Starting phenix.real_space_refine (version: dev) on Tue Feb 28 01:36:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/02_2023/7mei_23789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/02_2023/7mei_23789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/02_2023/7mei_23789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/02_2023/7mei_23789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/02_2023/7mei_23789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/02_2023/7mei_23789.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1453 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 39": "OE1" <-> "OE2" Residue "a GLU 76": "OE1" <-> "OE2" Residue "a ASP 85": "OD1" <-> "OD2" Residue "a PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 257": "NH1" <-> "NH2" Residue "a GLU 293": "OE1" <-> "OE2" Residue "a TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 500": "OE1" <-> "OE2" Residue "a ASP 526": "OD1" <-> "OD2" Residue "a ASP 592": "OD1" <-> "OD2" Residue "a GLU 593": "OE1" <-> "OE2" Residue "a ASP 602": "OD1" <-> "OD2" Residue "a PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 727": "OD1" <-> "OD2" Residue "a ARG 731": "NH1" <-> "NH2" Residue "a PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 791": "OD1" <-> "OD2" Residue "a PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 833": "OE1" <-> "OE2" Residue "a GLU 846": "OE1" <-> "OE2" Residue "a TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1005": "OE1" <-> "OE2" Residue "a TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 1206": "OD1" <-> "OD2" Residue "a GLU 1256": "OE1" <-> "OE2" Residue "a GLU 1307": "OE1" <-> "OE2" Residue "a GLU 1411": "OE1" <-> "OE2" Residue "b PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 61": "OD1" <-> "OD2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 183": "OE1" <-> "OE2" Residue "b TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 209": "OE1" <-> "OE2" Residue "b PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 332": "OD1" <-> "OD2" Residue "b PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 336": "NH1" <-> "NH2" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 398": "NH1" <-> "NH2" Residue "b PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 476": "NH1" <-> "NH2" Residue "b ASP 568": "OD1" <-> "OD2" Residue "b ARG 595": "NH1" <-> "NH2" Residue "b ARG 604": "NH1" <-> "NH2" Residue "b PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 629": "OD1" <-> "OD2" Residue "b TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 807": "NH1" <-> "NH2" Residue "b GLU 810": "OE1" <-> "OE2" Residue "b TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 872": "OE1" <-> "OE2" Residue "b GLU 924": "OE1" <-> "OE2" Residue "b GLU 945": "OE1" <-> "OE2" Residue "b PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 1190": "OD1" <-> "OD2" Residue "b TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 210": "OE1" <-> "OE2" Residue "c PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 124": "OE1" <-> "OE2" Residue "e GLU 6": "OE1" <-> "OE2" Residue "e GLU 40": "OE1" <-> "OE2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 169": "NH1" <-> "NH2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 119": "NH1" <-> "NH2" Residue "f ASP 145": "OD1" <-> "OD2" Residue "f GLU 149": "OE1" <-> "OE2" Residue "g PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 6": "OD1" <-> "OD2" Residue "g TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 118": "OD1" <-> "OD2" Residue "g ASP 135": "OD1" <-> "OD2" Residue "h GLU 27": "OE1" <-> "OE2" Residue "h GLU 106": "OE1" <-> "OE2" Residue "i ARG 30": "NH1" <-> "NH2" Residue "i ASP 72": "OD1" <-> "OD2" Residue "i PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 36": "OE1" <-> "OE2" Residue "k PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 33": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 874": "OD1" <-> "OD2" Residue "A TYR 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1135": "NH1" <-> "NH2" Residue "A ARG 1159": "NH1" <-> "NH2" Residue "A PHE 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1426": "OE1" <-> "OE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1004": "OE1" <-> "OE2" Residue "B GLU 1053": "OE1" <-> "OE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1101": "OD1" <-> "OD2" Residue "B GLU 1120": "OE1" <-> "OE2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1190": "OD1" <-> "OD2" Residue "B TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G ARG 58": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q ASP 132": "OD1" <-> "OD2" Residue "Q PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 100": "OD1" <-> "OD2" Residue "M TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 230": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69281 Number of models: 1 Model: "" Number of chains: 43 Chain: "N" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1519 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "O" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1524 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "a" Number of atoms: 11189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11189 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1355} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 9197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9197 Classifications: {'peptide': 1160} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'CIS': 12, 'PCIS': 2, 'PTRANS': 49, 'TRANS': 1096} Chain breaks: 8 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "d" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "f" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "g" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "h" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "i" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "j" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "k" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "l" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "r" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 11} Chain: "A" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11167 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1354} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 9227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9227 Classifications: {'peptide': 1166} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1103} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "Q" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1619 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1106 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3883 SG CYS a 110 143.101 89.974 132.080 1.00216.77 S ATOM 4188 SG CYS a 148 142.917 87.744 135.027 1.00265.00 S ATOM 4326 SG CYS a 167 143.261 91.067 134.548 1.00271.97 S ATOM 3554 SG CYS a 67 126.247 103.790 87.332 1.00242.80 S ATOM 3576 SG CYS a 70 127.947 104.231 86.113 1.00263.01 S ATOM 22954 SG CYS b1163 137.626 92.328 93.875 1.00771.81 S ATOM 22972 SG CYS b1166 136.101 94.287 96.768 1.00731.01 S ATOM 23097 SG CYS b1182 136.790 96.157 94.092 1.00879.94 S ATOM 23116 SG CYS b1185 138.927 94.473 97.078 1.00908.11 S ATOM 24076 SG CYS c 86 69.945 95.490 48.384 1.00652.87 S ATOM 24093 SG CYS c 88 71.597 98.265 50.169 1.00684.17 S ATOM 24126 SG CYS c 92 68.379 99.019 48.302 1.00633.55 S ATOM 24149 SG CYS c 95 68.698 97.094 51.719 1.00603.63 S ATOM 31775 SG CYS i 7 84.985 86.318 174.627 1.00606.34 S ATOM 31800 SG CYS i 10 86.706 88.767 172.133 1.00604.81 S ATOM 31966 SG CYS i 29 88.421 85.538 173.195 1.00592.83 S ATOM 31990 SG CYS i 32 87.811 88.226 175.798 1.00615.85 S ATOM 32317 SG CYS i 75 51.236 62.644 149.736 1.00999.99 S ATOM 32339 SG CYS i 78 49.640 64.668 151.653 1.00999.99 S ATOM 32555 SG CYS i 103 51.158 66.265 148.410 1.00999.99 S ATOM 32575 SG CYS i 106 53.415 65.413 151.439 1.00999.99 S ATOM 32703 SG CYS j 7 56.135 83.273 78.168 1.00416.77 S ATOM 32726 SG CYS j 10 54.938 82.468 74.776 1.00474.02 S ATOM 33006 SG CYS j 45 53.978 79.817 77.351 1.00511.53 S ATOM 33012 SG CYS j 46 52.452 83.105 76.612 