Starting phenix.real_space_refine on Wed Feb 21 09:50:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/02_2024/7aoc_11840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/02_2024/7aoc_11840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/02_2024/7aoc_11840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/02_2024/7aoc_11840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/02_2024/7aoc_11840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/02_2024/7aoc_11840.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 570 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 165 5.16 5 C 18860 2.51 5 N 5136 2.21 5 O 5557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 647": "OD1" <-> "OD2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ASP 719": "OD1" <-> "OD2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 819": "OD1" <-> "OD2" Residue "A ASP 855": "OD1" <-> "OD2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A ASP 882": "OD1" <-> "OD2" Residue "A TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 927": "OD1" <-> "OD2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A TYR 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1080": "OE1" <-> "OE2" Residue "A ASP 1103": "OD1" <-> "OD2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1122": "OD1" <-> "OD2" Residue "A TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A GLU 1274": "OE1" <-> "OE2" Residue "A ARG 1280": "NH1" <-> "NH2" Residue "A ASP 1302": "OD1" <-> "OD2" Residue "A ASP 1311": "OD1" <-> "OD2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1321": "OE1" <-> "OE2" Residue "A PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1481": "OD1" <-> "OD2" Residue "A GLU 1493": "OE1" <-> "OE2" Residue "A GLU 1501": "OE1" <-> "OE2" Residue "A GLU 1510": "OE1" <-> "OE2" Residue "A GLU 1554": "OE1" <-> "OE2" Residue "A ASP 1568": "OD1" <-> "OD2" Residue "A GLU 1588": "OE1" <-> "OE2" Residue "A PHE 1593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1615": "OE1" <-> "OE2" Residue "A PHE 1638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A ASP 1656": "OD1" <-> "OD2" Residue "A PHE 1672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 511": "OD1" <-> "OD2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 608": "OD1" <-> "OD2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 748": "OD1" <-> "OD2" Residue "B TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 770": "OD1" <-> "OD2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 795": "OD1" <-> "OD2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 858": "OE1" <-> "OE2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B GLU 870": "OE1" <-> "OE2" Residue "B ASP 877": "OD1" <-> "OD2" Residue "B ASP 880": "OD1" <-> "OD2" Residue "B ASP 900": "OD1" <-> "OD2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1027": "OD1" <-> "OD2" Residue "B PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1058": "OE1" <-> "OE2" Residue "B TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "B ASP 1134": "OD1" <-> "OD2" Residue "B PHE 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 128": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G ASP 149": "OD1" <-> "OD2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 8": "OD1" <-> "OD2" Residue "H PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "I PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ASP 36": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "K ASP 96": "OD1" <-> "OD2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29724 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1394, 11051 Classifications: {'peptide': 1394} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1327} Chain breaks: 12 Chain: "B" Number of atoms: 9148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9148 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 59, 'TRANS': 1099} Chain breaks: 3 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "A" 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: "B" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 483 SG CYS A 63 77.752 60.209 58.365 1.00 93.27 S ATOM 501 SG CYS A 66 74.149 61.180 57.450 1.00 95.46 S ATOM 565 SG CYS A 73 74.149 61.209 59.501 1.00 84.44 S ATOM 809 SG CYS A 103 81.341 18.476 87.647 1.00110.95 S ATOM 1540 SG CYS A 228 80.800 17.695 89.490 1.00102.85 S ATOM 1562 SG CYS A 231 82.126 13.918 87.382 1.00111.41 S ATOM 27663 SG CYS I 10 125.367 43.834 144.167 1.00100.65 S ATOM 27684 SG CYS I 13 126.037 44.283 140.827 1.00102.67 S ATOM 27789 SG CYS I 27 126.217 41.033 141.731 1.00128.76 S ATOM 27812 SG CYS I 30 127.155 42.411 141.870 1.00125.54 S ATOM 28111 SG CYS J 7 75.288 120.630 103.630 1.00 3.36 S ATOM 28134 SG CYS J 10 71.372 121.754 105.969 1.00 3.55 S ATOM 28406 SG CYS J 44 72.291 119.519 107.188 1.00 3.74 S ATOM 28412 SG CYS J 45 74.016 122.212 105.891 1.00 12.41 S ATOM 29399 SG CYS L 24 113.087 106.412 84.682 1.00 33.38 S ATOM 29418 SG CYS L 27 114.114 108.827 84.566 1.00 46.11 S ATOM 29525 SG CYS L 41 114.859 107.058 83.207 1.00 37.24 S ATOM 29551 SG CYS L 44 117.022 108.444 86.275 1.00 45.93 S Time building chain proxies: 14.54, per 1000 atoms: 0.49 Number of scatterers: 29724 At special positions: 0 Unit cell: (151.017, 155.271, 169.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 165 16.00 O 5557 8.00 N 5136 7.00 C 18860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B1089 " - pdb=" SG CYS B1092 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.53 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 73 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 66 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 63 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 103 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 228 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " Number of angles added : 21 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 43 sheets defined 36.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.551A pdb=" N VAL A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.793A pdb=" N VAL A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.840A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.706A pdb=" N LYS A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.795A pdb=" N PHE A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.407A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 385 through 411 Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 558 through 568 removed outlier: 3.622A pdb=" N GLN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.135A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 668 through 672 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.914A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 771 through 776 removed outlier: 4.337A pdb=" N TRP A 775 " --> pdb=" O PRO A 771 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 776 " --> pdb=" O GLY A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 776' Processing helix chain 'A' and resid 807 through 816 removed outlier: 3.521A pdb=" N SER A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 840 removed outlier: 3.545A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.727A pdb=" N VAL A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 1004 through 1022 removed outlier: 3.769A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 removed outlier: 3.524A pdb=" N LYS A1072 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A1074 " --> pdb=" O THR A1071 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1076 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 3.738A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.690A pdb=" N ILE A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.436A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.969A pdb=" N SER A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1138 through 1152 Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1171 through 1186 Processing helix chain 'A' and resid 1194 through 1209 Proline residue: A1205 - end of helix removed outlier: 3.867A pdb=" N MET A1209 " --> pdb=" O PRO A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1271 through 1274 Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 3.898A pdb=" N GLU A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1345 removed outlier: 4.178A pdb=" N GLN A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1516 Processing helix chain 'A' and resid 1548 through 1553 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.506A pdb=" N ILE A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1593 Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.902A pdb=" N LEU A1605 " --> pdb=" O ASP A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1631 through 1639 removed outlier: 3.534A pdb=" N LYS A1635 " --> pdb=" O SER A1631 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A1636 " --> pdb=" O PRO A1632 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A1639 " --> pdb=" O LYS A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1652 removed outlier: 3.581A pdb=" N PHE A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.503A pdb=" N VAL A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1676 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.205A pdb=" N GLN B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.032A pdb=" N GLY B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.825A pdb=" N ALA B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.843A pdb=" N ASN B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 205 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.153A pdb=" N LEU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.540A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.668A pdb=" N GLY B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 409 removed outlier: 4.022A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.768A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.595A pdb=" N MET B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.772A pdb=" N ALA B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.856A pdb=" N ASN B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.736A pdb=" N MET B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.681A pdb=" N ASN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.880A pdb=" N HIS B 749 " --> pdb=" O GLY B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 935 through 939 Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.619A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1022 through 1026 removed outlier: 4.197A pdb=" N SER B1026 " --> pdb=" O HIS B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1079 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.682A pdb=" N PHE C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.669A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.731A pdb=" N LYS C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.534A pdb=" N ASN C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.935A pdb=" N ILE D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.525A pdb=" N ARG E 10 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.660A pdb=" N PHE E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'F' and resid 76 through 93 removed outlier: 4.033A pdb=" N ALA F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.763A pdb=" N GLN F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 24 through 37 removed outlier: 4.379A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 4.307A pdb=" N LYS H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 40 removed outlier: 3.516A pdb=" N GLN I 38 " --> pdb=" O PRO I 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE I 39 " --> pdb=" O SER I 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA I 40 " --> pdb=" O GLU I 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 40' Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'J' and resid 21 through 26 removed outlier: 3.666A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 removed outlier: 3.871A pdb=" N LEU J 35 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 56 removed outlier: 3.565A pdb=" N GLY K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS K 56 " --> pdb=" O TYR K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.765A pdb=" N VAL K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1654 through 1655 removed outlier: 3.941A pdb=" N ASP A1655 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 14 " --> pdb=" O ASP A1655 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 13 " --> pdb=" O GLU B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 87 removed outlier: 11.160A pdb=" N LEU A 82 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ALA A 366 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N ILE A 84 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ASN A 364 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 86 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 482 through 483 removed outlier: 3.595A pdb=" N PHE B1056 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 494 removed outlier: 3.764A pdb=" N ILE A 630 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE A 503 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 619 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 490 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 518 removed outlier: 6.668A pdb=" N LYS A 592 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 544 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 594 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 767 removed outlier: 7.158A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 961 through 962 removed outlier: 3.905A pdb=" N ILE A 995 " --> pdb=" O GLY A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1044 through 1045 Processing sheet with id=AA9, first strand: chain 'A' and resid 1524 through 1529 removed outlier: 4.886A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1479 through 1482 removed outlier: 6.516A pdb=" N ALA A1298 " --> pdb=" O VAL A1281 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1281 " --> pdb=" O ALA A1298 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A1300 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A1279 " --> pdb=" O ARG A1300 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP A1302 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL I 44 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB3, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.733A pdb=" N ARG B 78 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B 115 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 139 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 117 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.607A pdb=" N VAL B 175 