Starting phenix.real_space_refine on Fri Mar 15 18:25:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkq_13477/03_2024/7pkq_13477.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkq_13477/03_2024/7pkq_13477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkq_13477/03_2024/7pkq_13477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkq_13477/03_2024/7pkq_13477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkq_13477/03_2024/7pkq_13477.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pkq_13477/03_2024/7pkq_13477.pdb" } resolution = 4.2 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= 0.004 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: 5 Type Number sf(0) Gaussians P 1114 5.49 5 S 115 5.16 5 C 39635 2.51 5 N 13038 2.21 5 O 16411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 838": "NH1" <-> "NH2" Residue "B ARG 839": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B ARG 853": "NH1" <-> "NH2" Residue "B GLU 854": "OE1" <-> "OE2" Residue "B ARG 857": "NH1" <-> "NH2" Residue "B ARG 869": "NH1" <-> "NH2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C GLU 425": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C ARG 856": "NH1" <-> "NH2" Residue "C ARG 860": "NH1" <-> "NH2" Residue "C GLU 880": "OE1" <-> "OE2" Residue "C GLU 882": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "C GLU 972": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 222": "OE1" <-> "OE2" Residue "L GLU 225": "OE1" <-> "OE2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L GLU 245": "OE1" <-> "OE2" Residue "L GLU 247": "OE1" <-> "OE2" Residue "L PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M GLU 138": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 183": "OE1" <-> "OE2" Residue "M GLU 191": "OE1" <-> "OE2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "M GLU 238": "OE1" <-> "OE2" Residue "M GLU 245": "OE1" <-> "OE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N GLU 123": "OE1" <-> "OE2" Residue "N GLU 124": "OE1" <-> "OE2" Residue "N GLU 215": "OE1" <-> "OE2" Residue "N GLU 225": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "N GLU 238": "OE1" <-> "OE2" Residue "N GLU 245": "OE1" <-> "OE2" Residue "N GLU 247": "OE1" <-> "OE2" Residue "O GLU 298": "OE1" <-> "OE2" Residue "O GLU 331": "OE1" <-> "OE2" Residue "O GLU 337": "OE1" <-> "OE2" Residue "O GLU 420": "OE1" <-> "OE2" Residue "O GLU 435": "OE1" <-> "OE2" Residue "O GLU 485": "OE1" <-> "OE2" Residue "O GLU 506": "OE1" <-> "OE2" Residue "P GLU 5": "OE1" <-> "OE2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 300": "OE1" <-> "OE2" Residue "P GLU 363": "OE1" <-> "OE2" Residue "P GLU 383": "OE1" <-> "OE2" Residue "P GLU 394": "OE1" <-> "OE2" Residue "P GLU 396": "OE1" <-> "OE2" Residue "d ARG 298": "NH1" <-> "NH2" Residue "d ARG 308": "NH1" <-> "NH2" Residue "d ARG 327": "NH1" <-> "NH2" Residue "d ARG 375": "NH1" <-> "NH2" Residue "d GLU 380": "OE1" <-> "OE2" Residue "f ARG 16": "NH1" <-> "NH2" Residue "f TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 32": "NH1" <-> "NH2" Residue "f ARG 53": "NH1" <-> "NH2" Residue "f ARG 54": "NH1" <-> "NH2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "f ARG 61": "NH1" <-> "NH2" Residue "p GLU 2": "OE1" <-> "OE2" Residue "p ARG 7": "NH1" <-> "NH2" Residue "p ARG 12": "NH1" <-> "NH2" Residue "p GLU 14": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p ARG 74": "NH1" <-> "NH2" Residue "r GLU 240": "OE1" <-> "OE2" Residue "r GLU 243": "OE1" <-> "OE2" Residue "r ARG 255": "NH1" <-> "NH2" Residue "r ARG 267": "NH1" <-> "NH2" Residue "r ARG 268": "NH1" <-> "NH2" Residue "r ARG 271": "NH1" <-> "NH2" Residue "r ARG 282": "NH1" <-> "NH2" Residue "r ARG 288": "NH1" <-> "NH2" Residue "w ARG 56": "NH1" <-> "NH2" Residue "w ARG 71": "NH1" <-> "NH2" Residue "w ARG 86": "NH1" <-> "NH2" Residue "w ARG 87": "NH1" <-> "NH2" Residue "w ARG 94": "NH1" <-> "NH2" Residue "w ARG 99": "NH1" <-> "NH2" Residue "w ARG 105": "NH1" <-> "NH2" Residue "w ARG 108": "NH1" <-> "NH2" Residue "w ARG 117": "NH1" <-> "NH2" Residue "w ARG 132": "NH1" <-> "NH2" Residue "w ARG 136": "NH1" <-> "NH2" Residue "w ARG 142": "NH1" <-> "NH2" Residue "w ARG 143": "NH1" <-> "NH2" Residue "w ARG 147": "NH1" <-> "NH2" Residue "w ARG 150": "NH1" <-> "NH2" Residue "w ARG 153": "NH1" <-> "NH2" Residue "w GLU 156": "OE1" <-> "OE2" Residue "w ARG 163": "NH1" <-> "NH2" Residue "w GLU 168": "OE1" <-> "OE2" Residue "w ARG 173": "NH1" <-> "NH2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "a GLU 161": "OE1" <-> "OE2" Residue "a GLU 163": "OE1" <-> "OE2" Residue "a GLU 232": "OE1" <-> "OE2" Residue "b GLU 134": "OE1" <-> "OE2" Residue "b ARG 138": "NH1" <-> "NH2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b ARG 150": "NH1" <-> "NH2" Residue "b GLU 222": "OE1" <-> "OE2" Residue "b GLU 270": "OE1" <-> "OE2" Residue "o GLU 180": "OE1" <-> "OE2" Residue "o GLU 282": "OE1" <-> "OE2" Residue "z GLU 107": "OE1" <-> "OE2" Residue "v GLU 25": "OE1" <-> "OE2" Residue "v GLU 77": "OE1" <-> "OE2" Residue "v GLU 114": "OE1" <-> "OE2" Residue "v GLU 116": "OE1" <-> "OE2" Residue "q GLU 5": "OE1" <-> "OE2" Residue "q GLU 47": "OE1" <-> "OE2" Residue "q GLU 68": "OE1" <-> "OE2" Residue "q GLU 148": "OE1" <-> "OE2" Residue "q GLU 170": "OE1" <-> "OE2" Residue "l ARG 32": "NH1" <-> "NH2" Residue "l GLU 82": "OE1" <-> "OE2" Residue "h ARG 50": "NH1" <-> "NH2" Residue "h GLU 147": "OE1" <-> "OE2" Residue "h GLU 152": "OE1" <-> "OE2" Residue "h ARG 178": "NH1" <-> "NH2" Residue "h GLU 285": "OE1" <-> "OE2" Residue "h GLU 304": "OE1" <-> "OE2" Residue "h GLU 318": "OE1" <-> "OE2" Residue "h GLU 326": "OE1" <-> "OE2" Residue "h GLU 336": "OE1" <-> "OE2" Residue "h GLU 360": "OE1" <-> "OE2" Residue "k GLU 122": "OE1" <-> "OE2" Residue "k GLU 168": "OE1" <-> "OE2" Residue "k GLU 172": "OE1" <-> "OE2" Residue "k GLU 173": "OE1" <-> "OE2" Residue "k TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 169": "OE1" <-> "OE2" Residue "j GLU 202": "OE1" <-> "OE2" Residue "j GLU 222": "OE1" <-> "OE2" Residue "m ARG 21": "NH1" <-> "NH2" Residue "m GLU 61": "OE1" <-> "OE2" Residue "m ARG 72": "NH1" <-> "NH2" Residue "m ARG 75": "NH1" <-> "NH2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m ARG 88": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 15": "NH1" <-> "NH2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n ARG 51": "NH1" <-> "NH2" Residue "n ARG 56": "NH1" <-> "NH2" Residue "n ARG 82": "NH1" <-> "NH2" Residue "n ARG 86": "NH1" <-> "NH2" Residue "n ARG 89": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u GLU 84": "OE1" <-> "OE2" Residue "s ARG 61": "NH1" <-> "NH2" Residue "s ARG 83": "NH1" <-> "NH2" Residue "i ARG 319": "NH1" <-> "NH2" Residue "i GLU 366": "OE1" <-> "OE2" Residue "x GLU 79": "OE1" <-> "OE2" Residue "x GLU 377": "OE1" <-> "OE2" Residue "x GLU 421": "OE1" <-> "OE2" Residue "x GLU 472": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c GLU 203": "OE1" <-> "OE2" Residue "y ARG 128": "NH1" <-> "NH2" Residue "y ARG 130": "NH1" <-> "NH2" Residue "y ARG 136": "NH1" <-> "NH2" Residue "y ARG 139": "NH1" <-> "NH2" Residue "y ARG 141": "NH1" <-> "NH2" Residue "y ARG 146": "NH1" <-> "NH2" Residue "y ARG 147": "NH1" <-> "NH2" Residue "y ARG 151": "NH1" <-> "NH2" Residue "y GLU 168": "OE1" <-> "OE2" Residue "y GLU 175": "OE1" <-> "OE2" Residue "y GLU 178": "OE1" <-> "OE2" Residue "y ARG 182": "NH1" <-> "NH2" Residue "y ARG 183": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70313 Number of models: 1 Model: "" Number of chains: 44 Chain: "B" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 386 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2766 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 344} Chain breaks: 6 Chain: "D" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2125 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 425} Link IDs: {'TRANS': 424} Chain breaks: 7 Unresolved non-hydrogen bonds: 850 Unresolved non-hydrogen angles: 1275 Unresolved non-hydrogen dihedrals: 425 Planarities with less than four sites: {'UNK:plan-1': 425} Unresolved non-hydrogen planarities: 425 Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 930 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'TRANS': 185} Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 186 Planarities with less than four sites: {'UNK:plan-1': 186} Unresolved non-hydrogen planarities: 186 Chain: "L" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1373 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Chain breaks: 1 Chain: "M" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 164} Chain breaks: 1 Chain: "N" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1479 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "O" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1710 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain breaks: 1 Chain: "P" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2601 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain breaks: 3 Chain: "U" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 165 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "V" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 760 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'TRANS': 151} Chain breaks: 5 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 152 Planarities with less than four sites: {'UNK:plan-1': 152} Unresolved non-hydrogen planarities: 152 Chain: "W" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 270 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'TRANS': 53} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'UNK:plan-1': 54} Unresolved non-hydrogen planarities: 54 Chain: "X" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 405 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'TRANS': 80} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'UNK:plan-1': 81} Unresolved non-hydrogen planarities: 81 Chain: "Y" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "Z" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 2855 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 571} Link IDs: {'TRANS': 570} Chain breaks: 18 Unresolved non-hydrogen bonds: 1142 Unresolved non-hydrogen angles: 1713 Unresolved non-hydrogen dihedrals: 571 Planarities with less than four sites: {'UNK:plan-1': 571} Unresolved non-hydrogen planarities: 571 Chain: "d" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 923 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 122} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "f" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "p" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 9, 'TRANS': 69} Chain: "r" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 459 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "w" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1245 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 151} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "1" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1986 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 23, 'rna3p': 69} Chain breaks: 1 Chain: "4" Number of atoms: 8811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 8811 Classifications: {'RNA': 415} Modifications used: {'rna2p_pur': 33, 'rna2p_pyr': 34, 'rna3p_pur': 178, 'rna3p_pyr': 170} Link IDs: {'rna2p': 66, 'rna3p': 348} Chain breaks: 8 Chain: "2" Number of atoms: 4533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 4533 Classifications: {'RNA': 213} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 15, 'rna3p_pur': 94, 'rna3p_pyr': 91} Link IDs: {'rna2p': 28, 'rna3p': 184} Chain: "3" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 8405 Classifications: {'RNA': 393} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 18, 'rna3p_pur': 185, 'rna3p_pyr': 153} Link IDs: {'rna2p': 55, 'rna3p': 337} Chain breaks: 2 Chain: "a" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1562 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "b" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1824 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1403 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain: "o" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1284 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "z" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 667 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain breaks: 1 Chain: "v" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1003 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1128 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 1 Chain: "l" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "h" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2711 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 24, 'TRANS': 326} Chain breaks: 2 Chain: "k" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 729 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "j" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1211 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'UNK:plan-1': 32} Unresolved non-hydrogen planarities: 32 Chain: "m" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Chain: "n" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 779 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "u" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "s" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 678 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Chain: "g" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 909 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "i" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1019 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 142} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "x" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2647 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 340} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "c" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1012 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "y" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 510 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 5, 'TRANS': 55} Time building chain proxies: 28.10, per 1000 atoms: 0.40 Number of scatterers: 70313 At special positions: 0 Unit cell: (171.76, 253.12, 288.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 1114 15.00 O 16411 8.00 N 13038 7.00 C 39635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 27.58 Conformation dependent library (CDL) restraints added in 5.4 seconds 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12632 Finding SS restraints... Secondary structure from input PDB file: 247 helices and 35 sheets defined 71.0% alpha, 11.0% beta 299 base pairs and 572 stacking pairs defined. Time for finding SS restraints: 19.83 Creating SS restraints... Processing helix chain 'B' and resid 852 through 868 removed outlier: 3.595A pdb=" N ASN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 299 removed outlier: 3.884A pdb=" N ARG C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 Processing helix chain 'C' and resid 315 through 334 Processing helix chain 'C' and resid 340 through 346 removed outlier: 4.330A pdb=" N LEU C 343 " --> pdb=" O ARG C 340 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER C 344 " --> pdb=" O GLY C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 399 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 409 through 437 removed outlier: 3.740A pdb=" N ALA C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 481 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 481 through 505 removed outlier: 3.541A pdb=" N GLN C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 560 Proline residue: C 557 - end of helix Processing helix chain 'C' and resid 564 through 574 Processing helix chain 'C' and resid 575 through 586 Processing helix chain 'C' and resid 586 through 596 removed outlier: 3.921A pdb=" N ALA C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 881 through 907 Processing helix chain 'C' and resid 969 through 980 removed outlier: 3.587A pdb=" N LEU C 980 " --> pdb=" O GLN C 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 141 removed outlier: 3.897A pdb=" N UNK D 132 " --> pdb=" O UNK D 128 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK D 141 " --> pdb=" O UNK D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 4.063A pdb=" N UNK D 156 " --> pdb=" O UNK D 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N UNK D 160 " --> pdb=" O UNK D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 211 removed outlier: 3.848A pdb=" N UNK D 205 " --> pdb=" O UNK D 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK D 211 " --> pdb=" O UNK D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 229 removed outlier: 4.275A pdb=" N UNK D 223 " --> pdb=" O UNK D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 262 removed outlier: 3.833A pdb=" N UNK D 246 " --> pdb=" O UNK D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 283 removed outlier: 3.510A pdb=" N UNK D 280 " --> pdb=" O UNK D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.595A pdb=" N UNK D 306 " --> pdb=" O UNK D 302 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N UNK D 307 " --> pdb=" O UNK D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 323 through 369 removed outlier: 4.369A pdb=" N UNK D 331 " --> pdb=" O UNK D 327 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N UNK D 343 " --> pdb=" O UNK D 339 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N UNK D 344 " --> pdb=" O UNK D 340 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N UNK D 357 " --> pdb=" O UNK D 353 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N UNK D 358 " --> pdb=" O UNK D 354 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N UNK D 361 " --> pdb=" O UNK D 357 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N UNK D 365 " --> pdb=" O UNK D 361 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK D 366 " --> pdb=" O UNK D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 408 removed outlier: 3.825A pdb=" N UNK D 397 " --> pdb=" O UNK D 393 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N UNK D 398 " --> pdb=" O UNK D 394 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N UNK D 399 " --> pdb=" O UNK D 395 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N UNK D 400 " --> pdb=" O UNK D 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N UNK D 403 " --> pdb=" O UNK D 399 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N UNK D 404 " --> pdb=" O UNK D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 removed outlier: 4.164A pdb=" N UNK D 420 " --> pdb=" O UNK D 416 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N UNK D 421 " --> pdb=" O UNK D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 449 removed outlier: 4.011A pdb=" N UNK D 436 " --> pdb=" O UNK D 432 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N UNK D 447 " --> pdb=" O UNK D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 489 through 494 Processing helix chain 'D' and resid 921 through 930 removed outlier: 3.918A pdb=" N UNK D 925 " --> pdb=" O UNK D 921 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N UNK D 928 " --> pdb=" O UNK D 924 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N UNK D 929 " --> pdb=" O UNK D 925 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK D 930 " --> pdb=" O UNK D 926 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 removed outlier: 3.598A pdb=" N UNK K 10 " --> pdb=" O UNK K 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK K 14 " --> pdb=" O UNK K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 42 removed outlier: 3.831A pdb=" N UNK K 30 " --> pdb=" O UNK K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 70 Processing helix chain 'K' and resid 78 through 96 Processing helix chain 'K' and resid 109 through 120 Processing helix chain 'K' and resid 126 through 143 Processing helix chain 'K' and resid 147 through 165 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 92 through 96 Processing helix chain 'L' and resid 203 through 217 Processing helix chain 'L' and resid 220 through 251 Processing helix chain 'M' and resid 75 through 88 Processing helix chain 'M' and resid 92 through 96 Processing helix chain 'M' and resid 198 through 202 Processing helix chain 'M' and resid 203 through 217 Processing helix chain 'M' and resid 220 through 252 Processing helix chain 'N' and resid 43 through 57 Processing helix chain 'N' and resid 73 through 88 removed outlier: 3.899A pdb=" N LEU N 77 " --> pdb=" O SER N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 97 removed outlier: 3.521A pdb=" N SER N 96 " --> pdb=" O PRO N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 Processing helix chain 'N' and resid 220 through 251 Processing helix chain 'O' and resid 272 through 301 removed outlier: 3.542A pdb=" N GLN O 276 " --> pdb=" O LEU O 272 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR O 279 " --> pdb=" O LEU O 275 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU O 301 " --> pdb=" O LEU O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 309 through 320 removed outlier: 4.513A pdb=" N ALA O 315 " --> pdb=" O GLY O 311 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA O 316 " --> pdb=" O ARG O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 342 Processing helix chain 'O' and resid 347 through 360 Processing helix chain 'O' and resid 370 through 377 Processing helix chain 'O' and resid 380 through 399 Processing helix chain 'O' and resid 410 through 425 Processing helix chain 'O' and resid 427 through 441 removed outlier: 3.549A pdb=" N VAL O 431 " --> pdb=" O ALA O 427 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS O 440 " --> pdb=" O SER O 436 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 460 Processing helix chain 'O' and resid 461 through 474 Processing helix chain 'O' and resid 481 through 497 removed outlier: 4.254A pdb=" N GLU O 485 " --> pdb=" O ALA O 481 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY O 487 " --> pdb=" O ALA O 483 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 508 removed outlier: 3.537A pdb=" N ALA O 501 " --> pdb=" O ASN O 497 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 29 through 38 Processing helix chain 'P' and resid 42 through 54 Processing helix chain 'P' and resid 55 through 57 No H-bonds generated for 'chain 'P' and resid 55 through 57' Processing helix chain 'P' and resid 58 through 76 Processing helix chain 'P' and resid 80 through 98 removed outlier: 3.962A pdb=" N VAL P 92 " --> pdb=" O LEU P 88 " (cutoff:3.500A) Proline residue: P 93 - end of helix Processing helix chain 'P' and resid 98 through 103 Processing helix chain 'P' and resid 104 through 119 Processing helix chain 'P' and resid 145 through 157 removed outlier: 3.601A pdb=" N VAL P 149 " --> pdb=" O PRO P 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 165 removed outlier: 3.898A pdb=" N LEU P 163 " --> pdb=" O ASN P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 182 removed outlier: 3.765A pdb=" N LEU P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 188 removed outlier: 3.699A pdb=" N TYR P 187 " --> pdb=" O PRO P 184 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY P 188 " --> pdb=" O GLN P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 204 Processing helix chain 'P' and resid 206 through 210 Processing helix chain 'P' and resid 211 through 226 Processing helix chain 'P' and resid 281 through 305 Processing helix chain 'P' and resid 314 through 333 Processing helix chain 'P' and resid 342 through 355 removed outlier: 4.201A pdb=" N VAL P 346 " --> pdb=" O PRO P 342 " (cutoff:3.500A) Processing helix chain 'P' and resid 360 through 375 removed outlier: 3.772A pdb=" N ALA P 364 " --> pdb=" O SER P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 378 through 391 Processing helix chain 'P' and resid 395 through 412 Processing helix chain 'U' and resid 9 through 16 removed outlier: 3.715A pdb=" N UNK U 14 " --> pdb=" O UNK U 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK U 15 " --> pdb=" O UNK U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 35 Processing helix chain 'V' and resid 48 through 75 removed outlier: 4.759A pdb=" N UNK V 54 " --> pdb=" O UNK V 50 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N UNK V 55 " --> pdb=" O UNK V 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK V 56 " --> pdb=" O UNK V 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N UNK V 60 " --> pdb=" O UNK V 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N UNK V 67 " --> pdb=" O UNK V 63 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N UNK V 68 " --> pdb=" O UNK V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 110 removed outlier: 3.668A pdb=" N UNK V 94 " --> pdb=" O UNK V 90 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N UNK V 96 " --> pdb=" O UNK V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 133 removed outlier: 3.727A pdb=" N UNK V 133 " --> pdb=" O UNK V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 148 Processing helix chain 'V' and resid 161 through 177 removed outlier: 4.190A pdb=" N UNK V 167 " --> pdb=" O UNK V 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N UNK V 172 " --> pdb=" O UNK V 168 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N UNK V 173 " --> pdb=" O UNK V 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 207 through 217 Processing helix chain 'X' and resid 37 through 52 Processing helix chain 'X' and resid 53 through 56 Processing helix chain 'X' and resid 71 through 77 Processing helix chain 'X' and resid 80 through 84 removed outlier: 4.154A pdb=" N UNK X 83 " --> pdb=" O UNK X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 91 removed outlier: 3.811A pdb=" N UNK X 91 " --> pdb=" O UNK X 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 16 removed outlier: 4.327A pdb=" N UNK Y 16 " --> pdb=" O UNK Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 35 Processing helix chain 'Y' and resid 45 through 67 removed outlier: 4.523A pdb=" N UNK Y 52 " --> pdb=" O UNK Y 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N UNK Y 53 " --> pdb=" O UNK Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 85 removed outlier: 4.237A pdb=" N UNK Y 74 " --> pdb=" O UNK Y 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 52 Processing helix chain 'Z' and resid 64 through 84 Processing helix chain 'Z' and resid 87 through 105 removed outlier: 4.443A pdb=" N UNK Z 94 " --> pdb=" O UNK Z 90 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N UNK Z 95 " --> pdb=" O UNK Z 91 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N UNK Z 96 " --> pdb=" O UNK Z 92 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N UNK Z 104 " --> pdb=" O UNK Z 100 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N UNK Z 105 " --> pdb=" O UNK Z 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 138 Processing helix chain 'Z' and resid 146 through 164 Processing helix chain 'Z' and resid 170 through 185 removed outlier: 4.862A pdb=" N UNK Z 178 " --> pdb=" O UNK Z 174 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N UNK Z 185 " --> pdb=" O UNK Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 208 Processing helix chain 'Z' and resid 212 through 234 Processing helix chain 'Z' and resid 258 through 274 Processing helix chain 'Z' and resid 282 through 312 Processing helix chain 'Z' and resid 339 through 353 Processing helix chain 'Z' and resid 358 through 377 Processing helix chain 'Z' and resid 385 through 407 removed outlier: 3.578A pdb=" N UNK Z 389 " --> pdb=" O UNK Z 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 429 Processing helix chain 'Z' and resid 439 through 464 Processing helix chain 'Z' and resid 487 through 502 Processing helix chain 'Z' and resid 508 through 536 Processing helix chain 'Z' and resid 539 through 553 removed outlier: 4.834A pdb=" N UNK Z 545 " --> pdb=" O UNK Z 541 " (cutoff:3.500A) Processing helix chain 'Z' and resid 573 through 579 removed outlier: 3.779A pdb=" N UNK Z 577 " --> pdb=" O UNK Z 573 " (cutoff:3.500A) Processing helix chain 'Z' and resid 584 through 592 removed outlier: 3.963A pdb=" N UNK Z 588 " --> pdb=" O UNK Z 584 " (cutoff:3.500A) Processing helix chain 'Z' and resid 656 through 665 Processing helix chain 'Z' and resid 673 through 693 removed outlier: 4.054A pdb=" N UNK Z 677 " --> pdb=" O UNK Z 673 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N UNK Z 693 " --> pdb=" O UNK Z 689 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 302 Processing helix chain 'd' and resid 307 through 323 removed outlier: 4.456A pdb=" N PHE d 311 " --> pdb=" O GLN d 307 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL d 312 " --> pdb=" O ARG d 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG d 323 " --> pdb=" O SER d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 330 through 337 Processing helix chain 'd' and resid 338 through 347 Processing helix chain 'd' and resid 351 through 362 Processing helix chain 'f' and resid 18 through 32 Processing helix chain 'f' and resid 72 through 74 No H-bonds generated for 'chain 'f' and resid 72 through 74' Processing helix chain 'f' and resid 75 through 85 Processing helix chain 'p' and resid 37 through 44 Processing helix chain 'p' and resid 49 through 59 Processing helix chain 'r' and resid 249 through 257 removed outlier: 4.293A pdb=" N LEU r 253 " --> pdb=" O ASN r 249 " (cutoff:3.500A) Processing helix chain 'r' and resid 266 through 270 removed outlier: 3.534A pdb=" N THR r 270 " --> pdb=" O ARG r 267 " (cutoff:3.500A) Processing helix chain 'r' and resid 273 through 288 Processing helix chain 'w' and resid 41 through 81 removed outlier: 3.653A pdb=" N ASP w 81 " --> pdb=" O LYS w 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 85 through 156 removed outlier: 4.858A pdb=" N LYS w 107 " --> pdb=" O LEU w 103 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG w 108 " --> pdb=" O LEU w 104 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG w 132 " --> pdb=" O VAL w 128 " (cutoff:3.500A) Processing helix chain 'w' and resid 163 through 165 No H-bonds generated for 'chain 'w' and resid 163 through 165' Processing helix chain 'w' and resid 166 through 173 Processing helix chain 'a' and resid 41 through 53 Processing helix chain 'a' and resid 62 through 72 removed outlier: 3.794A pdb=" N ARG a 66 " --> pdb=" O GLU a 62 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN a 72 " --> pdb=" O LEU a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 112 No H-bonds generated for 'chain 'a' and resid 110 through 112' Processing helix chain 'a' and resid 160 through 175 Processing helix chain 'b' and resid 119 through 128 Processing helix chain 'b' and resid 132 through 140 removed outlier: 3.707A pdb=" N LEU b 136 " --> pdb=" O ASP b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 202 removed outlier: 3.750A pdb=" N THR b 186 " --> pdb=" O ASP b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 213 through 215 No H-bonds generated for 'chain 'b' and resid 213 through 215' Processing helix chain 'b' and resid 216 through 227 Processing helix chain 'b' and resid 262 through 272 removed outlier: 4.051A pdb=" N GLN b 266 " --> pdb=" O GLN b 262 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE b 267 " --> pdb=" O PRO b 263 " (cutoff:3.500A) Processing helix chain 'b' and resid 376 through 386 Processing helix chain 'b' and resid 413 through 429 Processing helix chain 'b' and resid 431 through 440 Processing helix chain 'e' and resid 181 through 186 removed outlier: 3.683A pdb=" N GLU e 185 " --> pdb=" O GLU e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 237 through 252 Processing helix chain 'e' and resid 291 through 302 removed outlier: 3.914A pdb=" N GLU e 296 " --> pdb=" O ASP e 292 " (cutoff:3.500A) Processing helix chain 'e' and resid 316 through 331 removed outlier: 3.826A pdb=" N VAL e 320 " --> pdb=" O SER e 316 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN e 331 " --> pdb=" O ALA e 327 " (cutoff:3.500A) Processing helix chain 'e' and resid 333 through 337 removed outlier: 4.164A pdb=" N ASP e 336 " --> pdb=" O THR e 333 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY e 337 " --> pdb=" O PRO e 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 333 through 337' Processing helix chain 'o' and resid 108 through 116 Processing helix chain 'o' and resid 122 through 139 removed outlier: 3.724A pdb=" N GLN o 139 " --> pdb=" O ILE o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 169 Processing helix chain 'o' and resid 175 through 197 removed outlier: 4.080A pdb=" N ARG o 195 " --> pdb=" O THR o 191 " (cutoff:3.500A) Processing helix chain 'o' and resid 197 through 208 Processing helix chain 'o' and resid 256 through 268 Proline residue: o 262 - end of helix removed outlier: 3.956A pdb=" N ASP o 268 " --> pdb=" O LEU o 264 " (cutoff:3.500A) Processing helix chain 'o' and resid 268 through 287 removed outlier: 3.593A pdb=" N THR o 287 " --> pdb=" O LYS o 283 " (cutoff:3.500A) Processing helix chain 'z' and resid 37 through 40 Processing helix chain 'z' and resid 98 through 115 Processing helix chain 'v' and resid 16 through 25 removed outlier: 4.034A pdb=" N ARG v 22 " --> pdb=" O ALA v 18 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP v 23 " --> pdb=" O LYS v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 41 removed outlier: 3.751A pdb=" N TYR v 41 " --> pdb=" O VAL v 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 60 through 71 Processing helix chain 'v' and resid 72 through 76 Processing helix chain 'v' and resid 87 through 103 Processing helix chain 'v' and resid 105 through 117 Processing helix chain 'v' and resid 117 through 136 removed outlier: 3.841A pdb=" N LEU v 121 " --> pdb=" O LEU v 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 84 through 107 Processing helix chain 'q' and resid 143 through 172 removed outlier: 3.635A pdb=" N ALA q 147 " --> pdb=" O ASP q 143 " (cutoff:3.500A) Processing helix chain 'q' and resid 178 through 183 removed outlier: 3.669A pdb=" N LEU q 182 " --> pdb=" O SER q 178 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 19 Processing helix chain 'h' and resid 11 through 15 Processing helix chain 'h' and resid 19 through 31 removed outlier: 3.728A pdb=" N ALA h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU h 25 " --> pdb=" O ALA h 21 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 68 through 79 Processing helix chain 'h' and resid 81 through 99 Processing helix chain 'h' and resid 109 through 122 Processing helix chain 'h' and resid 134 through 137 Processing helix chain 'h' and resid 221 through 230 Processing helix chain 'h' and resid 249 through 255 Processing helix chain 'h' and resid 268 through 286 Processing helix chain 'h' and resid 290 through 294 Processing helix chain 'h' and resid 296 through 300 removed outlier: 3.771A pdb=" N TRP h 300 " --> pdb=" O LEU h 297 " (cutoff:3.500A) Processing helix chain 'h' and resid 301 through 319 removed outlier: 3.570A pdb=" N LEU h 305 " --> pdb=" O ASN h 301 " (cutoff:3.500A) Processing helix chain 'h' and resid 326 through 371 Processing helix chain 'k' and resid 158 through 163 Processing helix chain 'k' and resid 163 through 182 removed outlier: 3.864A pdb=" N ALA k 167 " --> pdb=" O GLN k 163 " (cutoff:3.500A) Processing helix chain 'k' and resid 194 through 208 removed outlier: 3.692A pdb=" N GLN k 198 " --> pdb=" O