1.00497.40 S ATOM 34156 SG CYS l 31 68.846 125.062 87.865 1.00283.35 S ATOM 34176 SG CYS l 34 65.722 126.606 87.732 1.00331.71 S ATOM 34280 SG CYS l 48 68.957 128.719 87.723 1.00280.24 S ATOM 34303 SG CYS l 51 67.076 127.079 90.872 1.00298.71 S ATOM 35614 SG CYS A 107 76.826 149.319 80.882 1.00250.70 S ATOM 35638 SG CYS A 110 74.863 149.330 80.371 1.00242.09 S ATOM 35943 SG CYS A 148 76.337 147.863 84.023 1.00294.76 S ATOM 36081 SG CYS A 167 75.422 146.045 80.155 1.00293.62 S ATOM 35309 SG CYS A 67 65.025 188.014 48.670 1.00231.64 S ATOM 35331 SG CYS A 70 62.878 187.237 50.949 1.00224.65 S ATOM 35384 SG CYS A 77 66.695 187.084 51.740 1.00202.98 S ATOM 54717 SG CYS B1163 57.914 181.039 64.831 1.00222.04 S ATOM 54735 SG CYS B1166 60.848 178.403 64.277 1.00229.02 S ATOM 54860 SG CYS B1182 59.730 179.977 60.924 1.00232.64 S ATOM 55839 SG CYS C 86 89.925 250.669 37.699 1.00323.13 S ATOM 55856 SG CYS C 88 90.001 247.301 35.931 1.00317.15 S ATOM 55889 SG CYS C 92 91.956 250.068 34.597 1.00296.54 S ATOM 55912 SG CYS C 95 93.131 248.452 37.800 1.00293.39 S ATOM 63534 SG CYS I 7 147.346 148.717 91.140 1.00276.12 S ATOM 63559 SG CYS I 10 144.878 149.094 88.041 1.00275.03 S ATOM 63725 SG CYS I 29 143.487 148.672 91.406 1.00273.60 S ATOM 63749 SG CYS I 32 145.614 145.848 89.918 1.00262.01 S ATOM 64076 SG CYS I 75 159.167 193.215 99.029 1.00273.06 S ATOM 64098 SG CYS I 78 160.746 193.033 97.924 1.00266.82 S ATOM 64334 SG CYS I 106 158.673 190.496 97.735 1.00279.11 S ATOM 64462 SG CYS J 7 117.432 239.389 57.241 1.00192.03 S ATOM 64485 SG CYS J 10 116.542 242.927 57.477 1.00191.68 S ATOM 64765 SG CYS J 45 118.172 241.609 60.548 1.00197.06 S ATOM 64771 SG CYS J 46 119.576 242.878 57.272 1.00203.76 S ATOM 65915 SG CYS L 31 113.628 210.553 21.511 1.00302.20 S ATOM 66039 SG CYS L 48 115.276 207.336 21.312 1.00309.77 S ATOM 66062 SG CYS L 51 118.041 209.737 21.576 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN a1801 " occ=0.95 residue: pdb="ZN ZN A1801 " occ=0.95 Time building chain proxies: 28.44, per 1000 atoms: 0.41 Number of scatterers: 69281 At special positions: 0 Unit cell: (195.48, 282.96, 193.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 16 29.99 S 374 16.00 P 179 15.00 Mg 4 11.99 O 13515 8.00 N 12103 7.00 C 43090 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: 23.59 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb=" ZN a1801 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 167 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 148 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 110 " pdb=" ZN a1802 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 67 " pdb="ZN ZN a1802 " - pdb=" NE2 HIS a 80 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 70 " pdb=" ZN b1301 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1166 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1185 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1182 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1163 " pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 88 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 95 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 92 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 86 " pdb=" ZN i 201 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 32 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 29 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 7 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 10 " pdb=" ZN i 202 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 78 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 75 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 106 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 103 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 10 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 46 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 45 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 7 " pdb=" ZN l 101 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 34 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 31 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 48 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 51 " Number of angles added : 63 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15566 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 82 sheets defined 37.0% alpha, 15.6% beta 60 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 15.60 Creating SS restraints... Processing helix chain 'a' and resid 23 through 31 Processing helix chain 'a' and resid 92 through 95 Processing helix chain 'a' and resid 96 through 105 Processing helix chain 'a' and resid 120 through 128 Processing helix chain 'a' and resid 132 through 142 Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 203 through 214 Processing helix chain 'a' and resid 215 through 222 removed outlier: 3.715A pdb=" N PHE a 219 " --> pdb=" O SER a 215 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR a 220 " --> pdb=" O VAL a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 235 removed outlier: 3.581A pdb=" N ILE a 235 " --> pdb=" O GLU a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 247 removed outlier: 3.551A pdb=" N VAL a 246 " --> pdb=" O PRO a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 282 removed outlier: 3.529A pdb=" N PHE a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 288 through 305 Processing helix chain 'a' and resid 324 through 330 Processing helix chain 'a' and resid 368 through 374 Processing helix chain 'a' and resid 384 through 395 Processing helix chain 'a' and resid 471 through 473 No H-bonds generated for 'chain 'a' and resid 471 through 473' Processing helix chain 'a' and resid 474 through 479 removed outlier: 3.634A pdb=" N TYR a 478 " --> pdb=" O VAL a 474 " (cutoff:3.500A) Processing helix chain 'a' and resid 494 through 502 Processing helix chain 'a' and resid 506 through 510 Processing helix chain 'a' and resid 524 through 535 Processing helix chain 'a' and resid 542 through 553 Processing helix chain 'a' and resid 573 through 581 removed outlier: 3.929A pdb=" N VAL a 580 " --> pdb=" O GLN a 576 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA a 581 " --> pdb=" O ILE a 577 " (cutoff:3.500A) Processing helix chain 'a' and resid 618 through 623 Processing helix chain 'a' and resid 628 through 637 Processing helix chain 'a' and resid 640 through 661 removed outlier: 3.933A pdb=" N LYS a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE a 655 " --> pdb=" O LYS a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 665 through 669 Processing helix chain 'a' and resid 672 through 699 Processing helix chain 'a' and resid 709 through 737 Processing helix chain 'a' and resid 741 through 749 removed outlier: 3.902A pdb=" N GLN a 745 " --> pdb=" O ASN a 741 " (cutoff:3.500A) Processing helix chain 'a' and resid 754 through 763 Processing helix chain 'a' and resid 809 through 843 removed outlier: 4.724A pdb=" N ALA a 832 " --> pdb=" O ALA a 828 " (cutoff:3.500A) Processing helix chain 'a' and resid 867 through 871 Processing helix chain 'a' and resid 889 through 898 Processing helix chain 'a' and resid 909 through 913 Processing helix chain 'a' and resid 922 through 947 Processing helix chain 'a' and resid 960 through 970 Processing helix chain 'a' and resid 982 through 997 removed outlier: 4.200A pdb=" N LYS a 991 " --> pdb=" O VAL a 987 " (cutoff:3.500A) Processing helix chain 'a' and resid 1004 through 1015 removed outlier: 3.627A pdb=" N GLN a1008 " --> pdb=" O ASN a1004 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) Processing helix chain 'a' and resid 1015 through 1026 Processing helix chain 'a' and resid 1027 through 1034 Processing helix chain 'a' and resid 1038 through 1056 Processing helix chain 'a' and resid 1063 through 1078 Proline residue: a1075 - end of helix removed outlier: 3.903A pdb=" N GLN a1078 " --> pdb=" O GLU a1074 " (cutoff:3.500A) Processing helix chain 'a' and resid 1096 through 1106 Processing helix chain 'a' and resid 1127 through 1139 Processing helix chain 