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.580A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.280A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.280A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 226 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS B 242 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 250 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 571 removed outlier: 5.553A pdb=" N ILE B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 563 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 610 " --> pdb=" O PHE B 628 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 725 through 729 removed outlier: 4.029A pdb=" N GLN B 885 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC4, first strand: chain 'B' and resid 902 through 903 removed outlier: 3.653A pdb=" N GLN B1019 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 932 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 902 through 903 removed outlier: 3.653A pdb=" N GLN B1019 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 809 through 810 removed outlier: 3.615A pdb=" N VAL B 845 " --> pdb=" O GLU B 858 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 923 through 924 Processing sheet with id=AC8, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AC9, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.742A pdb=" N VAL C 59 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 53 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 300 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 241 " --> pdb=" O GLN C 300 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 237 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASP C 306 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 235 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N TYR C 308 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N SER C 233 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N PHE C 310 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR C 231 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N VAL C 312 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL C 229 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 175 through 176 removed outlier: 6.894A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.664A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 263 through 267 removed outlier: 3.714A pdb=" N GLN C 274 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.905A pdb=" N TYR E 73 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 149 removed outlier: 4.231A pdb=" N LYS E 147 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 17 removed outlier: 3.954A pdb=" N ARG G 55 " --> pdb=" O ARG G 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 17 Processing sheet with id=AD9, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.781A pdb=" N GLY G 46 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 109 through 114 removed outlier: 6.179A pdb=" N LEU G 104 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE G 93 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 123 through 124 Processing sheet with id=AE3, first strand: chain 'H' and resid 15 through 17 removed outlier: 6.021A pdb=" N LEU H 101 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU H 100 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG H 82 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER H 96 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL H 80 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.682A pdb=" N THR I 25 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR I 34 " --> pdb=" O THR I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.595A pdb=" N ILE K 23 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.666A pdb=" N GLN K 80 " --> pdb=" O GLU K 61 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.63 Time building geometry restraints manager: 12.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9716 1.34 - 1.46: 5308 1.46 - 1.58: 15026 1.58 - 1.70: 0 1.70 - 1.81: 266 Bond restraints: 30316 Sorted by residual: bond pdb=" CA ASN B 147 " pdb=" C ASN B 147 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.37e-02 5.33e+03 1.40e+01 bond pdb=" CA ASN B 680 " pdb=" C ASN B 680 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.69e+00 bond pdb=" C GLN A 735 " pdb=" N ARG A 736 " ideal model delta sigma weight residual 1.325 1.289 0.036 1.25e-02 6.40e+03 8.22e+00 bond pdb=" C GLN E 169 " pdb=" N LEU E 170 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.45e-02 4.76e+03 7.09e+00 bond pdb=" N SER A1067 " pdb=" CA SER A1067 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 ... (remaining 30311 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.76: 568 104.76 - 112.10: 15016 112.10 - 119.43: 10040 119.43 - 126.77: 14974 126.77 - 134.10: 362 Bond angle restraints: 40960 Sorted by residual: angle pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" C ASP E 24 " ideal model delta sigma weight residual 110.80 126.20 -15.40 2.13e+00 2.20e-01 5.23e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 132.26 -10.56 1.80e+00 3.09e-01 3.44e+01 angle pdb=" N ASP A1066 " pdb=" CA ASP A1066 " pdb=" C ASP A1066 " ideal model delta sigma weight residual 110.80 122.16 -11.36 2.13e+00 2.20e-01 2.85e+01 angle pdb=" C ASP H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta sigma weight residual 121.70 130.90 -9.20 1.80e+00 3.09e-01 2.61e+01 angle pdb=" N SER G 99 " pdb=" CA SER G 99 " pdb=" C SER G 99 " ideal model delta sigma weight residual 114.62 108.94 5.68 1.14e+00 7.69e-01 2.49e+01 ... (remaining 40955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.39: 17425 26.39 - 52.79: 944 52.79 - 79.18: 61 79.18 - 105.57: 13 105.57 - 131.96: 1 Dihedral angle restraints: 18444 sinusoidal: 7554 harmonic: 10890 Sorted by residual: dihedral pdb=" CA HIS E 23 " pdb=" C HIS E 23 " pdb=" N ASP E 24 " pdb=" CA ASP E 24 " ideal model delta harmonic sigma weight residual -180.00 -48.04 -131.96 0 5.00e+00 4.00e-02 6.97e+02 dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual 180.00 -122.13 -57.87 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLU A1065 " pdb=" C GLU A1065 " pdb=" N ASP A1066 " pdb=" CA ASP A1066 " ideal model delta harmonic sigma weight residual -180.00 -138.67 -41.33 0 5.00e+00 4.00e-02 6.83e+01 ... (remaining 18441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3620 0.059 - 0.117: 861 0.117 - 0.176: 86 0.176 - 0.234: 6 0.234 - 0.292: 4 Chirality restraints: 4577 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE I 8 " pdb=" CA ILE I 8 " pdb=" CG1 ILE I 8 " pdb=" CG2 ILE I 8 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB VAL E 137 " pdb=" CA VAL E 137 " pdb=" CG1 VAL E 137 " pdb=" CG2 VAL E 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4574 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.056 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO A 85 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 786 " 0.025 2.00e-02 2.50e+03 2.17e-02 8.25e+00 pdb=" CG PHE A 786 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 786 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 786 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 786 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 786 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 786 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 895 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 896 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 896 