GLY k 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 123 through 142 Processing helix chain 'j' and resid 214 through 227 Processing helix chain 'j' and resid 247 through 253 removed outlier: 3.565A pdb=" N SER j 251 " --> pdb=" O PRO j 247 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 48 removed outlier: 3.764A pdb=" N VAL m 48 " --> pdb=" O VAL m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 86 through 93 Processing helix chain 'n' and resid 16 through 30 removed outlier: 4.054A pdb=" N ASP n 20 " --> pdb=" O GLY n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 44 removed outlier: 3.920A pdb=" N SER n 35 " --> pdb=" O GLU n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 57 Processing helix chain 'n' and resid 63 through 67 removed outlier: 4.001A pdb=" N ALA n 67 " --> pdb=" O ARG n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 102 Processing helix chain 'u' and resid 74 through 79 removed outlier: 3.543A pdb=" N PHE u 78 " --> pdb=" O ARG u 74 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 83 through 88 Processing helix chain 'g' and resid 123 through 138 removed outlier: 4.005A pdb=" N UNK g 138 " --> pdb=" O UNK g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 142 through 164 Processing helix chain 'g' and resid 177 through 188 Processing helix chain 'g' and resid 211 through 235 Processing helix chain 'g' and resid 242 through 256 removed outlier: 3.964A pdb=" N ALA g 246 " --> pdb=" O SER g 242 " (cutoff:3.500A) Processing helix chain 'g' and resid 259 through 275 removed outlier: 3.711A pdb=" N ASN g 275 " --> pdb=" O LEU g 271 " (cutoff:3.500A) Processing helix chain 'i' and resid 342 through 347 removed outlier: 3.970A pdb=" N TYR i 346 " --> pdb=" O PRO i 342 " (cutoff:3.500A) Processing helix chain 'i' and resid 349 through 364 Proline residue: i 359 - end of helix Processing helix chain 'i' and resid 379 through 399 Processing helix chain 'x' and resid 73 through 77 Processing helix chain 'x' and resid 84 through 88 removed outlier: 3.552A pdb=" N ALA x 87 " --> pdb=" O SER x 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE x 88 " --> pdb=" O ALA x 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 84 through 88' Processing helix chain 'x' and resid 102 through 113 Processing helix chain 'x' and resid 120 through 133 removed outlier: 3.546A pdb=" N ALA x 124 " --> pdb=" O ARG x 120 " (cutoff:3.500A) Processing helix chain 'x' and resid 148 through 162 Processing helix chain 'x' and resid 172 through 177 Processing helix chain 'x' and resid 195 through 216 Proline residue: x 211 - end of helix Processing helix chain 'x' and resid 223 through 230 removed outlier: 3.781A pdb=" N ARG x 227 " --> pdb=" O GLY x 223 " (cutoff:3.500A) Processing helix chain 'x' and resid 281 through 288 Processing helix chain 'x' and resid 293 through 314 removed outlier: 3.805A pdb=" N ALA x 297 " --> pdb=" O ASN x 293 " (cutoff:3.500A) Processing helix chain 'x' and resid 336 through 340 Processing helix chain 'x' and resid 368 through 373 Processing helix chain 'x' and resid 383 through 390 Processing helix chain 'x' and resid 433 through 448 removed outlier: 3.580A pdb=" N GLY x 448 " --> pdb=" O TYR x 444 " (cutoff:3.500A) Processing helix chain 'x' and resid 455 through 467 Processing helix chain 'x' and resid 469 through 476 Processing helix chain 'x' and resid 477 through 479 No H-bonds generated for 'chain 'x' and resid 477 through 479' Processing helix chain 'c' and resid 127 through 142 removed outlier: 3.577A pdb=" N ALA c 132 " --> pdb=" O ARG c 128 " (cutoff:3.500A) Processing helix chain 'c' and resid 160 through 174 removed outlier: 3.877A pdb=" N ALA c 164 " --> pdb=" O SER c 160 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 192 removed outlier: 3.697A pdb=" N ILE c 181 " --> pdb=" O ALA c 177 " (cutoff:3.500A) Processing helix chain 'y' and resid 126 through 135 Processing helix chain 'y' and resid 146 through 151 Processing helix chain 'y' and resid 154 through 160 removed outlier: 3.615A pdb=" N THR y 159 " --> pdb=" O GLY y 155 " (cutoff:3.500A) Processing helix chain 'y' and resid 174 through 185 removed outlier: 4.589A pdb=" N GLU y 180 " --> pdb=" O GLU y 176 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU y 185 " --> pdb=" O LEU y 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 835 through 837 Processing sheet with id=AA2, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA3, first strand: chain 'C' and resid 940 through 942 removed outlier: 3.560A pdb=" N TYR C 957 " --> pdb=" O VAL C 942 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 104 through 106 removed outlier: 3.953A pdb=" N LEU L 114 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS L 159 " --> pdb=" O ARG L 162 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG L 162 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU L 167 " --> pdb=" O HIS L 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS L 179 " --> pdb=" O GLU L 167 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU L 169 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE L 177 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 104 through 106 removed outlier: 3.813A pdb=" N THR M 115 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 104 through 107 removed outlier: 3.646A pdb=" N PHE N 153 " --> pdb=" O CYS N 168 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 168 " --> pdb=" O PHE N 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG N 162 " --> pdb=" O LYS N 159 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU N 169 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE N 177 " --> pdb=" O GLU N 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 69 through 70 removed outlier: 3.771A pdb=" N LEU f 3 " --> pdb=" O ARG f 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 8 through 10 Processing sheet with id=AA9, first strand: chain 'r' and resid 258 through 259 removed outlier: 3.530A pdb=" N ARG r 263 " --> pdb=" O SER r 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 104 through 108 removed outlier: 3.566A pdb=" N VAL a 107 " --> pdb=" O VAL a 95 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG a 94 " --> pdb=" O VAL a 90 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL a 90 " --> pdb=" O ARG a 94 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR a 96 " --> pdb=" O LEU a 88 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS a 86 " --> pdb=" O ASP a 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 202 through 206 removed outlier: 3.723A pdb=" N PHE a 195 " --> pdb=" O LEU a 206 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY a 194 " --> pdb=" O ASP a 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP a 190 " --> pdb=" O GLY a 194 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA a 196 " --> pdb=" O LEU a 188 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR a 238 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N MET a 230 " --> pdb=" O ARG a 236 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG a 236 " --> pdb=" O MET a 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 232 through 235 removed outlier: 6.627A pdb=" N VAL b 207 " --> pdb=" O TRP b 233 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TRP b 235 " --> pdb=" O VAL b 207 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL b 209 " --> pdb=" O TRP b 235 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL b 208 " --> pdb=" O VAL b 369 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU b 393 " --> pdb=" O VAL b 370 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR b 390 " --> pdb=" O PHE b 405 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL b 407 " --> pdb=" O THR b 390 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA b 392 " --> pdb=" O VAL b 407 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 193 through 206 removed outlier: 3.575A pdb=" N GLY e 222 " --> pdb=" O ASP e 193 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET e 218 " --> pdb=" O VAL e 197 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL e 199 " --> pdb=" O THR e 216 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR e 216 " --> pdb=" O VAL e 199 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG e 201 " --> pdb=" O GLU e 214 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU e 214 " --> pdb=" O ARG e 201 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N HIS e 203 " --> pdb=" O ARG e 212 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG e 212 " --> pdb=" O HIS e 203 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLY e 210 " --> pdb=" O PRO e 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'e' and resid 268 through 272 removed outlier: 3.683A pdb=" N HIS e 270 " --> pdb=" O ILE e 277 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE e 272 " --> pdb=" O LEU e 275 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER e 307 " --> pdb=" O MET e 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'z' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'z' and resid 42 through 49 removed outlier: 6.920A pdb=" N TRP z 62 " --> pdb=" O VAL z 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'q' and resid 6 through 12 removed outlier: 8.039A pdb=" N ILE q 7 " --> pdb=" O SER q 24 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER q 24 " --> pdb=" O ILE q 7 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL q 20 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 16.159A pdb=" N VAL q 69 " --> pdb=" O VAL q 39 " (cutoff:3.500A) removed outlier: 13.419A pdb=" N ARG q 41 " --> pdb=" O VAL q 69 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N TYR q 71 " --> pdb=" O ARG q 41 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS q 43 " --> pdb=" O TYR q 71 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL q 73 " --> pdb=" O LYS q 43 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG q 45 " --> pdb=" O VAL q 73 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP q 75 " --> pdb=" O ARG q 45 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG q 58 " --> pdb=" O VAL q 74 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR q 76 " --> pdb=" O ILE q 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE q 56 " --> pdb=" O THR q 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL q 57 " --> pdb=" O GLY q 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 42 through 52 removed outlier: 7.071A pdb=" N LYS l 66 " --> pdb=" O LEU l 47 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL l 49 " --> pdb=" O LEU l 64 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU l 64 " --> pdb=" O VAL l 49 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR l 51 " --> pdb=" O ARG l 62 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG l 62 " --> pdb=" O THR l 51 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL l 67 " --> pdb=" O ALA l 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA l 75 " --> pdb=" O VAL l 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU l 107 " --> pdb=" O LEU l 76 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER l 90 " --> pdb=" O CYS l 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS l 42 " --> pdb=" O VAL l 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 44 through 46 Processing sheet with id=AC2, first strand: chain 'h' and resid 103 through 106 Processing sheet with id=AC3, first strand: chain 'h' and resid 209 through 210 removed outlier: 3.997A pdb=" N ALA h 259 " --> pdb=" O MET h 220 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET h 220 " --> pdb=" O ALA h 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 209 through 210 removed outlier: 6.697A pdb=" N MET h 238 " --> pdb=" O ALA h 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'k' and resid 147 through 150 