) REVERT: H 94 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7685 (mmm) REVERT: J 97 MET cc_start: 0.9321 (mtt) cc_final: 0.9087 (mtt) REVERT: J 154 GLN cc_start: 0.8190 (tt0) cc_final: 0.7958 (tm-30) REVERT: J 298 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6290 (t80) REVERT: J 320 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6684 (tp30) REVERT: K 94 SER cc_start: 0.8689 (p) cc_final: 0.8264 (p) REVERT: M 94 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8731 (tpp) REVERT: M 360 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.7407 (mpt-90) REVERT: M 555 ILE cc_start: 0.8737 (mm) cc_final: 0.8534 (tt) REVERT: M 558 GLN cc_start: 0.7835 (mp10) cc_final: 0.7536 (mm110) REVERT: N 116 ASN cc_start: 0.8229 (t0) cc_final: 0.7899 (t0) REVERT: O 202 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: Q 100 GLU cc_start: 0.8012 (pt0) cc_final: 0.7758 (pt0) REVERT: Q 258 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8945 (tp) REVERT: T 81 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7761 (p) REVERT: U 82 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8661 (mtpm) REVERT: V 88 LEU cc_start: 0.8912 (tt) cc_final: 0.8639 (tp) REVERT: V 105 THR cc_start: 0.7034 (m) cc_final: 0.6689 (p) REVERT: W 86 MET cc_start: 0.8531 (mtp) cc_final: 0.8161 (ttm) REVERT: X 77 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: X 120 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8477 (mmt) REVERT: X 151 LYS cc_start: 0.8365 (tptt) cc_final: 0.7885 (tttm) REVERT: Y 74 TRP cc_start: 0.8904 (t-100) cc_final: 0.8572 (t-100) REVERT: Z 34 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: Z 35 LYS cc_start: 0.8609 (mttp) cc_final: 0.8342 (mtpt) REVERT: Z 49 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: a 72 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7819 (ttm110) REVERT: b 108 ASP cc_start: 0.7809 (m-30) cc_final: 0.7489 (m-30) REVERT: b 120 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7502 (mmt) REVERT: d 83 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8525 (mt) REVERT: f 63 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8227 (tttp) REVERT: h 53 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: h 88 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7438 (mmtm) REVERT: i 268 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8634 (tm-30) REVERT: i 278 MET cc_start: 0.8283 (mtp) cc_final: 0.8044 (ttm) REVERT: i 323 MET cc_start: 0.8152 (mtm) cc_final: 0.7951 (mpt) REVERT: i 334 THR cc_start: 0.9279 (m) cc_final: 0.8827 (p) REVERT: k 21 MET cc_start: 0.6707 (tmm) cc_final: 0.5643 (mmt) REVERT: l 140 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9109 (tt) REVERT: l 486 MET cc_start: 0.8424 (ttm) cc_final: 0.8159 (ttm) REVERT: l 495 ILE cc_start: 0.8669 (pp) cc_final: 0.8400 (mp) REVERT: n 10 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7301 (t70) REVERT: p 57 MET cc_start: 0.6530 (mmm) cc_final: 0.5148 (mtm) REVERT: p 59 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7831 (ttmm) REVERT: r 114 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: s 270 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.7679 (t80) REVERT: v 101 GLU cc_start: 0.7513 (tp30) cc_final: 0.7191 (mm-30) REVERT: w 209 VAL cc_start: 0.9004 (t) cc_final: 0.8756 (m) REVERT: w 223 ASN cc_start: 0.8295 (t0) cc_final: 0.7925 (t0) outliers start: 156 outliers final: 85 residues processed: 1190 average time/residue: 1.5078 time to fit residues: 2345.8776 Evaluate side-chains 1152 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1044 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 115 GLN Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain s residue 143 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 470 optimal weight: 0.9980 chunk 756 optimal weight: 8.9990 chunk 462 optimal weight: 8.9990 chunk 359 optimal weight: 0.8980 chunk 526 optimal weight: 0.9990 chunk 794 optimal weight: 2.9990 chunk 730 optimal weight: 4.9990 chunk 632 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 488 optimal weight: 6.9990 chunk 387 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 464 GLN M 569 GLN M 669 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 74 GLN V 129 GLN ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 ASN ** c 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 GLN l 23 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 104 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 68321 Z= 0.192 Angle : 0.557 11.298 92482 Z= 0.276 Chirality : 0.041 0.211 10058 Planarity : 0.005 0.061 11585 Dihedral : 10.949 179.829 10158 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.96 % Allowed : 20.39 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 8065 helix: 1.74 (0.08), residues: 4286 sheet: 0.20 (0.25), residues: 431 loop : -0.29 (0.11), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS l 534 PHE 0.030 0.001 PHE i 292 TYR 0.028 0.001 TYR Z 19 ARG 0.014 0.000 ARG p 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1036 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8447 (ppp) REVERT: E 68 MET cc_start: 0.8637 (mmp) cc_final: 0.8409 (mmp) REVERT: G 94 ASP cc_start: 0.4834 (p0) cc_final: 0.4087 (p0) REVERT: G 105 MET cc_start: 0.6401 (mmp) cc_final: 0.5842 (mmt) REVERT: G 117 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: H 38 ILE cc_start: 0.8606 (mm) cc_final: 0.8332 (mm) REVERT: H 66 LYS cc_start: 0.7450 (mtpp) cc_final: 0.7203 (mttm) REVERT: H 94 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7807 (mmm) REVERT: I 73 GLN cc_start: 0.7539 (mt0) cc_final: 0.7232 (pp30) REVERT: J 298 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6154 (t80) REVERT: K 94 SER cc_start: 0.8714 (p) cc_final: 0.8289 (p) REVERT: M 94 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8702 (tpp) REVERT: M 360 ARG cc_start: 0.7751 (mpt-90) cc_final: 0.7433 (mpt-90) REVERT: M 555 ILE cc_start: 0.8737 (mm) cc_final: 0.8535 (tt) REVERT: M 558 GLN