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 896 " 0.037 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 233 2.52 - 3.12: 23683 3.12 - 3.71: 44440 3.71 - 4.31: 61939 4.31 - 4.90: 104375 Nonbonded interactions: 234670 Sorted by model distance: nonbonded pdb=" OG SER B1097 " pdb=" OG SER B1117 " model vdw 1.929 2.440 nonbonded pdb=" OH TYR A 19 " pdb="ZN ZN B1301 " model vdw 1.993 2.230 nonbonded pdb=" OG SER B1117 " pdb="ZN ZN B1301 " model vdw 2.032 2.230 nonbonded pdb=" SG CYS A 103 " pdb=" CB CYS A 106 " model vdw 2.039 3.800 nonbonded pdb=" CB CYS A 106 " pdb="ZN ZN A1702 " model vdw 2.074 2.630 ... (remaining 234665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 4.210 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 82.800 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 30316 Z= 0.492 Angle : 0.878 15.399 40960 Z= 0.502 Chirality : 0.049 0.292 4577 Planarity : 0.005 0.085 5268 Dihedral : 15.048 131.965 11415 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.20 % Favored : 88.53 % Rotamer: Outliers : 0.33 % Allowed : 11.60 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.37 % 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: -4.08 (0.12), residues: 3688 helix: -2.06 (0.12), residues: 1205 sheet: -2.88 (0.19), residues: 536 loop : -3.14 (0.12), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 15 HIS 0.009 0.002 HIS A 612 PHE 0.050 0.002 PHE A 786 TYR 0.032 0.002 TYR A 19 ARG 0.009 0.001 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 636 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.4865 (tp30) cc_final: 0.4279 (pt0) REVERT: A 358 ASP cc_start: 0.7492 (m-30) cc_final: 0.7169 (p0) REVERT: A 479 MET cc_start: 0.7657 (mtt) cc_final: 0.7302 (mtp) REVERT: A 634 TYR cc_start: 0.8253 (m-80) cc_final: 0.7928 (m-80) REVERT: A 941 MET cc_start: 0.8839 (mtm) cc_final: 0.8626 (mtp) REVERT: A 966 GLU cc_start: 0.7338 (tp30) cc_final: 0.7132 (tp30) REVERT: A 1131 SER cc_start: 0.8520 (m) cc_final: 0.8284 (m) REVERT: A 1280 ARG cc_start: 0.7258 (ptp90) cc_final: 0.7041 (mtm110) REVERT: A 1337 LYS cc_start: 0.7017 (tptt) cc_final: 0.6649 (mttt) REVERT: A 1501 GLU cc_start: 0.6984 (mp0) cc_final: 0.6115 (tp30) REVERT: A 1530 LYS cc_start: 0.6104 (mttt) cc_final: 0.5816 (tmtt) REVERT: A 1557 ASN cc_start: 0.7234 (m110) cc_final: 0.7014 (p0) REVERT: A 1559 ILE cc_start: 0.8451 (tt) cc_final: 0.8241 (tp) REVERT: A 1601 ASP cc_start: 0.8613 (p0) cc_final: 0.8381 (p0) REVERT: A 1627 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6961 (mm-30) REVERT: B 1 MET cc_start: 0.3032 (tpt) cc_final: 0.2036 (tpt) REVERT: B 44 LEU cc_start: 0.8887 (tp) cc_final: 0.8371 (tt) REVERT: B 190 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.7993 (mmm-85) REVERT: B 424 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6721 (mmt90) REVERT: B 653 GLU cc_start: 0.8015 (mp0) cc_final: 0.7670 (mt-10) REVERT: B 705 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 861 HIS cc_start: 0.7010 (m170) cc_final: 0.6736 (m90) REVERT: B 943 MET cc_start: 0.9116 (mmt) cc_final: 0.8512 (mmt) REVERT: B 970 ILE cc_start: 0.9034 (mt) cc_final: 0.8828 (mt) REVERT: B 1024 MET cc_start: 0.5786 (ppp) cc_final: 0.5090 (tpt) REVERT: B 1168 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7237 (mtpt) REVERT: C 100 ASP cc_start: 0.8257 (t0) cc_final: 0.8004 (t0) REVERT: C 313 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6916 (tm-30) REVERT: E 40 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7302 (mm110) REVERT: E 166 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7171 (mmm160) REVERT: E 181 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7631 (mtp180) REVERT: G 75 ARG cc_start: 0.6458 (ttm170) cc_final: 0.6151 (ptm160) REVERT: H 35 ASP cc_start: 0.6151 (p0) cc_final: 0.5913 (p0) REVERT: J 48 MET cc_start: 0.8729 (mmm) cc_final: 0.8359 (tpp) REVERT: K 40 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8259 (tp-100) REVERT: L 49 MET cc_start: 0.8328 (mmm) cc_final: 0.7822 (mtm) outliers start: 11 outliers final: 2 residues processed: 643 average time/residue: 0.4812 time to fit residues: 470.6618 Evaluate side-chains 456 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 454 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.9990 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS A 60 ASN A 67 HIS A 79 HIS A 94 GLN A 108 HIS A 232 GLN A 257 GLN ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 533 ASN A 543 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 655 GLN A 735 GLN A 963 GLN ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 32 HIS ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 300 GLN B 386 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 HIS ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 887 HIS B1038 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 HIS ** B1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS C 300 GLN C 307 HIS D 51 ASN E 19 HIS E 20 GLN E 65 ASN E 98 ASN E 99 HIS ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN G 167 GLN H 37 ASN H 118 HIS I 41 ASN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30316 Z= 0.285 Angle : 0.715 11.821 40960 Z= 0.370 Chirality : 0.046 0.291 4577 Planarity : 0.005 0.085 5268 Dihedral : 6.311 60.115 4074 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.68 % Favored : 90.27 % Rotamer: Outliers : 3.91 % Allowed : 17.15 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.37 % 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: -3.00 (0.13), residues: 3688 helix: -0.79 (0.14), residues: 1236 sheet: -2.56 (0.20), residues: 550 loop : -2.68 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1553 HIS 0.015 0.001 HIS C 214 PHE 0.039 0.002 PHE A1638 TYR 0.042 0.002 TYR H 120 ARG 0.008 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 504 time to evaluate : 5.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.7524 (m-30) cc_final: 0.7175 (p0) REVERT: A 1053 ASP cc_start: 0.8501 (t0) cc_final: 0.8206 (t70) REVERT: A 1155 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7580 (tptm) REVERT: A 1307 ASP cc_start: 0.6532 (m-30) cc_final: 0.6120 (t0) REVERT: A 1342 LYS cc_start: 0.6052 (ttmt) cc_final: 0.5719 (ttmm) REVERT: A 1501 GLU cc_start: 0.6967 (mp0) cc_final: 0.6131 (tp30) REVERT: A 1557 ASN cc_start: 0.7265 (m110) cc_final: 0.7042 (p0) REVERT: B 1 MET cc_start: 0.3457 (tpt) cc_final: 0.2251 (tpt) REVERT: B 101 VAL cc_start: 0.9133 (t) cc_final: 0.8865 (p) REVERT: B 152 GLU cc_start: 0.8214 (tt0) cc_final: 0.7984 (tt0) REVERT: B 232 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7038 (pp) REVERT: B 254 MET cc_start: 0.8795 (tpp) cc_final: 0.8512 (ttm) REVERT: B 424 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6578 (mmt180) REVERT: B 705 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 861 HIS cc_start: 0.6976 (m170) cc_final: 0.6769 (m90) REVERT: B 943 MET cc_start: 0.8986 (mmt) cc_final: 0.8446 (mmt) REVERT: B 1024 MET cc_start: 0.5957 (ppp) cc_final: 0.4945 (tpt) REVERT: B 1162 LEU cc_start: 0.7473 (tp) cc_final: 0.7179 (mt) REVERT: B 1168 LYS cc_start: 0.7067 (mtpt) cc_final: 0.6412 (mtpt) REVERT: B 1169 MET cc_start: 0.8402 (pmm) cc_final: 0.8034 (ptp) REVERT: C 100 ASP cc_start: 0.8449 (t0) cc_final: 0.7999 (t0) REVERT: C 123 GLN cc_start: 0.7705 (mm-40) cc_final: 0.6979 (pm20) REVERT: C 179 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7615 (mm110) REVERT: E 13 