Starting phenix.real_space_refine on Wed Feb 21 18:18:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/02_2024/7aoe_11842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/02_2024/7aoe_11842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/02_2024/7aoe_11842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/02_2024/7aoe_11842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/02_2024/7aoe_11842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/02_2024/7aoe_11842.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 569 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 44 5.49 5 S 165 5.16 5 C 19404 2.51 5 N 5347 2.21 5 O 5862 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 TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 688": "OD1" <-> "OD2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ASP 719": "OD1" <-> "OD2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ASP 797": "OD1" <-> "OD2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 898": "OD1" <-> "OD2" Residue "A ASP 927": "OD1" <-> "OD2" Residue "A TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A ASP 1253": "OD1" <-> "OD2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A ARG 1280": "NH1" <-> "NH2" Residue "A ASP 1302": "OD1" <-> "OD2" Residue "A TYR 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1321": "OE1" <-> "OE2" Residue "A PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1493": "OE1" <-> "OE2" Residue "A GLU 1510": "OE1" <-> "OE2" Residue "A GLU 1554": "OE1" <-> "OE2" Residue "A PHE 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1579": "OE1" <-> "OE2" Residue "A PHE 1593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1601": "OD1" <-> "OD2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A PHE 1672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 80": "OD1" <-> "OD2" 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 GLU 158": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" 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 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 581": "OD1" <-> "OD2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 658": "OD1" <-> "OD2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B ASP 880": "OD1" <-> "OD2" Residue "B ASP 900": "OD1" <-> "OD2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1006": "OE1" <-> "OE2" Residue "B TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 114": "OE1" <-> "OE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 130": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" 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 67": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "K ASP 31": "OD1" <-> "OD2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K ASP 96": "OD1" <-> "OD2" Residue "K ASP 97": "OD1" <-> "OD2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30828 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 11102 Classifications: {'peptide': 1401} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1334} Chain breaks: 11 Chain: "B" Number of atoms: 9254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9254 Classifications: {'peptide': 1174} Link IDs: {'PTRANS': 60, 'TRANS': 1113} 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': 5, 'PTRANS': 7, 'TRANS': 194} 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: "U" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} 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 63 105.178 56.173 89.829 1.00 73.94 S ATOM 501 SG CYS A 66 104.500 54.333 89.518 1.00 69.95 S ATOM 565 SG CYS A 73 102.390 56.260 89.059 1.00 69.42 S ATOM 809 SG CYS A 103 74.652 45.015 131.808 1.00 93.16 S ATOM 835 SG CYS A 106 75.286 41.093 132.530 1.00 94.91 S ATOM 1540 SG CYS A 228 72.874 44.805 132.585 1.00102.92 S ATOM 1562 SG CYS A 231 75.022 43.102 136.179 1.00105.69 S ATOM 19731 SG CYS B1089 95.549 39.542 95.331 1.00 47.27 S ATOM 19756 SG CYS B1092 94.762 41.006 97.061 1.00 52.44 S ATOM 19912 SG CYS B1115 97.730 42.128 96.500 1.00 57.89 S ATOM 19935 SG CYS B1118 96.363 38.955 98.731 1.00 67.35 S ATOM 27820 SG CYS I 10 36.598 102.678 138.458 1.00 85.76 S ATOM 27841 SG CYS I 13 40.186 102.456 138.365 1.00 84.93 S ATOM 27946 SG CYS I 27 38.860 101.194 140.972 1.00104.55 S ATOM 27969 SG CYS I 30 39.264 102.522 140.348 1.00 95.27 S ATOM 28268 SG CYS J 7 63.115 93.491 42.813 1.00 17.17 S ATOM 28563 SG CYS J 44 59.353 91.760 42.704 1.00 20.42 S ATOM 28569 SG CYS J 45 61.478 94.155 41.227 1.00 18.78 S ATOM 29556 SG CYS L 24 90.933 112.237 71.571 1.00 36.02 S ATOM 29575 SG CYS L 27 91.349 114.118 71.395 1.00 36.10 S ATOM 29682 SG CYS L 41 93.551 113.693 72.623 1.00 50.40 S ATOM 29708 SG CYS L 44 91.838 114.994 72.540 1.00 52.02 S Time building chain proxies: 16.07, per 1000 atoms: 0.52 Number of scatterers: 30828 At special positions: 0 Unit cell: (161.652, 137.192, 156.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 165 16.00 P 44 15.00 O 5862 8.00 N 5347 7.00 C 19404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.73 Conformation dependent library (CDL) restraints added in 6.0 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 106 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1118 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1089 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1115 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " Number of angles added : 27 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7062 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 45 sheets defined 37.6% alpha, 13.1% beta 11 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 10.57 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.789A pdb=" N VAL A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.694A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.885A pdb=" N LEU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.630A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.721A pdb=" N LEU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) 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 470 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: 3.593A 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 633 through 641 removed outlier: 3.923A pdb=" N CYS A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 removed outlier: 3.570A pdb=" N ARG A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 686 through 698 removed outlier: 3.683A pdb=" N CYS A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.837A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 817 through 840 removed outlier: 3.906A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 removed outlier: 3.615A pdb=" N GLU A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 