'a' and resid 1142 through 1146 removed outlier: 3.568A pdb=" N VAL a1146 " --> pdb=" O THR a1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1142 through 1146' Processing helix chain 'a' and resid 1167 through 1173 Processing helix chain 'a' and resid 1198 through 1205 Processing helix chain 'a' and resid 1208 through 1220 removed outlier: 3.746A pdb=" N PHE a1220 " --> pdb=" O ILE a1216 " (cutoff:3.500A) Processing helix chain 'a' and resid 1255 through 1269 removed outlier: 3.511A pdb=" N MET a1259 " --> pdb=" O GLU a1255 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU a1269 " --> pdb=" O ASN a1265 " (cutoff:3.500A) Processing helix chain 'a' and resid 1315 through 1319 Processing helix chain 'a' and resid 1331 through 1339 Processing helix chain 'a' and resid 1340 through 1358 Processing helix chain 'a' and resid 1364 through 1377 removed outlier: 4.115A pdb=" N MET a1368 " --> pdb=" O ASN a1364 " (cutoff:3.500A) Processing helix chain 'a' and resid 1395 through 1401 removed outlier: 3.823A pdb=" N ARG a1399 " --> pdb=" O GLY a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1406 through 1416 Processing helix chain 'a' and resid 1423 through 1431 Processing helix chain 'a' and resid 1436 through 1441 removed outlier: 4.048A pdb=" N PHE a1441 " --> pdb=" O THR a1438 " (cutoff:3.500A) Processing helix chain 'a' and resid 1447 through 1453 Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 30 through 42 removed outlier: 3.872A pdb=" N ILE b 34 " --> pdb=" O SER b 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER b 35 " --> pdb=" O TRP b 31 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 57 removed outlier: 3.629A pdb=" N PHE b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 66 removed outlier: 4.154A pdb=" N ASP b 66 " --> pdb=" O ILE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 Processing helix chain 'b' and resid 179 through 184 Processing helix chain 'b' and resid 185 through 192 Processing helix chain 'b' and resid 246 through 250 removed outlier: 3.515A pdb=" N PHE b 250 " --> pdb=" O GLY b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 290 Processing helix chain 'b' and resid 293 through 302 removed outlier: 3.627A pdb=" N ILE b 297 " --> pdb=" O PRO b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 321 Proline residue: b 316 - end of helix removed outlier: 3.583A pdb=" N GLY b 321 " --> pdb=" O CYS b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 324 No H-bonds generated for 'chain 'b' and resid 322 through 324' Processing helix chain 'b' and resid 326 through 333 Processing helix chain 'b' and resid 348 through 359 Processing helix chain 'b' and resid 370 through 390 Processing helix chain 'b' and resid 408 through 430 removed outlier: 3.900A pdb=" N LEU b 416 " --> pdb=" O LEU b 412 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 464 removed outlier: 4.250A pdb=" N ILE b 448 " --> pdb=" O MET b 444 " (cutoff:3.500A) Processing helix chain 'b' and resid 487 through 496 removed outlier: 3.878A pdb=" N ARG b 496 " --> pdb=" O LEU b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 515 through 519 Processing helix chain 'b' and resid 551 through 561 removed outlier: 3.826A pdb=" N ILE b 555 " --> pdb=" O PRO b 551 " (cutoff:3.500A) Processing helix chain 'b' and resid 565 through 569 Processing helix chain 'b' and resid 592 through 606 removed outlier: 3.944A pdb=" N LEU b 596 " --> pdb=" O ASN b 592 " (cutoff:3.500A) Processing helix chain 'b' and resid 654 through 668 removed outlier: 3.629A pdb=" N ILE b 658 " --> pdb=" O ARG b 654 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP b 668 " --> pdb=" O THR b 664 " (cutoff:3.500A) Processing helix chain 'b' and resid 680 through 688 removed outlier: 3.524A pdb=" N GLY b 688 " --> pdb=" O LEU b 684 " (cutoff:3.500A) Processing helix chain 'b' and resid 695 through 699 removed outlier: 4.144A pdb=" N GLU b 699 " --> pdb=" O ALA b 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 695 through 699' Processing helix chain 'b' and resid 744 through 749 Processing helix chain 'b' and resid 750 through 756 removed outlier: 4.071A pdb=" N ILE b 755 " --> pdb=" O VAL b 751 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE b 756 " --> pdb=" O ALA b 752 " (cutoff:3.500A) Processing helix chain 'b' and resid 758 through 762 Processing helix chain 'b' and resid 763 through 775 removed outlier: 4.131A pdb=" N LYS b 775 " --> pdb=" O SER b 771 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 812 Processing helix chain 'b' and resid 843 through 849 Processing helix chain 'b' and resid 889 through 893 removed outlier: 3.584A pdb=" N LYS b 892 " --> pdb=" O THR b 889 " (cutoff:3.500A) Processing helix chain 'b' and resid 995 through 999 Processing helix chain 'b' and resid 1014 through 1017 Processing helix chain 'b' and resid 1023 through 1039 Processing helix chain 'b' and resid 1051 through 1063 removed outlier: 3.516A pdb=" N ILE b1055 " --> pdb=" O THR b1051 " (cutoff:3.500A) Processing helix chain 'b' and resid 1099 through 1103 Processing helix chain 'b' and resid 1131 through 1142 Processing helix chain 'b' and resid 1143 through 1153 Processing helix chain 'b' and resid 1197 through 1210 Processing helix chain 'c' and resid 26 through 40 Processing helix chain 'c' and resid 59 through 68 Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'c' and resid 92 through 96 removed outlier: 3.696A pdb=" N SER c 96 " --> pdb=" O ASP c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 118 removed outlier: 3.525A pdb=" N LEU c 118 " --> pdb=" O SER c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 204 through 209 Processing helix chain 'c' and resid 239 through 266 Processing helix chain 'd' and resid 51 through 75 removed outlier: 3.582A pdb=" N ALA d 55 " --> pdb=" O ASN d 51 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG d 56 " --> pdb=" O LEU d 52 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU d 57 " --> pdb=" O SER d 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS d 75 " --> pdb=" O LYS d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 134 removed outlier: 4.145A pdb=" N THR d 133 " --> pdb=" O LEU d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 152 removed outlier: 4.306A pdb=" N ASN d 150 " --> pdb=" O GLN d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 171 removed outlier: 3.841A pdb=" N SER d 169 " --> pdb=" O GLN d 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR d 170 " --> pdb=" O LEU d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 179 removed outlier: 4.059A pdb=" N VAL d 177 " --> pdb=" O HIS d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 183 removed outlier: 4.012A pdb=" N LEU d 183 " --> pdb=" O LEU d 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 180 through 183' Processing helix chain 'd' and resid 187 through 195 removed outlier: 4.166A pdb=" N ALA d 191 " --> pdb=" O THR d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 202 removed outlier: 4.044A pdb=" N ASN d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 216 removed outlier: 4.587A pdb=" N GLU d 213 " --> pdb=" O ARG d 209 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU d 214 " --> pdb=" O ILE d 210 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN d 216 " --> pdb=" O LYS d 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 26 removed outlier: 4.389A pdb=" N ARG e 7 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 36 removed outlier: 3.540A pdb=" N VAL e 35 " --> pdb=" O THR e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 47 Processing helix chain 'e' and resid 65 through 72 Processing helix chain 'e' and resid 89 through 104 Processing helix chain 'e' and resid 117 through 122 Processing helix chain 'e' and resid 157 through 169 Processing helix chain 'e' and resid 182 through 189 Processing helix chain 'f' and resid 86 through 103 Processing helix chain 'f' and resid 116 through 128 Processing helix chain 'g' and resid 14 through 18 Processing helix chain 'g' and resid 21 through 35 Processing