removed outlier: 6.163A pdb=" N GLY k 123 " --> pdb=" O GLN k 187 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ARG k 189 " --> pdb=" O GLY k 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL k 125 " --> pdb=" O ARG k 189 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS k 191 " --> pdb=" O VAL k 125 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILE k 127 " --> pdb=" O LYS k 191 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA k 215 " --> pdb=" O VAL k 186 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL k 188 " --> pdb=" O ALA k 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'j' and resid 203 through 211 Processing sheet with id=AC7, first strand: chain 'j' and resid 181 through 185 removed outlier: 3.626A pdb=" N GLU j 199 " --> pdb=" O SER n 108 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'j' and resid 241 through 243 removed outlier: 3.717A pdb=" N UNK j 288 " --> pdb=" O GLN j 242 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 84 through 85 Processing sheet with id=AD1, first strand: chain 's' and resid 44 through 45 removed outlier: 6.821A pdb=" N ILE s 44 " --> pdb=" O GLY s 63 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS s 65 " --> pdb=" O ILE s 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'g' and resid 192 through 195 Processing sheet with id=AD3, first strand: chain 'i' and resid 305 through 308 removed outlier: 6.442A pdb=" N THR i 337 " --> pdb=" O ALA i 373 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL i 375 " --> pdb=" O THR i 337 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'x' and resid 69 through 71 Processing sheet with id=AD5, first strand: chain 'x' and resid 165 through 169 removed outlier: 6.369A pdb=" N LEU x 165 " --> pdb=" O LEU x 330 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA x 332 " --> pdb=" O LEU x 165 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL x 167 " --> pdb=" O ALA x 332 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP x 334 " --> pdb=" O VAL x 167 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL x 169 " --> pdb=" O ASP x 334 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL x 329 " --> pdb=" O VAL x 401 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL x 403 " --> pdb=" O VAL x 329 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE x 331 " --> pdb=" O VAL x 403 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA x 405 " --> pdb=" O PHE x 331 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU x 333 " --> pdb=" O ALA x 405 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG x 137 " --> pdb=" O THR x 425 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL x 427 " --> pdb=" O ARG x 137 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU x 139 " --> pdb=" O VAL x 427 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'x' and resid 181 through 184 removed outlier: 3.513A pdb=" N ASP x 193 " --> pdb=" O ALA x 182 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG x 184 " --> pdb=" O GLY x 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'x' and resid 346 through 347 Processing sheet with id=AD8, first strand: chain 'c' and resid 216 through 222 2711 hydrogen bonds defined for protein. 7896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 734 hydrogen bonds 1228 hydrogen bond angles 0 basepair planarities 299 basepair parallelities 572 stacking parallelities Total time for adding SS restraints: 30.84 Time building geometry restraints manager: 29.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9808 1.31 - 1.44: 25240 1.44 - 1.57: 36288 1.57 - 1.70: 2211 1.70 - 1.84: 197 Bond restraints: 73744 Sorted by residual: bond pdb=" CA GLU r 240 " pdb=" CB GLU r 240 " ideal model delta sigma weight residual 1.527 1.589 -0.062 1.38e-02 5.25e+03 2.02e+01 bond pdb=" C ASN p 34 " pdb=" O ASN p 34 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.16e-02 7.43e+03 1.86e+01 bond pdb=" C VAL h 130 " pdb=" N VAL h 131 " ideal model delta sigma weight residual 1.333 1.280 0.053 1.27e-02 6.20e+03 1.73e+01 bond pdb=" N TYR f 59 " pdb=" CA TYR f 59 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.29e-02 6.01e+03 1.62e+01 bond pdb=" C ALA B 827 " pdb=" O ALA B 827 " ideal model delta sigma weight residual 1.236 1.264 -0.028 7.30e-03 1.88e+04 1.48e+01 ... (remaining 73739 not shown) Histogram of bond angle deviations from ideal: 91.98 - 100.81: 244 100.81 - 109.63: 21245 109.63 - 118.46: 44240 118.46 - 127.29: 36914 127.29 - 136.11: 2908 Bond angle restraints: 105551 Sorted by residual: angle pdb=" N ASN p 34 " pdb=" CA ASN p 34 " pdb=" C ASN p 34 " ideal model delta sigma weight residual 109.86 91.98 17.88 1.55e+00 4.16e-01 1.33e+02 angle pdb=" N LEU k 209 " pdb=" CA LEU k 209 " pdb=" C LEU k 209 " ideal model delta sigma weight residual 110.23 93.64 16.59 1.45e+00 4.76e-01 1.31e+02 angle pdb=" N GLY k 194 " pdb=" CA GLY k 194 " pdb=" C GLY k 194 " ideal model delta sigma weight residual 111.36 124.03 -12.67 1.17e+00 7.31e-01 1.17e+02 angle pdb=" N THR k 212 " pdb=" CA THR k 212 " pdb=" C THR k 212 " ideal model delta sigma weight residual 111.28 100.52 10.76 1.09e+00 8.42e-01 9.74e+01 angle pdb=" C TYR a 147 " pdb=" N THR a 148 " pdb=" CA THR a 148 " ideal model delta sigma weight residual 122.29 136.11 -13.82 1.48e+00 4.57e-01 8.73e+01 ... (remaining 105546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 42201 35.81 - 71.62: 3179 71.62 - 107.43: 354 107.43 - 143.24: 11 143.24 - 179.05: 8 Dihedral angle restraints: 45753 sinusoidal: 26410 harmonic: 19343 Sorted by residual: dihedral pdb=" CA PHE e 272 " pdb=" C PHE e 272 " pdb=" N HIS e 273 " pdb=" CA HIS e 273 " ideal model delta harmonic sigma weight residual -180.00 -126.58 -53.42 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA LEU C 932 " pdb=" C LEU C 932 " pdb=" N ARG C 933 " pdb=" CA ARG C 933 " ideal model delta harmonic sigma weight residual 180.00 128.42 51.58 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA PRO C 929 " pdb=" C PRO C 929 " pdb=" N ALA C 930 " pdb=" CA ALA C 930 " ideal model delta harmonic sigma weight residual -180.00 -129.09 -50.91 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 45750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 11089 0.111 - 0.222: 1854 0.222 - 0.333: 193 0.333 - 0.444: 26 0.444 - 0.555: 6 Chirality restraints: 13168 Sorted by residual: chirality pdb=" CB VAL v 56 " pdb=" CA VAL v 56 " pdb=" CG1 VAL v 56 " pdb=" CG2 VAL v 56 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.55 2.00e-01 2.50e+01 7.70e+00 chirality pdb=" CA UNK Y 19 " pdb=" N UNK Y 19 " pdb=" C UNK Y 19 " pdb=" CB UNK Y 19 " both_signs ideal model delta sigma weight residual False 2.52 1.97 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" P G 3 106 " pdb=" OP1 G 3 106 " pdb=" OP2 G 3 106 " pdb=" O5' G 3 106 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 13165 not shown) Planarity restraints: 9673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR l 114 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C TYR l 114 " -0.086 2.00e-02 2.50e+03 pdb=" O TYR l 114 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP l 115 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR w 67 " -0.031 2.00e-02 2.50e+03 3.29e-02 2.16e+01 pdb=" CG TYR w 67 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR w 67 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR w 67 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR w 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR w 67 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR w 67 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR w 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE b 181 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C PHE b 181 " -0.080 2.00e-02 2.50e+03 pdb=" O PHE b 181 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP b 182 " 0.028 2.00e-02 2.50e+03 ... (remaining 9670 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 3606 2.68 - 3.23: 62602 3.23 - 3.79: 129957 3.79 - 4.34: 151661 4.34 - 4.90: 221151 Nonbonded interactions: 568977 Sorted by model distance: nonbonded pdb=" CB UNK V 162 " pdb=" O2' U 4 48 " model vdw 2.123 3.440 nonbonded pdb=" N ASN p 34 " pdb=" O ASN p 34 " model vdw 2.137 2.496 nonbonded pdb=" OH TYR h 79 " pdb=" OD2 ASP h 114 " model vdw 2.155 2.440 nonbonded pdb=" CB UNK V 162 " pdb=" C2' U 4 48 " model vdw 2.187 3.870 nonbonded pdb=" O PRO x 143 " pdb=" NZ LYS x 148 " model vdw 2.249 2.520 ... (remaining 568972 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 'L' and (resid 74 through 138 or resid 147 through 253)) selection = (chain 'M' and (resid 74 through 138 or resid 147 through 253)) selection = (chain 'N' and (resid 74 through 138 or resid 147 through 253)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.470 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: 12.580 Check model and map are aligned: 0.840 Set scattering table: 0.520 Process input model: 162.870 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 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 : 0.009 0.107 73744 Z= 0.565 Angle : 1.419 20.562 105551 Z= 0.817 Chirality : 0.083 0.555 13168 Planarity : 0.009 0.113 9673 Dihedral : 21.641 179.054 33121 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 0.89 % Allowed : 2.42 % Favored : 96.69 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.38 % Twisted General : 0.58 % 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: -2.71 (0.11), residues: 4850 helix: -1.65 (0.09), residues: 2232 sheet: -0.68 (0.21), residues: 579 loop : -2.19 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP j 177 HIS 0.017 0.003 HIS e 262 PHE 0.060 0.005 PHE j 166 TYR 0.079 0.005 TYR w 67 ARG 0.033 0.002 ARG N 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 803 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8126 (m-40) cc_final: 0.7707 (m-40) REVERT: C 486 GLU cc_start: 0.7926 (pm20) cc_final: 0.7707 (tm-30) REVERT: C 893 ARG cc_start: 0.5173 (ttm170) cc_final: 0.4952 (mmt90) REVERT: C 902 PHE cc_start: 0.8774 (t80) cc_final: 0.8389 (t80) REVERT: L 159 LYS cc_start: 0.3379 (pttp) cc_final: 0.3045 (tptp) REVERT: M 167 GLU cc_start: 0.0003 (mm-30) cc_final: -0.0564 (tm-30) REVERT: M 193 MET cc_start: 0.1842 (tmm) cc_final: -0.0728 (mtt) REVERT: M 230 LEU cc_start: 0.5779 (tp) cc_final: 0.4866 (tp) REVERT: O 325 LEU cc_start: 0.6873 (pt) cc_final: 0.6624 (pt) REVERT: O 470 MET cc_start: 0.7470 (mmp) cc_final: 0.6897 (tmm) REVERT: O 505 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7325 (mtm-85) REVERT: P 43 LEU cc_start: 0.8595 (tt) cc_final: 0.8122 (mt) REVERT: P 46 MET cc_start: 0.8429 (ppp) cc_final: 0.8070 (mtm) REVERT: P 299 ASP cc_start: 0.8039 (m-30) cc_final: 0.7794 (p0) REVERT: p 71 TYR cc_start: 0.6296 (m-80) cc_final: 0.6087 (m-80) REVERT: w 111 THR cc_start: 0.7106 (m) cc_final: 0.6841 (m) REVERT: w 113 VAL cc_start: 0.8985 (t) cc_final: 0.8715 (t) REVERT: w 114 GLU cc_start: 0.8327 (mp0) cc_final: 0.8037 (mp0) REVERT: w 137 GLN cc_start: 0.8126 (pp30) cc_final: 0.7837 (tm-30) REVERT: a 177 MET cc_start: 0.1910 (mpp) cc_final: 0.1690 (mpp) REVERT: b 133 MET cc_start: 0.7018 (mtm) cc_final: 0.6777 (mtm) REVERT: b 137 MET cc_start: 0.7053 (mtt) cc_final: 0.6432 (mtt) REVERT: b 192 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7546 (mmt180) REVERT: b 243 CYS cc_start: 0.8694 (m) cc_final: 0.8416 (m) REVERT: b 273 LEU cc_start: 0.8625 (mt) cc_final: 0.8095 (tp) REVERT: b 395 ASN cc_start: 0.8517 (p0) cc_final: 0.7892 (t0) REVERT: o 205 ILE cc_start: 0.8678 (pt) cc_final: 0.8413 (pt) REVERT: o 282 GLU cc_start: 0.8541 (pp20) cc_final: 0.8339 (pp20) REVERT: z 58 LYS cc_start: 0.7318 (pttp) cc_final: 0.6870 (mmmt) REVERT: z 92 GLN cc_start: 0.1412 (tp40) cc_final: 0.1206 (tp40) REVERT: z 103 GLN cc_start: 0.8724 (tp40) cc_final: 0.8402 (pt0) REVERT: v 