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7900 (mmm160) REVERT: E 129 THR cc_start: 0.5177 (OUTLIER) cc_final: 0.4851 (p) REVERT: E 166 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7076 (mmm160) REVERT: E 193 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8389 (mt) REVERT: G 33 MET cc_start: 0.5926 (mmm) cc_final: 0.5561 (tpt) REVERT: J 48 MET cc_start: 0.8530 (mmm) cc_final: 0.8223 (tpp) REVERT: J 65 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7435 (pp) REVERT: L 49 MET cc_start: 0.8351 (mmm) cc_final: 0.8129 (mtm) outliers start: 129 outliers final: 81 residues processed: 590 average time/residue: 0.4771 time to fit residues: 450.8556 Evaluate side-chains 520 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 435 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1615 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 334 optimal weight: 8.9990 chunk 361 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1587 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN B 373 GLN B 374 HIS ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 30316 Z= 0.395 Angle : 0.741 11.147 40960 Z= 0.384 Chirality : 0.047 0.232 4577 Planarity : 0.006 0.085 5268 Dihedral : 6.336 55.218 4074 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.79 % Favored : 89.07 % Rotamer: Outliers : 5.57 % Allowed : 19.81 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.13), residues: 3688 helix: -0.43 (0.14), residues: 1245 sheet: -2.44 (0.21), residues: 546 loop : -2.58 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1553 HIS 0.012 0.002 HIS C 214 PHE 0.036 0.002 PHE A 786 TYR 0.044 0.002 TYR H 120 ARG 0.007 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 449 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: A 358 ASP cc_start: 0.7464 (m-30) cc_final: 0.7171 (p0) REVERT: A 449 ARG cc_start: 0.3977 (mtt90) cc_final: 0.3673 (mtt180) REVERT: A 662 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7994 (pp20) REVERT: A 814 GLU cc_start: 0.7983 (tp30) cc_final: 0.7714 (tp30) REVERT: A 1053 ASP cc_start: 0.8471 (t0) cc_final: 0.8184 (t0) REVERT: A 1277 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7521 (ttm110) REVERT: A 1342 LYS cc_start: 0.6105 (ttmt) cc_final: 0.5721 (ttmm) REVERT: A 1501 GLU cc_start: 0.6971 (mp0) cc_final: 0.6132 (tp30) REVERT: A 1557 ASN cc_start: 0.7375 (m110) cc_final: 0.7047 (p0) REVERT: A 1626 ILE cc_start: 0.8367 (mt) cc_final: 0.7938 (tt) REVERT: B 1 MET cc_start: 0.3525 (tpt) cc_final: 0.2211 (tpt) REVERT: B 80 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: B 101 VAL cc_start: 0.9148 (t) cc_final: 0.8907 (p) REVERT: B 254 MET cc_start: 0.8805 (tpp) cc_final: 0.8558 (ttm) REVERT: B 286 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7276 (tm-30) REVERT: B 424 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6605 (mmt180) REVERT: B 705 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 861 HIS cc_start: 0.7019 (m170) cc_final: 0.6693 (m90) REVERT: B 943 MET cc_start: 0.9110 (mmt) cc_final: 0.8478 (mmt) REVERT: B 1024 MET cc_start: 0.6089 (ppp) cc_final: 0.5044 (tpt) REVERT: C 100 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8137 (t0) REVERT: C 179 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8284 (mm-40) REVERT: E 106 TYR cc_start: 0.6914 (p90) cc_final: 0.6675 (p90) REVERT: E 166 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7100 (mmm160) REVERT: F 118 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8149 (ptpt) REVERT: J 48 MET cc_start: 0.8672 (mmm) cc_final: 0.8292 (tpp) REVERT: J 65 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7389 (pp) REVERT: K 36 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8324 (p) REVERT: L 42 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8105 (mtm110) outliers start: 184 outliers final: 116 residues processed: 584 average time/residue: 0.3952 time to fit residues: 375.9326 Evaluate side-chains 539 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 416 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 10.0000 chunk 251 optimal weight: 0.0010 chunk 173 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 335 optimal weight: 7.9990 chunk 355 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 374 HIS ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 ASN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN E 19 HIS G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30316 Z= 0.247 Angle : 0.664 10.710 40960 Z= 0.344 Chirality : 0.044 0.217 4577 Planarity : 0.005 0.085 5268 Dihedral : 6.055 55.157 4074 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.35 % Favored : 90.59 % Rotamer: Outliers : 5.30 % Allowed : 21.39 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 3688 helix: -0.11 (0.15), residues: 1241 sheet: -2.26 (0.21), residues: 548 loop : -2.39 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1553 HIS 0.011 0.001 HIS C 214 PHE 0.024 0.001 PHE A1638 TYR 0.039 0.001 TYR H 120 ARG 0.009 0.000 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 461 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6259 (tm-30) REVERT: A 107 HIS cc_start: 0.6066 (m-70) cc_final: 0.5567 (m90) REVERT: A 358 ASP cc_start: 0.7331 (m-30) cc_final: 0.7092 (p0) REVERT: A 449 ARG cc_start: 0.3752 (mtt90) cc_final: 0.3502 (mtt180) REVERT: A 751 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9112 (mt) REVERT: A 860 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: A 1053 ASP cc_start: 0.8473 (t0) cc_final: 0.8143 (t0) REVERT: A 1154 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7452 (p0) REVERT: A 1155 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7556 (mmtp) REVERT: A 1187 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8582 (mm) REVERT: A 1277 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7608 (ttm110) REVERT: A 1342 LYS cc_start: 0.6253 (ttmt) cc_final: 0.6045 (tttm) REVERT: A 1501 GLU cc_start: 0.6891 (mp0) cc_final: 0.6109 (tp30) REVERT: A 1557 ASN cc_start: 0.7469 (m110) cc_final: 0.7026 (p0) REVERT: A 1626 ILE cc_start: 0.8298 (mt) cc_final: 0.7920 (tt) REVERT: B 1 MET cc_start: 0.2844 (tpt) cc_final: 0.1374 (tpt) REVERT: B 55 LYS cc_start: 0.8289 (mmmm) cc_final: 0.8082 (mmmt) REVERT: B 80 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6928 (m-30) REVERT: B 101 VAL cc_start: 0.9064 (t) cc_final: 0.8813 (p) REVERT: B 254 MET cc_start: 0.8809 (tpp) cc_final: 0.8563 (ttt) REVERT: B 264 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 286 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 289 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 424 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6613 (mmt180) REVERT: B 705 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 861 HIS cc_start: 0.6984 (m170) cc_final: 0.6634 (m90) REVERT: B 943 MET cc_start: 0.9003 (mmt) cc_final: 0.8416 (mmt) REVERT: B 1024 MET cc_start: 0.6142 (ppp) cc_final: 0.4984 (tpt) REVERT: B 1169 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8185 (ptp) REVERT: C 100 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8044 (t0) REVERT: E 137 VAL cc_start: 0.5811 (OUTLIER) cc_final: 0.5571 (m) REVERT: E 166 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7056 (mmm160) REVERT: F 118 LYS cc_start: 0.8358 (pttt) cc_final: 0.8092 (ptpt) REVERT: J 65 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7454 (pp) REVERT: K 36 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8294 (p) REVERT: L 23 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8764 (mp) REVERT: L 42 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.8157 (mtm110) outliers start: 175 outliers final: 110 residues processed: 587 average time/residue: 0.4203 time to fit residues: 401.0838 Evaluate side-chains 543 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 419 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 319 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 HIS A 117 HIS ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN A1486 ASN A1519 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 HIS G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 30316 Z= 0.393 Angle : 0.725 12.377 40960 Z= 0.374 Chirality : 0.046 0.226 4577 Planarity : 0.005 0.086 5268 Dihedral : 6.169 54.246 4074 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.66 % Favored : 89.24 % Rotamer: Outliers : 6.60 % Allowed : 21.54 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 3688 helix: -0.08 (0.15), residues: 1243 sheet: -2.19 (0.21), residues: 537 loop : -2.36 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1553 HIS 0.015 0.002 HIS E 19 PHE 0.033 0.002 PHE A 786 TYR 0.040 0.002 TYR H 120 ARG 0.010 0.001 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 428 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: A 94 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6277 (tm-30) REVERT: A 220 HIS cc_start: 0.6007 (t70) cc_final: 0.5608 (t-90) REVERT: A 449 ARG cc_start: 0.3766 (mtt90) cc_final: 0.3503 (mtt180) REVERT: A 662 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8066 (pp20) REVERT: A 742 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 860 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6758 (mp10) REVERT: A 1053 ASP cc_start: 0.8631 (t0) cc_final: 0.8329 (t0) REVERT: A 1155 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7588 (mmtp) REVERT: A 1277 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7624 (ttm110) REVERT: A 1342 LYS cc_start: 0.6355 (ttmt) cc_final: 0.6047 (tttp) REVERT: A 1557 ASN cc_start: 0.7547 (m110) cc_final: 0.7064 (p0) REVERT: A 1626 ILE cc_start: 0.8333 (mt) cc_final: 0.7991 (tt) REVERT: B 1 MET cc_start: 0.4047 (tpt) cc_final: 0.2758 (tpt) REVERT: B 80 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: B 101 VAL cc_start: 0.9090 (t) cc_final: 0.8854 (p) REVERT: B 134 MET cc_start: 0.8490 (mtm) cc_final: 0.8095 (mtp) REVERT: B 254 MET cc_start: 0.8821 (tpp) cc_final: 0.8611 (ttt) REVERT: B 264 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8079 (t0) REVERT: B 286 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 289 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 424 ARG cc_start: 0.7230 (mtp180) cc_final: 0.6689 (mmt180) REVERT: B 705 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 861 HIS cc_start: 0.7004 (m170) cc_final: 0.6554 (m90) REVERT: B 943 MET cc_start: 0.9098 (mmt) cc_final: 0.8423 (mmt) REVERT: B 1024 MET cc_start: 0.6205 (ppp) cc_final: 0.5033 (tpt) REVERT: B 1169 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (ptp) REVERT: C 100 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8050 (t0) REVERT: E 166 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7055 (mmm160) REVERT: F 118 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8108 (ptpt) REVERT: J 10 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7683 (m) REVERT: J 65 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7313 (pp) REVERT: K 36 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8322 (p) REVERT: L 23 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8813 (mp) outliers start: 218 outliers final: 156 residues processed: 598 average time/residue: 0.3988 time to fit residues: 390.0736 Evaluate side-chains 594 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 423 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 909 LYS Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 356 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 374 HIS B 562 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30316 Z= 0.206 Angle : 0.639 11.605 40960 Z= 0.330 Chirality : 0.044 0.232 4577 Planarity : 0.005 0.085 5268 Dihedral : 5.855 53.734 4074 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.41 % Favored : 91.54 % Rotamer: Outliers : 5.30 % Allowed : 23.24 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3688 helix: 0.18 (0.15), residues: 1247 sheet: -1.99 (0.22), residues: 533 loop : -2.21 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 916 HIS 0.025 0.001 HIS A 79 PHE 0.025 0.001 PHE E 76 TYR 0.032 0.001 TYR H 120 ARG 0.010 0.000 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 450 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7384 (p90) cc_final: 0.6918 (p-80) REVERT: A 220 HIS cc_start: 0.6013 (t70) cc_final: 0.5665 (t-90) REVERT: A 449 ARG cc_start: 0.3663 (mtt90) cc_final: 0.3461 (mtt180) REVERT: A 479 MET cc_start: 0.7534 (mmm) cc_final: 0.7174 (mmt) REVERT: A 662 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: A 860 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: A 1053 ASP cc_start: 0.8444 (t0) cc_final: 0.8137 (t0) REVERT: A 1155 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7520 (mmtp) REVERT: A 1184 GLN cc_start: 0.8709 (tt0) cc_final: 0.8188 (tt0) REVERT: A 1557 ASN cc_start: 0.7529 (m110) cc_final: 0.7048 (p0) REVERT: A 1626 ILE cc_start: 0.8356 (mt) cc_final: 0.7991 (tt) REVERT: B 1 MET cc_start: 0.3125 (tpt) cc_final: 0.1629 (tpt) REVERT: B 101 VAL cc_start: 0.8975 (t) cc_final: 0.8734 (p) REVERT: B 264 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8052 (t0) REVERT: B 289 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 424 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6634 (mmt90) REVERT: B 518 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8272 (pp) REVERT: B 688 MET cc_start: 0.7494 (mtm) cc_final: 0.7265 (mtm) REVERT: B 705 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7551 (tp-100) REVERT: B 861 HIS cc_start: 0.6925 (m170) cc_final: 0.6392 (m90) REVERT: B 943 MET cc_start: 0.8969 (mmt) cc_final: 0.8396 (mmt) REVERT: B 1024 MET cc_start: 0.6237 (ppp) cc_final: 0.4896 (tpt) REVERT: B 1060 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: B 1169 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8099 (ptp) REVERT: E 166 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7045 (mmm160) REVERT: G 33 MET cc_start: 0.5984 (mmm) cc_final: 0.5575 (mmm) REVERT: J 65 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7279 (pp) REVERT: K 36 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8294 (p) REVERT: L 21 ILE cc_start: 0.8878 (mm) cc_final: 0.8634 (mt) outliers start: 175 outliers final: 112 residues processed: 579 average time/residue: 0.4030 time to fit residues: 379.2299 Evaluate side-chains 536 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 415 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS A 590 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 373 GLN B 374 HIS ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 HIS G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 30316 Z= 0.413 Angle : 0.739 12.771 40960 Z= 0.382 Chirality : 0.047 0.227 4577 Planarity : 0.005 0.086 5268 Dihedral : 6.156 53.576 4074 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.28 % Favored : 88.67 % Rotamer: Outliers : 6.18 % Allowed : 23.36 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3688 