cc_start: 0.7830 (mp10) cc_final: 0.7544 (mm110) REVERT: Q 100 GLU cc_start: 0.8021 (pt0) cc_final: 0.7716 (pt0) REVERT: Q 258 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8959 (tp) REVERT: T 81 SER cc_start: 0.8097 (m) cc_final: 0.7770 (p) REVERT: V 16 THR cc_start: 0.4955 (OUTLIER) cc_final: 0.4606 (m) REVERT: V 88 LEU cc_start: 0.8926 (tt) cc_final: 0.8649 (tp) REVERT: V 105 THR cc_start: 0.7034 (m) cc_final: 0.6694 (p) REVERT: W 86 MET cc_start: 0.8547 (mtp) cc_final: 0.8327 (mtm) REVERT: X 77 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: X 120 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8484 (mmm) REVERT: X 151 LYS cc_start: 0.8359 (tptt) cc_final: 0.7904 (tttm) REVERT: Y 74 TRP cc_start: 0.8908 (t-100) cc_final: 0.8568 (t-100) REVERT: Z 34 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: Z 49 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: a 72 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7823 (ttm110) REVERT: b 108 ASP cc_start: 0.7827 (m-30) cc_final: 0.7502 (m-30) REVERT: b 120 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7512 (mmt) REVERT: d 83 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (mt) REVERT: f 63 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8221 (tttp) REVERT: h 88 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7421 (mmtm) REVERT: i 268 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8654 (tm-30) REVERT: i 278 MET cc_start: 0.8351 (mtp) cc_final: 0.8094 (ttm) REVERT: i 323 MET cc_start: 0.8182 (mtm) cc_final: 0.7919 (mpt) REVERT: i 334 THR cc_start: 0.9290 (m) cc_final: 0.8825 (p) REVERT: k 1 MET cc_start: 0.7149 (ttt) cc_final: 0.6828 (ttp) REVERT: k 21 MET cc_start: 0.6693 (tmm) cc_final: 0.5660 (mmt) REVERT: l 140 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9115 (tt) REVERT: l 486 MET cc_start: 0.8448 (ttm) cc_final: 0.8185 (ttm) REVERT: n 10 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7257 (t70) REVERT: n 58 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7734 (mttp) REVERT: o 114 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7904 (mtpm) REVERT: p 57 MET cc_start: 0.6442 (mmm) cc_final: 0.5061 (mtm) REVERT: r 114 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8459 (tm-30) REVERT: s 270 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7707 (t80) REVERT: v 21 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7369 (mtm-85) REVERT: v 101 GLU cc_start: 0.7584 (tp30) cc_final: 0.7227 (mm-30) REVERT: w 209 VAL cc_start: 0.9017 (t) cc_final: 0.8745 (m) REVERT: w 223 ASN cc_start: 0.8319 (t0) cc_final: 0.7943 (t0) REVERT: w 297 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8345 (tm) outliers start: 138 outliers final: 91 residues processed: 1127 average time/residue: 1.5155 time to fit residues: 2226.1966 Evaluate side-chains 1125 residues out of total 7120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1013 time to evaluate : 5.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 140 CYS Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain J residue 298 TYR Chi-restraints excluded: chain K residue 107 SER Chi-restraints excluded: chain L residue 73 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 364 ASP Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 657 ASP Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 101 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 CYS Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 202 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 110 SER Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 104 GLU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 MET Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 154 GLN Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain d residue 83 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain l residue 46 LEU Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain m residue 27 ILE Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 10 ASP Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 85 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 205 VAL Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 270 PHE Chi-restraints excluded: chain u residue 56 CYS Chi-restraints excluded: chain u residue 66 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 797 random chunks: chunk 502 optimal weight: 0.0270 chunk 673 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 582 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 633 optimal weight: 0.7980 chunk 265 optimal weight: 0.0470 chunk 650 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 116 optimal weight: 0.0980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN F 25 GLN ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 HIS M 464 GLN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 GLN V 129 GLN ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 GLN j 10 ASN l 23 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 518 GLN ** p 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 139 GLN u 104 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104547 restraints weight = 88663.381| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.41 r_work: 0.2912 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 68321 Z= 0.141 Angle : 0.526 11.574 92482 Z= 0.260 Chirality : 0.039 0.200 10058 Planarity : 0.004 0.063 11585 Dihedral : 10.523 179.570 10158 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 1.76 % Allowed : 20.64 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.02 % 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: 1.34 (0.10), residues: 8065 helix: 1.84 (0.08), residues: 4280 sheet: 0.25 (0.25), residues: 441 loop : -0.22 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP l 144 HIS 0.006 0.001 HIS l 534 PHE 0.031 0.001 PHE i 292 TYR 0.028 0.001 TYR l 422 ARG 0.019 0.000 ARG E 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29928.78 seconds wall clock time: 517 minutes 34.28 seconds (31054.28 seconds total)