936 through 944 removed outlier: 4.047A pdb=" N MET A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.748A 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 1026 removed outlier: 3.637A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1024 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.039A pdb=" N TYR A1031 " --> pdb=" O ARG A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1077 removed outlier: 4.068A pdb=" N HIS A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1076 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1072 through 1077' Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 3.709A pdb=" N SER A1082 " --> pdb=" O GLN A1078 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.768A pdb=" N ILE A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.188A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.865A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.582A pdb=" N LYS A1127 " --> pdb=" O PRO A1123 " (cutoff:3.500A) 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: 3.757A 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 1275 removed outlier: 3.785A pdb=" N VAL A1275 " --> pdb=" O VAL A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1271 through 1275' Processing helix chain 'A' and resid 1305 through 1313 Processing helix chain 'A' and resid 1316 through 1345 removed outlier: 3.533A pdb=" N GLN A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1515 Processing helix chain 'A' and resid 1548 through 1555 removed outlier: 3.622A pdb=" N GLU A1554 " --> pdb=" O LYS A1550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.741A pdb=" N GLY A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1595 removed outlier: 3.587A pdb=" N VAL A1595 " --> pdb=" O SER A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.826A 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 1633 through 1639 removed outlier: 4.442A pdb=" N GLU A1639 " --> pdb=" O LYS A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1652 Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.682A 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 14 removed outlier: 3.556A pdb=" N ASN B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.237A 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: 3.851A pdb=" N GLY B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.577A 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: 3.858A pdb=" N ASN B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.796A pdb=" N LEU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.750A pdb=" N GLU B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.689A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.849A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.531A pdb=" N MET B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.687A 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 Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.563A 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: 3.618A 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 795 through 800 removed outlier: 4.174A pdb=" N LYS B 799 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 795 through 800' 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: 3.896A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1059 through 1068 Processing helix chain 'B' and resid 1069 through 1079 Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 3.581A pdb=" N ASN B1156 " --> pdb=" O PRO B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.522A pdb=" N ALA C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.707A pdb=" N VAL C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.724A pdb=" N PHE C 119 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.605A pdb=" N PHE C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.613A pdb=" N VAL C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.053A 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 344 Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.692A pdb=" N VAL E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.739A pdb=" N PHE E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.520A pdb=" N LYS E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 122' Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.594A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.742A 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: 3.874A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE G 37 " --> pdb=" O MET G 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 4.086A pdb=" N LYS H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.902A pdb=" N THR J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.658A pdb=" N LEU J 35 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 50 removed outlier: 4.522A pdb=" N ILE J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'K' and resid 43 through 56 removed outlier: 3.616A pdb=" N GLY K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.731A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 15 removed outlier: 4.471A 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 81 removed outlier: 3.927A pdb=" N ILE A 365 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.623A pdb=" N SER A 490 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 619 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.986A pdb=" N SER A 493 " --> pdb=" O MET A 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 6.852A pdb=" N LYS A 592 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE A 544 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A 594 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AA7, first strand: chain 'A' and resid 734 through 736 removed outlier: 6.201A pdb=" N ILE H 75 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 767 removed outlier: 7.609A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 961 through 962 removed outlier: 3.753A pdb=" N GLY A 961 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 995 " --> pdb=" O GLY A 961 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1050 through 1052 removed outlier: 7.111A pdb=" N VAL A1051 " --> pdb=" O VAL A1059 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1524 through 1530 removed outlier: 4.751A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A1530 " --> pdb=" O LYS A1541 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS A1541 " --> pdb=" O LYS A1530 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1477 through 1482 removed outlier: 5.371A pdb=" N GLN A1278 " --> pdb=" O ASP A1302 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL I 44 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB5, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.548A