helix: 0.03 (0.15), residues: 1254 sheet: -2.10 (0.21), residues: 548 loop : -2.28 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 37 HIS 0.010 0.001 HIS B 338 PHE 0.034 0.002 PHE A 786 TYR 0.040 0.002 TYR H 120 ARG 0.011 0.001 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 429 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: A 94 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: A 220 HIS cc_start: 0.6137 (t70) cc_final: 0.5727 (t-90) REVERT: A 662 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: A 742 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 860 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: A 1053 ASP cc_start: 0.8618 (t0) cc_final: 0.8413 (t0) REVERT: A 1184 GLN cc_start: 0.8805 (tt0) cc_final: 0.8305 (tt0) REVERT: A 1557 ASN cc_start: 0.7544 (m110) cc_final: 0.7173 (p0) REVERT: A 1626 ILE cc_start: 0.8227 (mt) cc_final: 0.7942 (tt) REVERT: B 1 MET cc_start: 0.4106 (tpt) cc_final: 0.2661 (tpt) REVERT: B 101 VAL cc_start: 0.9092 (t) cc_final: 0.8830 (p) REVERT: B 134 MET cc_start: 0.8547 (mtm) cc_final: 0.8157 (mtp) REVERT: B 264 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8021 (t0) REVERT: B 286 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 289 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7818 (mp) REVERT: B 424 ARG cc_start: 0.7366 (mtp180) cc_final: 0.6790 (mmt180) REVERT: B 688 MET cc_start: 0.7655 (mtm) cc_final: 0.7380 (mtm) REVERT: B 705 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 820 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6245 (mtm110) REVERT: B 861 HIS cc_start: 0.6889 (m170) cc_final: 0.6502 (m90) REVERT: B 943 MET cc_start: 0.9153 (mmt) cc_final: 0.8409 (mmt) REVERT: B 1024 MET cc_start: 0.6073 (ppp) cc_final: 0.4859 (tpt) REVERT: B 1060 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: B 1169 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8374 (ptp) REVERT: C 221 GLN cc_start: 0.8144 (pt0) cc_final: 0.7892 (pt0) REVERT: E 195 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8083 (mtt180) REVERT: J 10 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7713 (m) REVERT: J 65 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7329 (pp) outliers start: 204 outliers final: 144 residues processed: 588 average time/residue: 0.3938 time to fit residues: 381.1297 Evaluate side-chains 567 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 410 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1264 CYS Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1601 ASP Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 HIS A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 373 GLN B 562 GLN B 640 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30316 Z= 0.236 Angle : 0.667 11.453 40960 Z= 0.342 Chirality : 0.044 0.208 4577 Planarity : 0.005 0.086 5268 Dihedral : 5.912 53.431 4074 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.76 % Favored : 91.21 % Rotamer: Outliers : 5.39 % Allowed : 24.27 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.25 % 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: -1.98 (0.13), residues: 3688 helix: 0.22 (0.15), residues: 1251 sheet: -2.04 (0.21), residues: 548 loop : -2.19 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 916 HIS 0.010 0.001 HIS A 79 PHE 0.028 0.001 PHE A 372 TYR 0.034 0.001 TYR H 120 ARG 0.010 0.000 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 433 time to evaluate : 3.165 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: A 31 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: A 94 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: A 220 HIS cc_start: 0.6116 (t70) cc_final: 0.5712 (t-90) REVERT: A 662 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: A 860 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: A 1053 ASP cc_start: 0.8619 (t0) cc_final: 0.8405 (t0) REVERT: A 1154 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 1155 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7437 (mmmt) REVERT: A 1184 GLN cc_start: 0.8639 (tt0) cc_final: 0.8164 (tt0) REVERT: A 1300 ARG cc_start: 0.7463 (ttt180) cc_final: 0.7145 (ttt-90) REVERT: A 1342 LYS cc_start: 0.6587 (ttpp) cc_final: 0.6223 (ttmm) REVERT: A 1557 ASN cc_start: 0.7553 (m110) cc_final: 0.7175 (p0) REVERT: A 1626 ILE cc_start: 0.8359 (mt) cc_final: 0.8090 (tt) REVERT: B 1 MET cc_start: 0.4047 (tpt) cc_final: 0.2609 (tpt) REVERT: B 134 MET cc_start: 0.8453 (mtm) cc_final: 0.8038 (mtp) REVERT: B 264 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8028 (t0) REVERT: B 283 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6993 (p0) REVERT: B 286 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 289 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 346 PHE cc_start: 0.9126 (t80) cc_final: 0.8801 (t80) REVERT: B 424 ARG cc_start: 0.7242 (mtp180) cc_final: 0.6711 (mmt90) REVERT: B 657 MET cc_start: 0.7207 (mtt) cc_final: 0.6854 (mtt) REVERT: B 688 MET cc_start: 0.7674 (mtm) cc_final: 0.7406 (mtm) REVERT: B 820 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6158 (mtm110) REVERT: B 861 HIS cc_start: 0.6786 (m170) cc_final: 0.6407 (m90) REVERT: B 943 MET cc_start: 0.9042 (mmt) cc_final: 0.8329 (mmt) REVERT: B 1024 MET cc_start: 0.6024 (ppp) cc_final: 0.4793 (tpt) REVERT: B 1060 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: B 1169 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8175 (ptp) REVERT: E 20 GLN cc_start: 0.8585 (mt0) cc_final: 0.8348 (mt0) REVERT: G 33 MET cc_start: 0.5952 (mmm) cc_final: 0.5735 (mmm) REVERT: G 52 ASP cc_start: 0.7223 (p0) cc_final: 0.5960 (m-30) REVERT: J 10 CYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7619 (m) outliers start: 178 outliers final: 132 residues processed: 570 average time/residue: 0.3936 time to fit residues: 367.1192 Evaluate side-chains 560 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 416 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1601 ASP Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 0.6980 chunk 339 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 330 optimal weight: 0.3980 chunk 198 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 chunk 312 optimal weight: 0.1980 chunk 329 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30316 Z= 0.183 Angle : 0.636 10.691 40960 Z= 0.325 Chirality : 0.043 0.210 4577 Planarity : 0.005 0.086 5268 Dihedral : 5.635 52.806 4074 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.60 % Favored : 91.38 % Rotamer: Outliers : 4.39 % Allowed : 25.39 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3688 helix: 0.40 (0.15), residues: 1260 sheet: -1.92 (0.22), residues: 536 loop : -2.11 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 916 HIS 0.011 0.001 HIS A 79 PHE 0.016 0.001 PHE A 247 TYR 0.029 0.001 TYR A 896 ARG 0.010 0.000 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 448 time to evaluate : 3.671 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: A 31 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: A 94 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6166 (tm-30) REVERT: A 220 HIS cc_start: 0.6048 (t70) cc_final: 0.5658 (t-90) REVERT: A 449 ARG cc_start: 0.3658 (mtt90) cc_final: 0.3449 (mtt180) REVERT: A 479 MET cc_start: 0.7527 (mmm) cc_final: 0.7319 (mmt) REVERT: A 617 MET cc_start: 0.9217 (mtm) cc_final: 0.9009 (mtt) REVERT: A 860 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: A 