helix chain 'i' and resid 61 through 65 removed outlier: 3.710A pdb=" N ASP i 65 " --> pdb=" O ILE i 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 28 Processing helix chain 'j' and resid 31 through 40 Processing helix chain 'j' and resid 43 through 52 removed outlier: 3.813A pdb=" N ARG j 47 " --> pdb=" O ARG j 43 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET j 49 " --> pdb=" O CYS j 45 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'k' and resid 6 through 10 removed outlier: 3.549A pdb=" N LEU k 9 " --> pdb=" O ARG k 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 52 removed outlier: 3.684A pdb=" N GLY k 43 " --> pdb=" O ASP k 39 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU k 45 " --> pdb=" O THR k 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN k 52 " --> pdb=" O ALA k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 112 Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.593A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.541A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 removed outlier: 4.033A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.656A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.774A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.919A pdb=" N ARG A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.629A pdb=" N LEU A 509 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.712A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.073A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 640 through 661 removed outlier: 3.660A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.016A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.558A pdb=" N GLN A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 4.637A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 913 through 917 removed outlier: 4.613A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 960 through 972 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.919A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.509A pdb=" N GLN A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.526A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.734A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1163 through 1166 Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 3.610A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.599A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.645A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 4.169A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.865A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.070A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.526A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 42 removed outlier: 4.293A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 59 through 66 removed outlier: 4.018A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.677A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.560A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.588A pdb=" N CYS B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.853A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.503A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.165A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.673A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 4.562A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.664A pdb=" N GLU B 699 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.941A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.592A pdb=" N SER B 754 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 750 through 755' Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.713A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.332A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 4.307A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.341A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.405A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.758A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.752A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1174 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.740A pdb=" N SER C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 76 removed outlier: 3.870A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.850A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.593A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.672A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.575A pdb=" N ILE D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.184A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.413A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.877A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.549A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.553A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 25 removed outlier: 3.522A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 44 through 53 removed outlier: 4.209A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.739A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.597A pdb=" N GLU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.818A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'Q' and resid 23 through 35 removed outlier: 3.657A pdb=" N MET Q 27 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 removed outlier: 3.748A pdb=" N GLU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 447 Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.797A pdb=" N SER M 64 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN M 65 " --> pdb=" O GLU M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 65' Processing helix chain 'M' and resid 74 through 82 removed outlier: 3.503A pdb=" N LYS M 80 " --> pdb=" O PHE M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.503A pdb=" N GLU M 238 " --> pdb=" O HIS M 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'a' and resid 82 through 83 removed outlier: 3.769A pdb=" N GLY a 82 " --> pdb=" O VAL a 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'a' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'a' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE a 468 " --> pdb=" O ARG a 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL a 352 " --> pdb=" O PHE a 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 365 through 367 removed outlier: 5.628A pdb=" N VAL a 366 " --> pdb=" O ILE a 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 376 through 379 removed outlier: 3.523A pdb=" N VAL a 432 " --> pdb=" O GLU a 378 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL a 405 " --> pdb=" O ILE a 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 512 through 513 removed outlier: 3.724A pdb=" N LYS a 518 " --> pdb=" O SER a 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 587 through 589 removed outlier: 3.549A pdb=" N LEU a 588 " --> pdb=" O ILE a 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 849 through 850 removed outlier: 6.967A pdb=" N THR a 856 " --> pdb=" O ILE a 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 1283 through 1292 removed outlier: 3.542A pdb=" N MET a1285 " --> pdb=" O VAL a1305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 1224 through 1228 removed outlier: 4.067A pdb=" N LEU a1236 " --> pdb=" O LEU a1197 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL a1242 " --> pdb=" O TRP a1191 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP a1191 " --> pdb=" O VAL a1242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA a1149 " --> pdb=" O GLU a1196 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER a1150 " --> pdb=" O ARG i 45 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG i 45 " --> pdb=" O SER a1150 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE a1152 " --> pdb=" O VAL i 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE g 79 " --> pdb=" O ILE g 45 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE g 45 " --> pdb=" O PHE g 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 69 through 73 removed outlier: 3.548A pdb=" N GLY b 93 " --> pdb=" O ASP b 131 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP b 131 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE b 95 " --> pdb=" O PHE b 129 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE b 129 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL b 97 " --> pdb=" O GLY b 127 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY b 127 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER b 126 " --> pdb=" O ARG b 169 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG b 169 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU b 128 " --> pdb=" O ILE b 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 101 through 103 removed outlier: 3.985A pdb=" N VAL b 102 " --> pdb=" O HIS b 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 203 through 204 Processing sheet with id=AC2, first strand: chain 'b' and resid 404 through 407 Processing sheet with id=AC3, first strand: chain 'b' and resid 224 through 227 removed outlier: 4.276A pdb=" N HIS b 236 " --> pdb=" O LEU b 258 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 258 " --> pdb=" O HIS b 236 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 240 " --> pdb=" O LEU b 254 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN b 255 " --> pdb=" O THR b 272 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR b 268 " --> pdb=" O TYR b 259 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE b 269 " --> pdb=" O ILE b 280 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE b 280 " --> pdb=" O ILE b 269 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA b 271 " --> pdb=" O GLN b 278 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN b 278 " --> pdb=" O ALA b 271 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU b 273 " --> pdb=" O ILE b 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'b' and resid 650 through 651 removed outlier: 3.545A pdb=" N GLU b 650 " --> pdb=" O GLU b 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 585 through 590 removed outlier: 3.684A pdb=" N HIS b 587 " --> pdb=" O VAL b 580 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL b 580 " --> pdb=" O HIS b 587 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL b 589 " --> pdb=" O THR b 578 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR b 578 " --> pdb=" O VAL b 589 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 792 through 796 removed outlier: 3.702A pdb=" N ILE b 795 " --> pdb=" O LEU b 854 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG b 857 " --> pdb=" O VAL b 968 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL b 966 " --> pdb=" O TYR b 859 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 861 " --> pdb=" O VAL b 964 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG b 967 " --> pdb=" O GLN b 951 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN b 951 " --> pdb=" O ARG b 967 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG b 969 " --> pdb=" O VAL b 949 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL b 949 " --> pdb=" O ARG b 969 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE b1086 " --> pdb=" O ILE b 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE b 827 " --> pdb=" O PHE b1086 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU b1010 " --> pdb=" O ASN b 822 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE b 824 " --> pdb=" O LEU b1010 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE b1012 " --> pdb=" O ILE b 824 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA b 826 " --> pdb=" O ILE b1012 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET b 839 " --> pdb=" O GLY b 991 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR b 993 " --> pdb=" O MET b 839 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET b 841 " --> pdb=" O THR b 993 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 910 through 912 removed outlier: 6.819A pdb=" N THR b 939 " --> pdb=" O ILE b 911 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 1158 through 1162 Processing sheet with id=AD3, first strand: chain 'c' and resid 8 through 13 removed outlier: 6.609A pdb=" N ASP c 19 " --> pdb=" O ARG c 11 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA c 13 " --> pdb=" O ASN c 17 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN c 17 " --> pdb=" O ALA c 13 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE c 20 " --> pdb=" O MET c 230 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET c 230 " --> pdb=" O PHE c 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 119 through 120 removed outlier: 5.649A pdb=" N LYS c 160 " --> pdb=" O ILE c 46 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE c 46 " --> pdb=" O LYS c 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE l 67 " --> pdb=" O VAL c 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 72 through 74 removed outlier: 4.238A pdb=" N HIS c 131 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 111 through 112 Processing sheet with id=AD7, first strand: chain 'd' and resid 36 through 37 Processing sheet with id=AD8, first strand: chain 'e' and resid 60 through 62 removed outlier: 7.127A pdb=" N TRP e 79 " --> pdb=" O ILE e 109 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL e 111 " --> pdb=" O TRP e 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 143 through 147 removed outlier: 3.683A pdb=" N VAL g 92 " --> pdb=" O GLU g 100 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU g 100 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS g 107 " --> pdb=" O ALA g 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'h' and resid 95 through 98 removed outlier: 4.289A pdb=" N TYR h 95 " --> pdb=" O ILE h 144 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE h 144 " --> pdb=" O TYR h 95 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU h 27 " --> pdb=" O SER h 13 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL h 15 " --> pdb=" O ARG h 25 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG h 25 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU h 122 " --> pdb=" O ASP h 41 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR h 116 " --> pdb=" O MET h 123 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU h 125 " --> pdb=" O VAL h 114 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL h 114 " --> pdb=" O LEU h 125 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU h 111 " --> pdb=" O GLU h 106 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU h 106 " --> pdb=" O LEU h 111 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA h 113 " --> pdb=" O PHE h 104 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE h 104 " --> pdb=" O ALA h 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR h 115 " --> pdb=" O TYR h 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 14 through 18 Processing sheet with id=AE5, first strand: chain 'i' and resid 84 through 87 Processing sheet with id=AE6, first strand: chain 'k' and resid 19 through 24 removed outlier: 4.535A pdb=" N ALA k 30 " --> pdb=" O ASP k 24 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE k 71 " --> pdb=" O PHE k 35 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.605A pdb=" N VAL A 17 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 83 through 90 removed outlier: 10.202A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AF1, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.756A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.099A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.553A pdb=" N ALA A 349 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AF5, first strand: chain 'A' and resid 588 through 589 removed outlier: 7.087A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.574A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 879 through 882 removed outlier: 3.610A pdb=" N GLN A 881 " --> pdb=" O TRP A 954 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1283 through 1292 removed outlier: 3.547A pdb=" N TYR A1328 