124 LEU cc_start: 0.8611 (tp) cc_final: 0.8269 (tp) REVERT: q 31 LYS cc_start: 0.8839 (tptm) cc_final: 0.8579 (tptm) REVERT: q 170 GLU cc_start: 0.7158 (tp30) cc_final: 0.6920 (tp30) REVERT: h 225 LEU cc_start: 0.9598 (tp) cc_final: 0.9312 (tp) REVERT: h 239 CYS cc_start: 0.9012 (m) cc_final: 0.8698 (m) REVERT: h 301 ASN cc_start: 0.7889 (t0) cc_final: 0.6897 (t0) REVERT: h 302 MET cc_start: 0.7410 (ttm) cc_final: 0.6932 (tpp) REVERT: k 153 VAL cc_start: 0.1502 (OUTLIER) cc_final: 0.1231 (m) REVERT: k 154 VAL cc_start: 0.3494 (OUTLIER) cc_final: 0.3290 (m) REVERT: j 120 GLN cc_start: 0.4844 (tm-30) cc_final: 0.4072 (tt0) REVERT: n 22 MET cc_start: 0.3539 (ttt) cc_final: 0.3161 (ppp) REVERT: n 38 LYS cc_start: 0.4378 (mtmm) cc_final: 0.4065 (tptt) REVERT: n 90 LEU cc_start: 0.4202 (OUTLIER) cc_final: 0.3715 (mp) REVERT: n 95 ILE cc_start: 0.6545 (mt) cc_final: 0.6209 (mm) REVERT: g 192 MET cc_start: 0.5562 (mmp) cc_final: 0.3817 (pmm) REVERT: x 123 MET cc_start: 0.0537 (mtm) cc_final: -0.1022 (ttt) outliers start: 34 outliers final: 12 residues processed: 835 average time/residue: 0.6992 time to fit residues: 960.7453 Evaluate side-chains 533 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 518 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 629 optimal weight: 0.6980 chunk 565 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 381 optimal weight: 40.0000 chunk 302 optimal weight: 40.0000 chunk 584 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 355 optimal weight: 8.9990 chunk 435 optimal weight: 9.9990 chunk 677 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 271 HIS O 370 HIS O 394 ASN O 398 GLN O 419 GLN P 406 GLN f 63 HIS ** p 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 364 GLN ** b 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 417 HIS e 267 HIS v 101 GLN l 87 GLN h 15 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 264 HIS ** k 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 197 GLN ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 31 ASN s 65 HIS ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 281 GLN x 295 GLN c 145 GLN c 146 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 73744 Z= 0.312 Angle : 0.843 11.555 105551 Z= 0.422 Chirality : 0.043 0.288 13168 Planarity : 0.007 0.089 9673 Dihedral : 22.533 178.252 24242 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.31 % Favored : 93.53 % Rotamer: Outliers : 0.45 % Allowed : 6.83 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.78 (0.11), residues: 4850 helix: -0.55 (0.10), residues: 2317 sheet: -0.60 (0.21), residues: 564 loop : -2.04 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP s 6 HIS 0.011 0.002 HIS w 49 PHE 0.027 0.003 PHE C 908 TYR 0.034 0.003 TYR f 31 ARG 0.013 0.001 ARG w 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 631 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8071 (m-40) cc_final: 0.7725 (m-40) REVERT: C 325 LEU cc_start: 0.9007 (tp) cc_final: 0.8788 (tt) REVERT: C 593 LEU cc_start: 0.8666 (mm) cc_final: 0.8156 (pp) REVERT: C 893 ARG cc_start: 0.5189 (ttm170) cc_final: 0.4979 (mmt90) REVERT: C 932 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7222 (tp) REVERT: C 933 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7296 (mmp80) REVERT: L 157 VAL cc_start: 0.1781 (t) cc_final: 0.1547 (p) REVERT: M 127 VAL cc_start: 0.1799 (t) cc_final: 0.1572 (t) REVERT: M 167 GLU cc_start: 0.0362 (mm-30) cc_final: -0.0302 (tm-30) REVERT: M 230 LEU cc_start: 0.5579 (tp) cc_final: 0.4885 (tp) REVERT: O 277 ASP cc_start: 0.8546 (m-30) cc_final: 0.8317 (p0) REVERT: O 474 MET cc_start: 0.6814 (mmm) cc_final: 0.6364 (mmt) REVERT: P 43 LEU cc_start: 0.8683 (tt) cc_final: 0.8270 (mp) REVERT: P 69 LEU cc_start: 0.9268 (tp) cc_final: 0.9067 (tp) REVERT: p 33 LEU cc_start: 0.6550 (mm) cc_final: 0.6260 (mm) REVERT: r 242 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7460 (tp) REVERT: r 243 GLU cc_start: 0.7055 (mp0) cc_final: 0.6728 (mp0) REVERT: w 67 TYR cc_start: 0.8273 (m-80) cc_final: 0.7959 (m-80) REVERT: w 77 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8767 (mttt) REVERT: w 105 ARG cc_start: 0.7293 (ptt180) cc_final: 0.5782 (tmm-80) REVERT: w 129 GLN cc_start: 0.8653 (tm-30) cc_final: 0.7720 (tm-30) REVERT: w 172 ASN cc_start: 0.8034 (m110) cc_final: 0.7547 (m110) REVERT: a 75 LEU cc_start: 0.6910 (mp) cc_final: 0.6668 (mp) REVERT: a 155 LEU cc_start: 0.8369 (tt) cc_final: 0.8040 (tt) REVERT: b 268 MET cc_start: 0.8245 (tpt) cc_final: 0.7993 (tpt) REVERT: o 151 MET cc_start: 0.8186 (mmm) cc_final: 0.7081 (mmm) REVERT: o 176 MET cc_start: 0.8512 (ttm) cc_final: 0.8083 (ttm) REVERT: o 267 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: o 268 ASP cc_start: 0.8070 (t0) cc_final: 0.7815 (t0) REVERT: z 58 LYS cc_start: 0.7383 (pttp) cc_final: 0.6669 (mmmt) REVERT: z 92 GLN cc_start: 0.1707 (tp40) cc_final: 0.1477 (tp40) REVERT: v 124 LEU cc_start: 0.8570 (tp) cc_final: 0.8318 (tp) REVERT: q 31 LYS cc_start: 0.8920 (tptm) cc_final: 0.8645 (tptm) REVERT: h 247 ILE cc_start: 0.9178 (pt) cc_final: 0.8913 (pt) REVERT: h 251 MET cc_start: 0.8894 (pmm) cc_final: 0.8435 (pmm) REVERT: j 255 ARG cc_start: 0.4386 (ttm110) cc_final: 0.3780 (mpt180) REVERT: n 22 MET cc_start: 0.3189 (ttt) cc_final: 0.2279 (ppp) REVERT: n 38 LYS cc_start: 0.4178 (mtmm) cc_final: 0.3355 (tptt) REVERT: u 72 THR cc_start: -0.0042 (OUTLIER) cc_final: -0.0455 (m) REVERT: g 192 MET cc_start: 0.5739 (mmp) cc_final: 0.4203 (pmm) REVERT: g 250 GLU cc_start: 0.1733 (mt-10) cc_final: 0.0843 (pt0) REVERT: i 314 HIS cc_start: 0.2364 (t70) cc_final: 0.1978 (t70) REVERT: i 422 TRP cc_start: 0.2727 (p90) cc_final: 0.2193 (p90) REVERT: x 123 MET cc_start: 0.1861 (mtm) cc_final: 0.0173 (ttt) outliers start: 17 outliers final: 3 residues processed: 644 average time/residue: 0.6869 time to fit residues: 738.0765 Evaluate side-chains 483 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 476 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 40.0000 chunk 210 optimal weight: 10.0000 chunk 563 optimal weight: 5.9990 chunk 461 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 678 optimal weight: 20.0000 chunk 733 optimal weight: 0.1980 chunk 604 optimal weight: 4.9990 chunk 673 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 544 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 394 ASN O 398 GLN ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 249 ASN w 115 GLN w 172 ASN ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 187 ASN x 295 GLN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 73744 Z= 0.225 Angle : 0.711 12.189 105551 Z= 0.357 Chirality : 0.039 0.252 13168 Planarity : 0.005 0.085 9673 Dihedral : 22.340 177.583 24242 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.60 % Favored : 93.30 % Rotamer: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.22 (0.12), residues: 4850 helix: 0.05 (0.10), residues: 2311 sheet: -0.45 (0.22), residues: 553 loop : -1.91 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 233 HIS 0.012 0.001 HIS b 142 PHE 0.026 0.002 PHE s 87 TYR 0.027 0.002 TYR f 31 ARG 0.031 0.001 ARG h 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 641 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8239 (m-40) cc_final: 0.7686 (m-40) REVERT: C 325 LEU cc_start: 0.9064 (tp) cc_final: 0.8830 (tt) REVERT: C 951 THR cc_start: 0.8721 (m) cc_final: 0.8499 (m) REVERT: L 157 VAL cc_start: 0.1507 (t) cc_final: 0.1123 (p) REVERT: M 167 GLU cc_start: 0.1091 (mm-30) cc_final: 0.0695 (tm-30) REVERT: O 500 GLN cc_start: 0.8960 (pm20) cc_final: 0.8465 (tt0) REVERT: P 111 TYR cc_start: 0.7921 (t80) cc_final: 0.7685 (t80) REVERT: P 299 ASP cc_start: 0.8197 (m-30) cc_final: 0.7994 (m-30) REVERT: P 406 GLN cc_start: 0.7058 (tp40) cc_final: 0.6739 (tp-100) REVERT: d 379 LEU cc_start: 0.8471 (tp) cc_final: 0.7955 (tt) REVERT: p 33 LEU cc_start: 0.6403 (mm) cc_final: 0.6108 (mm) REVERT: w 105 ARG cc_start: 0.7252 (ptt180) cc_final: 0.6888 (ptp90) REVERT: w 129 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7799 (tm-30) REVERT: w 172 ASN cc_start: 0.8072 (m-40) cc_final: 0.7577 (m110) REVERT: a 102 ASN cc_start: 0.7950 (t0) cc_final: 0.6811 (t0) REVERT: a 155 LEU cc_start: 0.8631 (tt) cc_final: 0.8332 (tt) REVERT: e 264 LEU cc_start: 0.8945 (mt) cc_final: 0.8575 (mt) REVERT: o 151 MET cc_start: 0.8302 (mmm) cc_final: 0.7151 (mmm) REVERT: o 203 TYR cc_start: 0.8895 (t80) cc_final: 0.8674 (t80) REVERT: o 282 GLU cc_start: 0.8568 (pp20) cc_final: 0.8249 (pp20) REVERT: z 58 LYS cc_start: 0.7398 (pttp) cc_final: 0.6801 (mmmt) REVERT: z 59 LEU cc_start: 0.8311 (mm) cc_final: 0.8076 (mt) REVERT: q 31 LYS cc_start: 0.8960 (tptm) cc_final: 0.8619 (tptm) REVERT: l 122 ARG cc_start: 0.3351 (ptt180) cc_final: 0.1066 (tpt170) REVERT: h 115 MET cc_start: 0.7820 (tmm) cc_final: 0.7577 (tmm) REVERT: h 213 LYS cc_start: 0.8531 (tptp) cc_final: 0.8289 (mmmt) REVERT: j 255 ARG cc_start: 0.4658 (ttm110) cc_final: 0.4061 (mpt180) REVERT: n 22 MET cc_start: 0.2891 (ttt) cc_final: 0.1958 (ppp) REVERT: g 192 MET cc_start: 0.5925 (mmp) cc_final: 0.4690 (pmm) REVERT: i 314 HIS cc_start: 0.2659 (t70) cc_final: 0.2332 (t70) REVERT: x 123 MET cc_start: 0.1299 (mtm) cc_final: -0.0284 (ttt) REVERT: c 253 TRP cc_start: 0.6544 (m-10) cc_final: 0.6043 (m-10) outliers start: 6 outliers final: 3 residues processed: 646 average time/residue: 0.6878 time to fit residues: 744.4383 Evaluate side-chains 481 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 478 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 7.9990 chunk 510 optimal weight: 7.9990 chunk 352 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 323 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 681 optimal weight: 0.9980 chunk 721 optimal weight: 0.1980 chunk 355 optimal weight: 10.0000 chunk 645 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 291 HIS O 370 HIS O 398 GLN ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 115 GLN w 172 ASN ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 225 HIS ** b 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN h 64 GLN ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 45 ASN x 295 GLN x 461 HIS ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 127 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 73744 Z= 0.188 Angle : 0.654 11.479 105551 Z= 0.328 Chirality : 0.037 0.239 13168 Planarity : 0.005 0.059 9673 Dihedral : 22.168 177.295 24242 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.94 % Favored : 93.96 % Rotamer: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.12), residues: 4850 helix: 0.40 (0.11), residues: 2313 sheet: -0.29 (0.22), residues: 543 loop : -1.78 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 899 HIS 0.011 0.001 HIS b 142 PHE 0.023 0.002 PHE C 908 TYR 0.030 0.002 TYR c 167 ARG 0.009 0.001 ARG h 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 618 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8253 (m-40) cc_final: 0.7756 (m-40) REVERT: L 157 VAL cc_start: 0.1599 (t) cc_final: 0.1152 (p) REVERT: M 167 GLU cc_start: 0.1127 (mm-30) cc_final: 0.0665 (tm-30) REVERT: O 291 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.6168 (p90) REVERT: O 294 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6608 (tm-30) REVERT: d 341 MET cc_start: 0.7509 (mmm) cc_final: 0.7210 (mmt) REVERT: f 76 ILE cc_start: 0.9406 (mm) cc_final: 0.9145 (mm) REVERT: p 33 LEU cc_start: 0.6640 (mm) cc_final: 0.6335 (mm) REVERT: p 71 TYR cc_start: 0.5870 (t80) cc_final: 0.5480 (t80) REVERT: w 67 TYR cc_start: 0.8051 (m-80) cc_final: 0.7810 (m-80) REVERT: w 105 ARG cc_start: 0.7228 (ptt180) cc_final: 0.5672 (tmm-80) REVERT: w 129 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7715 (tm-30) REVERT: a 75 LEU cc_start: 0.7106 (mp) cc_final: 0.6880 (mp) REVERT: a 102 ASN cc_start: 0.7716 (t0) cc_final: 0.6863 (t0) REVERT: a 155 LEU cc_start: 0.8563 (tt) cc_final: 0.8309 (tt) REVERT: a 230 MET cc_start: -0.1830 (mmt) cc_final: -0.2123 (mmt) REVERT: o 151 MET cc_start: 0.8306 (mmm) cc_final: 0.7281 (mmm) REVERT: o 176 MET cc_start: 0.8315 (ttm) cc_final: 0.8042 (ttm) REVERT: o 181 ILE cc_start: 0.9032 (mm) cc_final: 0.8693 (mm) REVERT: o 282 GLU cc_start: 0.8553 (pp20) cc_final: 0.8301 (pp20) REVERT: z 58 LYS cc_start: 0.7374 (pttp) cc_final: 0.6780 (mmmt) REVERT: z 107 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8101 (tm-30) REVERT: q 31 LYS cc_start: 0.8908 (tptm) cc_final: 0.8543 (tptm) REVERT: l 122 ARG cc_start: 0.3738 (ptt180) cc_final: 0.1191 (tpt170) REVERT: h 251 MET cc_start: 0.8685 (pmm) cc_final: 0.8230 (pmm) REVERT: j 255 ARG cc_start: 0.4726 (ttm110) cc_final: 0.4160 (mpt180) REVERT: n 22 MET cc_start: 0.2638 (ttt) cc_final: 0.1752 (ppp) REVERT: g 192 MET cc_start: 0.5740 (mmp) cc_final: 0.4223 (pmm) REVERT: x 123 MET cc_start: 0.1218 (mtm) cc_final: -0.0163 (ttt) REVERT: c 253 TRP cc_start: 0.6390 (m-10) cc_final: 0.6108 (m-10) outliers start: 4 outliers final: 1 residues processed: 620 average time/residue: 0.6685 time to fit residues: 698.6906 Evaluate side-chains 471 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 469 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 7.9990 chunk 409 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 536 optimal weight: 9.9990 chunk 297 optimal weight: 50.0000 chunk 615 optimal weight: 0.9990 chunk 498 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 368 optimal weight: 30.0000 chunk 647 optimal weight: 50.0000 chunk 181 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN M 176 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 394 ASN O 398 GLN O 440 HIS ** P 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 123 HIS w 172 ASN ** b 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 273 HIS ** o 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN h 64 GLN ** h 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 ASN ** s 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 73744 Z= 0.357 Angle : 0.862 11.476 105551 Z= 0.429 Chirality : 0.043 0.272 13168 Planarity : 0.007 0.096 9673 Dihedral : 22.415 173.218 24242 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.39 % Favored : 91.53 % Rotamer: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4850 helix: -0.04 (0.10), residues: 2315 sheet: -0.60 (0.21), residues: 563 loop : -1.98 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP b 235 HIS 0.016 0.002 HIS b 142 PHE 0.041 0.003 PHE c 185 TYR 0.033 0.003 TYR o 129 ARG 0.028 0.001 ARG h 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 566 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8188 (m-40) cc_final: 0.7688 (m-40) REVERT: L 157 VAL cc_start: 0.1460 (t) cc_final: 0.1006 (p) REVERT: L 186 GLU cc_start: 0.4837 (tp30) cc_final: 0.4125 (mt-10) REVERT: M 167 GLU cc_start: 0.1346 (mm-30) cc_final: 0.0370 (tm-30) REVERT: O 342 LEU cc_start: 0.7628 (pp) cc_final: 0.7210 (tt) REVERT: O 500 GLN cc_start: 0.9119 (pm20) cc_final: 0.8714 (pm20) REVERT: P 33 LEU cc_start: 0.8871 (mp) cc_final: 0.8565 (tt) REVERT: P 111 TYR cc_start: 0.7826 (t80) cc_final: 0.7542 (t80) REVERT: P 317 ASP cc_start: 0.8435 (m-30) cc_final: 0.8190 (m-30) REVERT: d 293 LYS cc_start: 0.3887 (tttm) cc_final: 0.2002 (tptt) REVERT: w 67 TYR cc_start: 0.8236 (m-80) cc_final: 0.8014 (m-80) REVERT: w 105 ARG cc_start: 0.7400 (ptt180) cc_final: 0.5658 (tmm-80) REVERT: w 129 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8131 (tm-30) REVERT: w 172 ASN cc_start: 0.8261 (m-40) cc_final: 0.7834 (m110) REVERT: o 151 MET cc_start: 0.8282 (mmm) cc_final: 0.7153 (mmm) REVERT: q 31 LYS cc_start: 0.9078 (tptm) cc_final: 0.8713 (tptm) REVERT: l 17 GLN cc_start: 0.4579 (tp-100) cc_final: 0.3772 (tp40) REVERT: l 122 ARG cc_start: 0.3686 (ptt180) cc_final: 0.1297 (tpt170) REVERT: h 96 ASP cc_start: 0.8865 (p0) cc_final: 0.8586 (p0) REVERT: h 247 ILE cc_start: 0.9118 (pt) cc_final: 0.8828 (pt) REVERT: h 251 MET cc_start: 0.8832 (pmm) cc_final: 0.8357 (pmm) REVERT: j 255 ARG cc_start: 0.5221 (ttm110) cc_final: 0.4394 (mpt180) REVERT: m 76 GLU cc_start: 0.2832 (OUTLIER) cc_final: 0.2490 (tp30) REVERT: n 22 MET cc_start: 0.2714 (ttt) cc_final: 0.1548 (ppp) REVERT: g 192 MET cc_start: 0.5957 (mmp) cc_final: 0.5188 (ptp) REVERT: x 123 MET cc_start: 0.1744 (mtm) cc_final: 0.0127 (ttt) REVERT: c 253 TRP cc_start: 0.6532 (m-10) cc_final: 0.6158 (m-10) outliers start: 4 outliers final: 2 residues processed: 570 average time/residue: 0.6563 time to fit residues: 635.6687 Evaluate side-chains 442 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 439 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 20.0000 chunk 649 optimal weight: 0.0020 chunk 142 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 721 optimal weight: 0.9980 chunk 599 optimal weight: 5.9990 chunk 334 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 238 optimal weight: 40.0000 chunk 378 optimal weight: 50.0000 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 GLN O 370 HIS O 503 GLN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 115 GLN w 123 HIS ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 25 HIS ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 GLN h 60 ASN h 64 GLN h 216 GLN ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 197 GLN n 17 ASN s 65 HIS ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 73744 Z= 0.219 Angle : 0.690 12.093 105551 Z= 0.346 Chirality : 0.038 0.271 13168 Planarity : 0.005 0.065 9673 Dihedral : 22.225 171.420 24242 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.12), residues: 4850 helix: 0.31 (0.10), residues: 2316 sheet: -0.38 (0.22), residues: 540 loop : -1.86 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP s 6 HIS 0.012 0.001 HIS b 142 PHE 0.038 0.002 PHE c 185 TYR 0.031 0.002 TYR c 167 ARG 0.030 0.001 ARG y 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.7979 (m-40) cc_final: 0.7375 (m-40) REVERT: L 157 VAL cc_start: 0.1398 (t) cc_final: 0.0961 (p) REVERT: M 167 GLU cc_start: 0.1374 (mm-30) cc_final: 0.0370 (tm-30) REVERT: O 294 GLN cc_start: 0.7621 (tm-30) cc_final: 0.6809 (tm-30) REVERT: O 342 LEU cc_start: 0.7736 (pp) cc_final: 0.7337 (tt) REVERT: P 391 ARG cc_start: 0.7826 (mtt180) cc_final: 0.6691 (tpt90) REVERT: d 293 LYS cc_start: 0.3985 (tttm) cc_final: 0.2345 (tptt) REVERT: f 76 ILE cc_start: 0.9505 (mm) cc_final: 0.9272 (mm) REVERT: w 67 TYR cc_start: 0.8169 (m-80) cc_final: 0.7879 (m-80) REVERT: w 105 ARG cc_start: 0.7180 (ptt180) cc_final: 0.5682 (tmm-80) REVERT: w 129 GLN cc_start: 0.8604 (tm-30) cc_final: 0.7755 (tm-30) REVERT: a 75 LEU cc_start: 0.7573 (mp) cc_final: 0.7314 (mp) REVERT: a 147 TYR cc_start: 0.7447 (t80) cc_final: 0.7172 (t80) REVERT: b 411 GLU cc_start: 0.8209 (mp0) cc_final: 0.7858 (mp0) REVERT: o 151 MET cc_start: 0.8494 (mmm) cc_final: 0.8016 (mmm) REVERT: o 181 ILE cc_start: 0.9086 (mm) cc_final: 0.8882 (mm) REVERT: o 261 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7195 (ttp80) REVERT: v 110 PHE cc_start: 0.7485 (t80) cc_final: 0.7261 (t80) REVERT: q 31 LYS cc_start: 0.9037 (tptm) cc_final: 0.8682 (tptm) REVERT: l 122 ARG cc_start: 0.3577 (ptt180) cc_final: 0.1132 (tpt170) REVERT: h 96 ASP cc_start: 0.8771 (p0) cc_final: 0.8456 (p0) REVERT: h 336 GLU cc_start: 0.8394 (pp20) cc_final: 0.8089 (mm-30) REVERT: n 22 MET cc_start: 0.2498 (ttt) cc_final: 0.1372 (ppp) REVERT: i 314 HIS cc_start: 0.2889 (t70) cc_final: 0.2441 (t70) REVERT: x 123 MET cc_start: 0.1769 (mtm) cc_final: 0.0133 (ttt) REVERT: c 253 TRP cc_start: 0.6367 (m-10) cc_final: 0.6112 (m-10) outliers start: 1 outliers final: 0 residues processed: 585 average time/residue: 0.7150 time to fit residues: 719.3748 Evaluate side-chains 457 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 527 optimal weight: 4.9990 chunk 408 optimal weight: 10.0000 chunk 607 optimal weight: 0.8980 chunk 403 optimal weight: 20.0000 chunk 719 optimal weight: 50.0000 chunk 449 optimal weight: 20.0000 chunk 438 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN L 236 GLN N 134 GLN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 394 ASN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 123 HIS ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 126 HIS k 128 GLN n 17 ASN n 85 HIS s 65 HIS ** s 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 73744 Z= 0.267 Angle : 0.730 11.447 105551 Z= 0.364 Chirality : 0.039 0.257 13168 Planarity : 0.005 0.082 9673 Dihedral : 22.234 172.251 24242 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.14 % Favored : 91.77 % Rotamer: Outliers : 0.08 % Allowed : 2.60 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.01 (0.12), residues: 4850 helix: 0.29 (0.10), residues: 2312 sheet: -0.46 (0.22), residues: 532 loop : -1.86 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 423 HIS 0.014 0.001 HIS b 142 PHE 0.033 0.002 PHE c 185 TYR 0.036 0.002 TYR o 129 ARG 0.013 0.001 ARG g 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 556 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8066 (m-40) cc_final: 0.7490 (m-40) REVERT: L 157 VAL cc_start: 0.1908 (t) cc_final: 0.1479 (p) REVERT: M 167 GLU cc_start: 0.1615 (mm-30) cc_final: 0.0398 (tm-30) REVERT: O 276 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7361 (mp10) REVERT: O 342 LEU cc_start: 0.7782 (pp) cc_final: 0.7296 (tt) REVERT: O 474 MET cc_start: 0.6560 (mmm) cc_final: 0.5627 (mmm) REVERT: P 46 MET cc_start: 0.8608 (ppp) cc_final: 0.8351 (ppp) REVERT: P 199 MET cc_start: 0.8507 (ttm) cc_final: 0.8260 (ttm) REVERT: P 391 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6729 (tpt90) REVERT: d 293 LYS cc_start: 0.4021 (tttm) cc_final: 0.2279 (tptt) REVERT: w 105 ARG cc_start: 0.7224 (ptt180) cc_final: 0.5482 (tmm-80) REVERT: w 129 GLN cc_start: 0.8696 (tm-30) cc_final: 0.7992 (tm-30) REVERT: a 147 TYR cc_start: 0.7617 (t80) cc_final: 0.7345 (t80) REVERT: b 411 GLU cc_start: 0.8221 (mp0) cc_final: 0.7933 (mp0) REVERT: b 430 ILE cc_start: 0.8610 (tp) cc_final: 0.8410 (tp) REVERT: o 151 MET cc_start: 0.8511 (mmm) cc_final: 0.7947 (mmm) REVERT: q 31 LYS cc_start: 0.8988 (tptm) cc_final: 0.8609 (tptm) REVERT: l 122 ARG cc_start: 0.3321 (ptt180) cc_final: 0.0937 (tpt170) REVERT: h 96 ASP cc_start: 0.8793 (p0) cc_final: 0.8498 (p0) REVERT: h 251 MET cc_start: 0.8894 (pmm) cc_final: 0.8437 (pmm) REVERT: h 301 ASN cc_start: 0.8305 (t0) cc_final: 0.7458 (t0) REVERT: h 302 MET cc_start: 0.7705 (ttp) cc_final: 0.7397 (ttm) REVERT: n 22 MET cc_start: 0.2511 (ttt) cc_final: 0.1432 (ppp) REVERT: n 25 MET cc_start: 0.4076 (ptt) cc_final: 0.3355 (ptt) REVERT: x 123 MET cc_start: 0.1945 (mtm) cc_final: 0.0252 (ttt) REVERT: c 251 LYS cc_start: 0.6241 (mppt) cc_final: 0.5789 (mppt) REVERT: c 253 TRP cc_start: 0.6552 (m-10) cc_final: 0.6165 (m-10) outliers start: 3 outliers final: 1 residues processed: 559 average time/residue: 0.6639 time to fit residues: 631.8697 Evaluate side-chains 440 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 439 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 20.0000 chunk 287 optimal weight: 40.0000 chunk 429 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 141 optimal weight: 50.0000 chunk 139 optimal weight: 0.6980 chunk 457 optimal weight: 20.0000 chunk 489 optimal weight: 1.9990 chunk 355 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 565 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 398 GLN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 115 GLN w 123 HIS w 172 ASN a 116 HIS ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 ASN ** s 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN c 148 HIS ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 73744 Z= 0.191 Angle : 0.657 11.843 105551 Z= 0.328 Chirality : 0.037 0.256 13168 Planarity : 0.005 0.062 