1053 ASP cc_start: 0.8403 (t0) cc_final: 0.8172 (t0) REVERT: A 1169 LEU cc_start: 0.7554 (mt) cc_final: 0.7332 (mp) REVERT: A 1184 GLN cc_start: 0.8525 (tt0) cc_final: 0.8072 (tt0) REVERT: A 1300 ARG cc_start: 0.7499 (ttt180) cc_final: 0.7247 (ttt90) REVERT: A 1342 LYS cc_start: 0.6493 (ttpp) cc_final: 0.6044 (ttmm) REVERT: A 1557 ASN cc_start: 0.7469 (m110) cc_final: 0.7065 (p0) REVERT: A 1627 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6591 (tp30) REVERT: B 1 MET cc_start: 0.3412 (tpt) cc_final: 0.2000 (tpt) REVERT: B 24 ASP cc_start: 0.8037 (m-30) cc_final: 0.7811 (m-30) REVERT: B 54 GLU cc_start: 0.7588 (pm20) cc_final: 0.7319 (pt0) REVERT: B 264 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7966 (t0) REVERT: B 283 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6978 (p0) REVERT: B 286 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 289 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 346 PHE cc_start: 0.9061 (t80) cc_final: 0.8743 (t80) REVERT: B 424 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6736 (mmt180) REVERT: B 657 MET cc_start: 0.7325 (mtt) cc_final: 0.7003 (mtt) REVERT: B 688 MET cc_start: 0.7497 (mtm) cc_final: 0.7280 (mtm) REVERT: B 705 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7571 (tp-100) REVERT: B 820 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6009 (mtm110) REVERT: B 861 HIS cc_start: 0.6791 (m170) cc_final: 0.6386 (m90) REVERT: B 943 MET cc_start: 0.8928 (mmt) cc_final: 0.8316 (mmt) REVERT: B 1024 MET cc_start: 0.6091 (ppp) cc_final: 0.4846 (tpt) REVERT: B 1072 LEU cc_start: 0.8944 (tt) cc_final: 0.8681 (tt) REVERT: B 1078 MET cc_start: 0.8409 (tmm) cc_final: 0.7859 (ttp) REVERT: B 1169 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7998 (ptp) REVERT: E 20 GLN cc_start: 0.8647 (mt0) cc_final: 0.8434 (mt0) REVERT: E 165 LEU cc_start: 0.8974 (mt) cc_final: 0.8634 (mp) REVERT: E 195 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7879 (mtt180) REVERT: G 33 MET cc_start: 0.5858 (mmm) cc_final: 0.5440 (mmm) REVERT: G 52 ASP cc_start: 0.7211 (p0) cc_final: 0.6009 (m-30) REVERT: G 64 MET cc_start: 0.6898 (tpp) cc_final: 0.6643 (tpt) REVERT: L 21 ILE cc_start: 0.8955 (mm) cc_final: 0.8696 (mt) outliers start: 145 outliers final: 114 residues processed: 562 average time/residue: 0.4001 time to fit residues: 364.7776 Evaluate side-chains 546 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 422 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1264 CYS Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1601 ASP Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1627 GLU Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 7.9990 chunk 349 optimal weight: 0.0670 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 374 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30316 Z= 0.263 Angle : 0.663 11.168 40960 Z= 0.340 Chirality : 0.044 0.201 4577 Planarity : 0.005 0.087 5268 Dihedral : 5.669 52.832 4074 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.33 % Favored : 90.65 % Rotamer: Outliers : 4.00 % Allowed : 26.05 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.23 % 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: -1.75 (0.14), residues: 3688 helix: 0.43 (0.15), residues: 1258 sheet: -1.94 (0.22), residues: 539 loop : -2.07 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1489 HIS 0.025 0.001 HIS A 439 PHE 0.022 0.001 PHE G 69 TYR 0.037 0.002 TYR E 106 ARG 0.010 0.001 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 415 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: A 94 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: A 220 HIS cc_start: 0.6119 (t70) cc_final: 0.5708 (t-90) REVERT: A 334 ARG cc_start: 0.6935 (ptm160) cc_final: 0.6720 (ttm170) REVERT: A 479 MET cc_start: 0.7540 (mmm) cc_final: 0.7339 (mmt) REVERT: A 860 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.6701 (mp10) REVERT: A 1169 LEU cc_start: 0.7534 (mt) cc_final: 0.7320 (mp) REVERT: A 1184 GLN cc_start: 0.8631 (tt0) cc_final: 0.8163 (tt0) REVERT: A 1236 MET cc_start: 0.6557 (ttp) cc_final: 0.6295 (ptm) REVERT: A 1300 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7280 (ttt90) REVERT: A 1342 LYS cc_start: 0.6514 (ttpp) cc_final: 0.6129 (ttmm) REVERT: A 1557 ASN cc_start: 0.7551 (m110) cc_final: 0.7201 (p0) REVERT: A 1627 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6574 (tp30) REVERT: B 1 MET cc_start: 0.3494 (tpt) cc_final: 0.2154 (tpt) REVERT: B 54 GLU cc_start: 0.7599 (pm20) cc_final: 0.7323 (pt0) REVERT: B 264 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7891 (t0) REVERT: B 283 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 289 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7764 (mt) REVERT: B 346 PHE cc_start: 0.9104 (t80) cc_final: 0.8772 (t80) REVERT: B 424 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6805 (mmt180) REVERT: B 657 MET cc_start: 0.7474 (mtt) cc_final: 0.7215 (mtt) REVERT: B 688 MET cc_start: 0.7533 (mtm) cc_final: 0.7231 (mtm) REVERT: B 705 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7577 (tp-100) REVERT: B 820 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6133 (mtm110) REVERT: B 861 HIS cc_start: 0.6767 (m170) cc_final: 0.6402 (m90) REVERT: B 943 MET cc_start: 0.9010 (mmt) cc_final: 0.8326 (mmt) REVERT: B 1024 MET cc_start: 0.6061 (ppp) cc_final: 0.4812 (tpt) REVERT: B 1169 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8169 (ptp) REVERT: E 20 GLN cc_start: 0.8694 (mt0) cc_final: 0.8465 (mt0) REVERT: E 195 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7990 (mtt180) REVERT: G 52 ASP cc_start: 0.7171 (p0) cc_final: 0.5926 (m-30) outliers start: 132 outliers final: 115 residues processed: 523 average time/residue: 0.3901 time to fit residues: 332.1557 Evaluate side-chains 530 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 405 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 906 ASP Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1264 CYS Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1601 ASP Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1627 GLU Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 0.7980 chunk 310 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 14 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 373 GLN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN G 167 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.148880 restraints weight = 40207.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137362 restraints weight = 78862.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134733 restraints weight = 59803.963| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 30316 Z= 0.331 Angle : 0.699 11.376 40960 Z= 0.359 Chirality : 0.045 0.211 4577 Planarity : 0.005 0.087 5268 Dihedral : 5.821 52.957 4072 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.71 % Favored : 89.26 % Rotamer: Outliers : 4.60 % Allowed : 25.66 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.23 % 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: -1.82 (0.14), residues: 3688 helix: 0.35 (0.15), residues: 1257 sheet: -1.99 (0.22), residues: 536 loop : -2.09 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1489 HIS 0.023 0.001 HIS A 439 PHE 0.026 0.002 PHE A 786 TYR 0.036 0.002 TYR H 120 ARG 0.008 0.001 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6890.99 seconds wall clock time: 127 minutes 34.09 seconds (7654.09 seconds total)