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.356A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.511A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AG5, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AG6, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AG7, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.522A pdb=" N GLN B 224 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 544 through 547 removed outlier: 6.538A pdb=" N CYS B 544 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 633 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 546 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.328A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AH2, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.518A pdb=" N ALA B 793 " --> pdb=" O PHE B 856 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 4.466A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1158 through 1162 Processing sheet with id=AH5, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.800A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.144A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.856A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.986A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AI1, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.357A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.503A pdb=" N ARG E 200 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 86 through 93 removed outlier: 5.430A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.895A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 54 through 58 removed outlier: 3.782A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AI7, first strand: chain 'I' and resid 84 through 87 Processing sheet with id=AI8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AI9, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.149A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL M 68 " --> pdb=" O CYS M 219 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU M 221 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU M 70 " --> pdb=" O GLU M 221 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN M 223 " --> pdb=" O LEU M 70 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 72 " --> pdb=" O GLN M 223 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET M 225 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN M 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL Q 378 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.149A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL M 134 " --> pdb=" O VAL M 215 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR M 217 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU M 132 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR Q 116 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN Q 122 " --> pdb=" O ALA Q 397 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) 2556 hydrogen bonds defined for protein. 7089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 36.33 Time building geometry restraints manager: 25.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 22184 1.34 - 1.46: 15427 1.46 - 1.58: 32329 1.58 - 1.71: 333 1.71 - 1.83: 602 Bond restraints: 70875 Sorted by residual: bond pdb=" O3' C R 15 " pdb=" P C R 16 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.51e+01 bond pdb=" C CYS b 523 " pdb=" N PRO b 524 " ideal model delta sigma weight residual 1.334 1.305 0.029 8.40e-03 1.42e+04 1.18e+01 bond pdb=" O3' A r 46 " pdb=" P U r 47 " ideal model delta sigma weight residual 1.607 1.555 0.052 1.50e-02 4.44e+03 1.18e+01 bond pdb=" O3' DA O -47 " pdb=" P DT O -46 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.10e+01 bond pdb=" O3' U R 13 " pdb=" P C R 14 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.05e+01 ... (remaining 70870 not shown) Histogram of bond angle deviations from ideal: 96.05 - 103.67: 1391 103.67 - 111.30: 30634 111.30 - 118.92: 27321 118.92 - 126.54: 35833 126.54 - 134.17: 1311 Bond angle restraints: 96490 Sorted by residual: angle pdb=" C CYS B1166 " pdb=" CA CYS B1166 " pdb=" CB CYS B1166 " ideal model delta sigma weight residual 110.88 96.70 14.18 1.57e+00 4.06e-01 8.15e+01 angle pdb=" O3' U r 40 " pdb=" C3' U r 40 " pdb=" C2' U r 40 " ideal model delta sigma weight residual 113.70 101.01 12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" O2' U r 47 " pdb=" C2' U r 47 " pdb=" C1' U r 47 " ideal model delta sigma weight residual 108.40 96.13 12.27 1.50e+00 4.44e-01 6.69e+01 angle pdb=" O3' DG O -39 " pdb=" C3' DG O -39 " pdb=" C2' DG O -39 " ideal model delta sigma weight residual 111.50 99.50 12.00 1.50e+00 4.44e-01 6.40e+01 angle pdb=" N PRO Q 421 " pdb=" CA PRO Q 421 " pdb=" CB PRO Q 421 " ideal model delta sigma weight residual 103.27 110.17 -6.90 9.00e-01 1.23e+00 5.88e+01 ... (remaining 96485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 41368 35.82 - 71.64: 1304 71.64 - 107.45: 84 107.45 - 143.27: 7 143.27 - 179.09: 3 Dihedral angle restraints: 42766 sinusoidal: 18734 harmonic: 24032 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -133.35 -46.65 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA LYS B 510 " pdb=" C LYS B 510 " pdb=" N PRO B 511 " pdb=" CA PRO B 511 " ideal model delta harmonic sigma weight residual -180.00 -134.49 -45.51 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA PHE A 252 " pdb=" C PHE A 252 " pdb=" N ASN A 253 " pdb=" CA ASN A 253 " ideal model delta harmonic sigma weight residual 180.00 138.67 41.33 0 5.00e+00 4.00e-02 6.83e+01 ... (remaining 42763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 10481 0.106 - 0.212: 378 0.212 - 0.319: 6 0.319 - 0.425: 3 0.425 - 0.531: 1 Chirality restraints: 10869 Sorted by residual: chirality pdb=" C2' U r 40 " pdb=" C3' U r 40 " pdb=" O2' U r 40 " pdb=" C1' U r 40 " both_signs ideal model delta sigma weight residual False -2.75 -2.22 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CA CYS B1166 " pdb=" N CYS B1166 " pdb=" C CYS B1166 " pdb=" CB CYS B1166 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C3' DA O -42 " pdb=" C4' DA O -42 " pdb=" O3' DA O -42 " pdb=" C2' DA O -42 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 10866 not shown) Planarity restraints: 11891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 510 " 0.065 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO B 511 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 511 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 511 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U r 40 " 0.035 2.00e-02 2.50e+03 2.06e-02 9.52e+00 pdb=" N1 U r 40 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U r 40 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U r 40 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U r 40 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U r 40 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U r 40 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U r 40 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U r 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C r 39 " 0.042 2.00e-02 2.50e+03 1.97e-02 8.71e+00 pdb=" N1 C r 39 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C r 39 " -0.007 2.00e-02 2.50e+03 pdb=" O2 C r 39 " -0.016 2.00e-02 2.50e+03 pdb=" N3 C r 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C r 39 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C r 39 " 0.024 2.00e-02 2.50e+03 pdb=" C5 C r 39 " -0.014 2.00e-02 2.50e+03 pdb=" C6 C r 39 " -0.019 2.00e-02 2.50e+03 ... (remaining 11888 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 3 1.97 - 2.71: 3993 2.71 - 3.44: 110854 3.44 - 4.17: 167907 4.17 - 4.90: 280550 Nonbonded interactions: 563307 Sorted by model distance: nonbonded pdb=" OP1 U R 13 " pdb="MG MG R 101 " model vdw 1.242 2.170 nonbonded pdb=" O CYS a 67 " pdb="ZN ZN a1802 " model vdw 1.888 2.230 nonbonded pdb=" OD2 ASP a 481 " pdb="MG MG a1803 " model vdw 1.934 2.170 nonbonded pdb=" OP2 C r 48 " pdb="MG MG a1803 " model vdw 1.984 2.170 nonbonded pdb=" O CYS A 67 " pdb="ZN ZN A1802 " model vdw 1.999 2.230 ... (remaining 563302 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 'A' and (resid 2 through 314 or (resid 315 