9673 Dihedral : 22.091 171.035 24242 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 0.03 % Allowed : 1.26 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.75 (0.12), residues: 4850 helix: 0.57 (0.11), residues: 2300 sheet: -0.37 (0.22), residues: 540 loop : -1.79 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP q 145 HIS 0.013 0.001 HIS b 142 PHE 0.023 0.002 PHE o 198 TYR 0.028 0.002 TYR f 31 ARG 0.010 0.001 ARG e 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 587 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.7999 (m-40) cc_final: 0.7561 (m-40) REVERT: L 157 VAL cc_start: 0.1845 (t) cc_final: 0.1404 (p) REVERT: M 167 GLU cc_start: 0.1655 (mm-30) cc_final: 0.0450 (tm-30) REVERT: O 276 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7444 (pm20) REVERT: O 294 GLN cc_start: 0.7683 (tm-30) cc_final: 0.6885 (tm-30) REVERT: O 338 LEU cc_start: 0.9159 (mm) cc_final: 0.8895 (mm) REVERT: O 342 LEU cc_start: 0.7720 (pp) cc_final: 0.7291 (tt) REVERT: P 199 MET cc_start: 0.8403 (ttm) cc_final: 0.8188 (ttm) REVERT: P 391 ARG cc_start: 0.7789 (mtt180) cc_final: 0.6710 (tpt90) REVERT: d 293 LYS cc_start: 0.3897 (tttm) cc_final: 0.2314 (tptt) REVERT: f 76 ILE cc_start: 0.9475 (mm) cc_final: 0.9262 (mm) REVERT: w 105 ARG cc_start: 0.7177 (ptt180) cc_final: 0.5492 (tmm-80) REVERT: w 109 VAL cc_start: 0.9175 (m) cc_final: 0.8933 (t) REVERT: w 129 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8330 (tm-30) REVERT: a 75 LEU cc_start: 0.7605 (mp) cc_final: 0.7340 (mp) REVERT: a 147 TYR cc_start: 0.7528 (t80) cc_final: 0.7314 (t80) REVERT: a 230 MET cc_start: -0.1637 (mmt) cc_final: -0.1944 (mmt) REVERT: b 175 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7086 (mtp180) REVERT: b 411 GLU cc_start: 0.8086 (mp0) cc_final: 0.7829 (mp0) REVERT: e 264 LEU cc_start: 0.8776 (mt) cc_final: 0.8359 (mt) REVERT: o 151 MET cc_start: 0.8570 (mmm) cc_final: 0.8053 (mmm) REVERT: o 182 MET cc_start: 0.8293 (mtt) cc_final: 0.7947 (mtt) REVERT: z 109 GLN cc_start: 0.8278 (pp30) cc_final: 0.7767 (pp30) REVERT: z 113 GLN cc_start: 0.7723 (mp-120) cc_final: 0.7220 (mm-40) REVERT: q 31 LYS cc_start: 0.8948 (tptm) cc_final: 0.8723 (tptm) REVERT: l 107 LEU cc_start: 0.7870 (mt) cc_final: 0.7630 (mt) REVERT: l 122 ARG cc_start: 0.3050 (ptt180) cc_final: 0.0667 (tpt170) REVERT: h 115 MET cc_start: 0.7803 (tmm) cc_final: 0.7578 (tmm) REVERT: h 165 ARG cc_start: 0.9101 (mtm110) cc_final: 0.8828 (mtm-85) REVERT: h 251 MET cc_start: 0.8933 (pmm) cc_final: 0.8536 (pmm) REVERT: h 301 ASN cc_start: 0.8171 (t0) cc_final: 0.7498 (t0) REVERT: n 22 MET cc_start: 0.2189 (ttt) cc_final: 0.1324 (ppp) REVERT: n 25 MET cc_start: 0.3692 (ptt) cc_final: 0.2974 (ptt) REVERT: i 314 HIS cc_start: 0.2644 (t70) cc_final: 0.2213 (t70) REVERT: x 123 MET cc_start: 0.1831 (mtm) cc_final: 0.0185 (ttt) REVERT: c 251 LYS cc_start: 0.6109 (mppt) cc_final: 0.5809 (mppt) REVERT: c 253 TRP cc_start: 0.6453 (m-10) cc_final: 0.6148 (m-10) outliers start: 1 outliers final: 0 residues processed: 588 average time/residue: 0.6621 time to fit residues: 660.3941 Evaluate side-chains 459 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 10.0000 chunk 688 optimal weight: 0.0070 chunk 628 optimal weight: 10.0000 chunk 670 optimal weight: 40.0000 chunk 403 optimal weight: 20.0000 chunk 291 optimal weight: 50.0000 chunk 526 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 605 optimal weight: 0.5980 chunk 633 optimal weight: 40.0000 chunk 667 optimal weight: 20.0000 overall best weight: 3.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 291 HIS O 394 ASN O 398 GLN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 123 HIS ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 85 ASN ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 ASN s 45 ASN ** s 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 73744 Z= 0.212 Angle : 0.675 12.771 105551 Z= 0.336 Chirality : 0.037 0.260 13168 Planarity : 0.005 0.069 9673 Dihedral : 22.038 172.109 24242 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 0.05 % Allowed : 1.13 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.71 (0.12), residues: 4850 helix: 0.61 (0.11), residues: 2308 sheet: -0.40 (0.22), residues: 532 loop : -1.77 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP z 44 HIS 0.019 0.001 HIS b 142 PHE 0.022 0.002 PHE v 92 TYR 0.033 0.002 TYR w 67 ARG 0.007 0.001 ARG e 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 568 time to evaluate : 4.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 ASN cc_start: 0.8009 (m-40) cc_final: 0.7609 (m-40) REVERT: L 157 VAL cc_start: 0.1997 (t) cc_final: 0.1698 (p) REVERT: M 167 GLU cc_start: 0.1689 (mm-30) cc_final: 0.0481 (tm-30) REVERT: O 294 GLN cc_start: 0.7768 (tm-30) cc_final: 0.6932 (tm-30) REVERT: P 299 ASP cc_start: 0.8326 (m-30) cc_final: 0.8106 (m-30) REVERT: P 391 ARG cc_start: 0.7755 (mtt180) cc_final: 0.6688 (tpt90) REVERT: d 293 LYS cc_start: 0.4002 (tttm) cc_final: 0.2339 (tptt) REVERT: w 105 ARG cc_start: 0.7240 (ptt180) cc_final: 0.5446 (tmm-80) REVERT: w 115 GLN cc_start: 0.7831 (pt0) cc_final: 0.7481 (pt0) REVERT: w 129 GLN cc_start: 0.8650 (tm-30) cc_final: 0.7706 (tm-30) REVERT: a 75 LEU cc_start: 0.7474 (mp) cc_final: 0.7205 (mp) REVERT: a 230 MET cc_start: -0.1576 (mmt) cc_final: -0.1852 (mmt) REVERT: b 175 ARG cc_start: 0.7481 (mtt90) cc_final: 0.6996 (mtp180) REVERT: e 264 LEU cc_start: 0.8815 (mt) cc_final: 0.8510 (mt) REVERT: o 132 GLN cc_start: 0.8335 (mp10) cc_final: 0.7963 (mp10) REVERT: o 151 MET cc_start: 0.8568 (mmm) cc_final: 0.7885 (mmm) REVERT: z 109 GLN cc_start: 0.8292 (pp30) cc_final: 0.7814 (pp30) REVERT: z 113 GLN cc_start: 0.7715 (mp-120) cc_final: 0.7230 (mm-40) REVERT: q 31 LYS cc_start: 0.8962 (tptm) cc_final: 0.8540 (tptm) REVERT: l 122 ARG cc_start: 0.2978 (ptt180) cc_final: 0.0688 (tpt170) REVERT: h 115 MET cc_start: 0.7906 (tmm) cc_final: 0.7647 (tmm) REVERT: h 251 MET cc_start: 0.8840 (pmm) cc_final: 0.8409 (pmm) REVERT: n 22 MET cc_start: 0.1896 (ttt) cc_final: 0.1457 (ppp) REVERT: n 25 MET cc_start: 0.3888 (ptt) cc_final: 0.3156 (ptt) REVERT: i 314 HIS cc_start: 0.2696 (t70) cc_final: 0.2266 (t70) REVERT: x 123 MET cc_start: 0.1812 (mtm) cc_final: 0.0171 (ttt) REVERT: c 251 LYS cc_start: 0.6227 (mppt) cc_final: 0.5820 (mppt) REVERT: c 253 TRP cc_start: 0.6669 (m-10) cc_final: 0.6452 (m-10) outliers start: 2 outliers final: 0 residues processed: 570 average time/residue: 0.6411 time to fit residues: 627.9204 Evaluate side-chains 452 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 20.0000 chunk 708 optimal weight: 40.0000 chunk 432 optimal weight: 20.0000 chunk 336 optimal weight: 8.9990 chunk 492 optimal weight: 0.0010 chunk 743 optimal weight: 6.9990 chunk 684 optimal weight: 50.0000 chunk 591 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 457 optimal weight: 20.0000 chunk 362 optimal weight: 20.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN O 370 HIS ** O 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 398 GLN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 123 HIS w 172 ASN ** b 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 GLN ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 GLN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 17 ASN ** s 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN x 383 ASN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 73744 Z= 0.404 Angle : 0.932 15.462 105551 Z= 0.463 Chirality : 0.046 0.315 13168 Planarity : 0.007 0.137 9673 Dihedral : 22.518 172.949 24242 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.36 % Favored : 90.54 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.62 (0.11), residues: 4850 helix: -0.25 (0.10), residues: 2298 sheet: -0.83 (0.21), residues: 550 loop : -2.09 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP b 423 HIS 0.032 0.003 HIS w 64 PHE 0.035 0.003 PHE e 272 TYR 0.035 0.003 TYR h 221 ARG 0.017 0.001 ARG w 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9700 Ramachandran restraints generated. 4850 Oldfield, 0 Emsley, 4850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 534 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 157 VAL cc_start: 0.2041 (t) cc_final: 0.1376 (p) REVERT: O 430 LEU cc_start: 0.8253 (tp) cc_final: 0.7996 (tp) REVERT: O 434 TRP cc_start: 0.7232 (m100) cc_final: 0.6564 (m100) REVERT: P 111 TYR cc_start: 0.7915 (t80) cc_final: 0.7613 (t80) REVERT: P 377 ARG cc_start: 0.8522 (mtt180) cc_final: 0.7265 (tmt170) REVERT: P 391 ARG cc_start: 0.7906 (mtt180) cc_final: 0.6867 (tpt90) REVERT: d 293 LYS cc_start: 0.3826 (tttm) cc_final: 0.1844 (tptt) REVERT: p 1 MET cc_start: 0.6112 (pmm) cc_final: 0.4332 (ptt) REVERT: w 105 ARG cc_start: 0.7370 (ptt180) cc_final: 0.5646 (tmm-80) REVERT: w 129 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8096 (tm-30) REVERT: a 70 ARG cc_start: 0.8084 (ppt170) cc_final: 0.6743 (tpt90) REVERT: a 86 LYS cc_start: 0.8555 (tppt) cc_final: 0.8134 (mptt) REVERT: a 93 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7129 (tm-30) REVERT: b 243 CYS cc_start: 0.8691 (m) cc_final: 0.8469 (m) REVERT: o 132 GLN cc_start: 0.8708 (mp10) cc_final: 0.8220 (mp10) REVERT: o 151 MET cc_start: 0.8539 (mmm) cc_final: 0.8166 (mpp) REVERT: o 214 TYR cc_start: 0.7288 (t80) cc_final: 0.6684 (t80) REVERT: q 31 LYS cc_start: 0.9049 (tptm) cc_final: 0.8831 (tptm) REVERT: l 91 MET cc_start: 0.6090 (ttp) cc_final: 0.5270 (ttp) REVERT: l 122 ARG cc_start: 0.2898 (ptt180) cc_final: 0.0525 (tpt170) REVERT: h 261 VAL cc_start: 0.8504 (p) cc_final: 0.8258 (p) REVERT: n 22 MET cc_start: 0.2017 (ttt) cc_final: 0.1495 (ppp) REVERT: n 25 MET cc_start: 0.4594 (ptt) cc_final: 0.3616 (ptt) REVERT: x 123 MET cc_start: 0.1852 (mtm) cc_final: 0.0229 (ttt) REVERT: x 469 ASN cc_start: 0.5649 (t0) cc_final: 0.5175 (m-40) REVERT: c 253 TRP cc_start: 0.6790 (m-10) cc_final: 0.6375 (m-10) outliers start: 1 outliers final: 0 residues processed: 535 average time/residue: 0.6547 time to fit residues: 599.8464 Evaluate side-chains 421 residues out of total 3904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 470 optimal weight: 5.9990 chunk 630 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 545 optimal weight: 8.9990 chunk 87 optimal weight: 40.0000 chunk 164 optimal weight: 9.9990 chunk 592 optimal weight: 3.9990 chunk 248 optimal weight: 40.0000 chunk 608 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 931 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 394 ASN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 313 GLN ** d 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 123 HIS ** b 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 85 ASN ** h 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 197 GLN n 17 ASN ** s 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 295 GLN ** c 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.138834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.117942 restraints weight = 325231.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.117151 restraints weight = 443107.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117941 restraints weight = 300185.498| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 73744 Z= 0.239 Angle : 0.739 12.533 105551 Z= 0.368 Chirality : 0.039 0.280 13168 Planarity : 0.005 0.081 9673 Dihedral : 22.270 171.629 24242 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.04 % Favored : 91.88 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4850 helix: 0.07 (0.10), residues: 2300 sheet: -0.71 (0.22), residues: 532 loop : -2.02 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP s 6 HIS 0.018 0.002 HIS b 413 PHE 0.023 0.002 PHE v 92 TYR 0.081 0.002 TYR a 147 ARG 0.021 0.001 ARG r 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11664.61 seconds wall clock time: 208 minutes 3.94 seconds (12483.94 seconds total)