through 318 and (name N or nam \ e CA or name C or name O or name CB )) or resid 319 through 1454 or resid 1801 t \ hrough 1803)) selection = (chain 'a' and (resid 2 through 174 or (resid 175 and (name N or name CA or name \ C or name O or name CB )) or resid 176 through 317 or (resid 318 and (name N or \ name CA or name C or name O or name CB )) or resid 319 through 325 or (resid 32 \ 6 through 327 and (name N or name CA or name C or name O or name CB )) or resid \ 328 through 329 or (resid 330 and (name N or name CA or name C or name O or name \ CB )) or resid 331 through 1403 or (resid 1404 and (name N or name CA or name C \ or name O or name CB )) or resid 1405 through 1406 or (resid 1407 and (name N o \ r name CA or name C or name O or name CB )) or resid 1408 through 1454 or resid \ 1801 through 1803)) } ncs_group { reference = (chain 'B' and (resid 20 through 502 or resid 509 through 867 or (resid 868 and \ (name N or name CA or name C or name O or name CB )) or resid 869 through 1223 o \ r resid 1301)) selection = (chain 'b' and (resid 20 through 469 or (resid 470 through 472 and (name N or na \ me CA or name C or name O or name CB )) or resid 473 through 1223 or resid 1301) \ ) } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 171)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 16 6.06 5 P 179 5.49 5 Mg 4 5.21 5 S 374 5.16 5 C 43090 2.51 5 N 12103 2.21 5 O 13515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.95 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.080 Extract box with map and model: 12.290 Check model and map are aligned: 0.770 Process input model: 171.640 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Set scattering table: 0.500 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.005 0.062 70875 Z= 0.348 Angle : 0.828 14.899 96490 Z= 0.483 Chirality : 0.047 0.531 10869 Planarity : 0.004 0.097 11891 Dihedral : 16.675 179.091 27200 Min Nonbonded Distance : 1.242 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.32 % Favored : 88.61 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.11 % 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: -1.69 (0.09), residues: 8171 helix: 0.33 (0.10), residues: 2620 sheet: -0.98 (0.14), residues: 1258 loop : -2.17 (0.09), residues: 4293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 362 time to evaluate : 6.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 367 average time/residue: 0.6551 time to fit residues: 419.5656 Evaluate side-chains 328 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 6.035 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3213 time to fit residues: 10.0278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 702 optimal weight: 9.9990 chunk 630 optimal weight: 9.9990 chunk 349 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 425 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 chunk 652 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 485 optimal weight: 10.0000 chunk 755 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1009 ASN ** a1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 70875 Z= 0.389 Angle : 0.760 19.174 96490 Z= 0.401 Chirality : 0.045 0.219 10869 Planarity : 0.005 0.104 11891 Dihedral : 15.487 174.201 10824 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.07 % Favored : 87.90 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.09 % 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: -1.70 (0.09), residues: 8171 helix: 0.39 (0.10), residues: 2691 sheet: -1.05 (0.14), residues: 1292 loop : -2.24 (0.09), residues: 4188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 342 time to evaluate : 7.002 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 outliers start: 37 outliers final: 17 residues processed: 355 average time/residue: 0.6883 time to fit residues: 427.6609 Evaluate side-chains 340 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 323 time to evaluate : 6.121 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5636 time to fit residues: 25.8359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 419 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 628 optimal weight: 10.0000 chunk 514 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 756 optimal weight: 10.0000 chunk 817 optimal weight: 50.0000 chunk 674 optimal weight: 7.9990 chunk 750 optimal weight: 50.0000 chunk 258 optimal weight: 6.9990 chunk 607 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 794 ASN ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 70875 Z= 0.359 Angle : 0.730 19.572 96490 Z= 0.383 Chirality : 0.044 0.239 10869 Planarity : 0.005 0.102 11891 Dihedral : 15.463 177.478 10824 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.64 % Favored : 88.32 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.08 % 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: -1.60 (0.09), residues: 8171 helix: 0.51 (0.10), residues: 2694 sheet: -1.00 (0.14), residues: 1242 loop : -2.22 (0.09), residues: 4235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 338 time to evaluate : 6.133 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 outliers start: 83 outliers final: 36 residues processed: 412 average time/residue: 0.6588 time to fit residues: 476.6821 Evaluate side-chains 362 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 326 time to evaluate : 6.051 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5074 time to fit residues: 43.1022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 747 optimal weight: 40.0000 chunk 569 optimal weight: 9.9990 chunk 392 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 361 optimal weight: 0.0870 chunk 508 optimal weight: 4.9990 chunk 759 optimal weight: 0.3980 chunk 804 optimal weight: 20.0000 chunk 396 optimal weight: 8.9990 chunk 719 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 395 GLN b 776 GLN ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 768 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 35 GLN I 87 GLN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 70875 Z= 0.221 Angle : 0.678 19.526 96490 Z= 0.351 Chirality : 0.043 0.232 10869 Planarity : 0.004 0.095 11891 Dihedral : 15.381 178.242 10824 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.65 % Favored : 89.33 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.06 % 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: -1.37 (0.09), residues: 8171 helix: 0.79 (0.10), residues: 2698 sheet: -0.90 (0.15), residues: 1248 loop : -2.13 (0.09), residues: 4225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 342 time to evaluate : 6.172 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 outliers start: 101 outliers final: 32 residues processed: 424 average time/residue: 0.6785 time to fit residues: 507.9496 Evaluate side-chains 361 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 329 time to evaluate : 6.142 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5294 time to fit residues: 40.9192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 669 optimal weight: 8.9990 chunk 456 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 598 optimal weight: 20.0000 chunk 331 optimal weight: 2.9990 chunk 686 optimal weight: 9.9990 chunk 555 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 410 optimal weight: 2.9990 chunk 721 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 659 HIS ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1195 HIS e 5 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 70875 Z= 0.291 Angle : 0.700 19.645 96490 Z= 0.362 Chirality : 0.043 0.246 10869 Planarity : 0.005 0.091 11891 Dihedral : 15.385 178.405 10824 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.27 % Favored : 88.70 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 8171 helix: 0.78 (0.10), residues: 2703 sheet: -0.88 (0.15), residues: 1249 loop : -2.11 (0.09), residues: 4219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 337 time to evaluate : 6.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 35 residues processed: 428 average time/residue: 0.6462 time to fit residues: 488.0201 Evaluate side-chains 366 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 331 time to evaluate : 6.091 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5176 time to fit residues: 42.6931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 270 optimal weight: 7.9990 chunk 724 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 472 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 804 optimal weight: 30.0000 chunk 668 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 422 optimal weight: 40.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 70875 Z= 0.284 Angle : 0.707 19.731 96490 Z= 0.363 Chirality : 0.043 0.225 10869 Planarity : 0.004 0.087 11891 Dihedral : 15.396 179.067 10824 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.98 % Favored : 89.00 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.05 % 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: -1.31 (0.09), residues: 8171 helix: 0.79 (0.10), residues: 2706 sheet: -0.85 (0.15), residues: 1251 loop : -2.08 (0.09), residues: 4214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 341 time to evaluate : 6.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 35 residues processed: 416 average time/residue: 0.6651 time to fit residues: 486.2337 Evaluate side-chains 365 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 330 time to evaluate : 6.150 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5173 time to fit residues: 42.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 776 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 458 optimal weight: 7.9990 chunk 587 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 677 optimal weight: 0.3980 chunk 449 optimal weight: 9.9990 chunk 801 optimal weight: 40.0000 chunk 501 optimal weight: 8.9990 chunk 488 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 776 GLN ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 96 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 70875 Z= 0.255 Angle : 0.704 19.864 96490 Z= 0.359 Chirality : 0.043 0.227 10869 Planarity : 0.004 0.085 11891 Dihedral : 15.376 179.681 10824 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.77 % Favored : 89.21 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.04 % 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: -1.25 (0.09), residues: 8171 helix: 0.87 (0.10), residues: 2704 sheet: -0.82 (0.15), residues: 1245 loop : -2.06 (0.09), residues: 4222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 334 time to evaluate : 6.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 25 residues processed: 400 average time/residue: 0.6693 time to fit residues: 469.2800 Evaluate side-chains 353 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 328 time to evaluate : 6.088 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5126 time to fit residues: 32.8174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 496 optimal weight: 8.9990 chunk 320 optimal weight: 8.9990 chunk 478 optimal weight: 10.0000 chunk 241 optimal weight: 30.0000 chunk 157 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 509 optimal weight: 0.9990 chunk 546 optimal weight: 6.9990 chunk 396 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 630 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 70875 Z= 0.288 Angle : 0.722 19.805 96490 Z= 0.368 Chirality : 0.043 0.219 10869 Planarity : 0.004 0.083 11891 Dihedral : 15.384 179.868 10824 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.99 % Favored : 88.99 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.09), residues: 8171 helix: 0.83 (0.10), residues: 2711 sheet: -0.86 (0.15), residues: 1253 loop : -2.08 (0.09), residues: 4207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 337 time to evaluate : 6.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 22 residues processed: 385 average time/residue: 0.6914 time to fit residues: 465.0365 Evaluate side-chains 352 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 330 time to evaluate : 6.037 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5497 time to fit residues: 30.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 729 optimal weight: 0.7980 chunk 768 optimal weight: 10.0000 chunk 700 optimal weight: 50.0000 chunk 747 optimal weight: 20.0000 chunk 449 optimal weight: 9.9990 chunk 325 optimal weight: 0.1980 chunk 586 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 675 optimal weight: 0.9990 chunk 706 optimal weight: 5.9990 chunk 744 optimal weight: 50.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 587 HIS ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 70875 Z= 0.191 Angle : 0.708 19.821 96490 Z= 0.355 Chirality : 0.043 0.212 10869 Planarity : 0.004 0.080 11891 Dihedral : 15.293 179.702 10824 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.01 % Favored : 89.96 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.05 % 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: -1.15 (0.10), residues: 8171 helix: 0.96 (0.10), residues: 2711 sheet: -0.73 (0.15), residues: 1204 loop : -2.00 (0.09), residues: 4256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 344 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 7 residues processed: 369 average time/residue: 0.6766 time to fit residues: 437.1339 Evaluate side-chains 340 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 333 time to evaluate : 6.120 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6299 time to fit residues: 15.9531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 490 optimal weight: 4.9990 chunk 790 optimal weight: 3.9990 chunk 482 optimal weight: 20.0000 chunk 374 optimal weight: 5.9990 chunk 549 optimal weight: 0.7980 chunk 828 optimal weight: 5.9990 chunk 762 optimal weight: 0.7980 chunk 660 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 509 optimal weight: 0.9980 chunk 404 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1076 HIS ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 70875 Z= 0.179 Angle : 0.713 20.026 96490 Z= 0.355 Chirality : 0.043 0.235 10869 Planarity : 0.004 0.078 11891 Dihedral : 15.228 179.871 10824 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.66 % Favored : 90.31 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.09), residues: 8171 helix: 0.97 (0.10), residues: 2716 sheet: -0.67 (0.15), residues: 1203 loop : -1.97 (0.09), residues: 4252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 344 time to evaluate : 6.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 359 average time/residue: 0.6906 time to fit residues: 435.2999 Evaluate side-chains 347 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 336 time to evaluate : 6.073 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5645 time to fit residues: 19.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 524 optimal weight: 8.9990 chunk 703 optimal weight: 0.2980 chunk 202 optimal weight: 8.9990 chunk 608 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 661 optimal weight: 20.0000 chunk 276 optimal weight: 0.9980 chunk 678 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 131 HIS ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.050927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.034874 restraints weight = 634104.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.035287 restraints weight = 364241.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.035758 restraints weight = 255596.495| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 70875 Z= 0.178 Angle : 0.708 19.916 96490 Z= 0.353 Chirality : 0.043 0.207 10869 Planarity : 0.004 0.077 11891 Dihedral : 15.194 179.667 10824 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.30 % Favored : 90.67 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 8171 helix: 1.00 (0.10), residues: 2721 sheet: -0.60 (0.15), residues: 1222 loop : -1.94 (0.09), residues: 4228 =============================================================================== Job complete usr+sys time: 10790.22 seconds wall clock time: 194 minutes 50.91 seconds (11690.91 seconds total)