pdb=" N ARG B 78 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER B 115 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET B 139 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU B 117 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 180 through 182 Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.632A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET B 184 " --> pdb=" O HIS B 480 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.577A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 250 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 572 removed outlier: 4.022A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 561 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU B 625 " --> pdb=" O TRP B 558 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 628 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 610 " --> pdb=" O PHE B 628 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 646 through 649 Processing sheet with id=AC3, first strand: chain 'B' and resid 725 through 729 removed outlier: 3.917A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET L 49 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC5, first strand: chain 'B' and resid 932 through 934 removed outlier: 8.297A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 754 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 809 through 810 Processing sheet with id=AC7, first strand: chain 'B' and resid 843 through 845 removed outlier: 7.307A pdb=" N GLU B 858 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 923 through 924 Processing sheet with id=AC9, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AD1, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD2, first strand: chain 'B' and resid 1119 through 1121 removed outlier: 3.592A pdb=" N TRP B1132 " --> pdb=" O PHE B1140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 53 removed outlier: 6.722A pdb=" N VAL C 59 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 53 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N ARG C 303 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N HIS C 241 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N ARG C 305 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N THR C 239 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS C 307 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 237 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.441A pdb=" N VAL C 140 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 112 through 113 removed outlier: 4.059A pdb=" N ARG C 192 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.738A pdb=" N GLU C 148 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.798A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AD9, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.541A pdb=" N LYS D 13 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 8 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 55 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP G 77 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN G 53 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.541A pdb=" N LYS D 13 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 8 " --> pdb=" O GLU D 15 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.789A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AE4, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.894A pdb=" N GLY G 46 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 109 through 114 removed outlier: 7.124A pdb=" N HIS G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 96 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY G 102 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 169 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.612A pdb=" N SER H 15 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE H 42 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 95 " --> pdb=" O MET H 102 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG H 82 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AE8, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.518A pdb=" N ILE K 23 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 34 through 35 1108 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 14.29 Time building geometry restraints manager: 14.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9098 1.33 - 1.46: 6431 1.46 - 1.58: 15657 1.58 - 1.70: 87 1.70 - 1.83: 266 Bond restraints: 31539 Sorted by residual: bond pdb=" CA ARG B1032 " pdb=" CB ARG B1032 " ideal model delta sigma weight residual 1.527 1.467 0.060 2.48e-02 1.63e+03 5.92e+00 bond pdb=" C ASP A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.336 1.313 0.023 9.80e-03 1.04e+04 5.44e+00 bond pdb=" CA ASP A 700 " pdb=" C ASP A 700 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.80e-02 3.09e+03 5.19e+00 bond pdb=" CB TRP A 695 " pdb=" CG TRP A 695 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 5.00e+00 bond pdb=" C LEU A 624 " pdb=" N PRO A 625 " ideal model delta sigma weight residual 1.333 1.308 0.025 1.20e-02 6.94e+03 4.30e+00 ... (remaining 31534 not shown) Histogram of bond angle deviations from ideal: 96.06 - 103.68: 588 103.68 - 111.29: 13349 111.29 - 118.90: 12084 118.90 - 126.52: 16273 126.52 - 134.13: 522 Bond angle restraints: 42816 Sorted by residual: angle pdb=" C GLU A1065 " pdb=" N ASP A1066 " pdb=" CA ASP A1066 " ideal model delta sigma weight residual 121.54 133.95 -12.41 1.91e+00 2.74e-01 4.22e+01 angle pdb=" C GLN K 112 " pdb=" N LEU K 113 " pdb=" CA LEU K 113 " ideal model delta sigma weight residual 123.15 108.87 14.28 2.23e+00 2.01e-01 4.10e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 132.32 -10.62 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C ASP H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta sigma weight residual 121.70 132.04 -10.34 1.80e+00 3.09e-01 3.30e+01 angle pdb=" C SER A1067 " pdb=" N LEU A1068 " pdb=" CA LEU A1068 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 ... (remaining 42811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16690 18.02 - 36.04: 1870 36.04 - 54.06: 398 54.06 - 72.08: 89 72.08 - 90.10: 32 Dihedral angle restraints: 19079 sinusoidal: 8127 harmonic: 10952 Sorted by residual: 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 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA LYS B 274 " pdb=" C LYS B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta harmonic sigma weight residual 180.00 133.59 46.41 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" CA PRO B 498 " pdb=" C PRO B 498 " pdb=" N GLU B 499 " pdb=" CA GLU B 499 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 ... (remaining 19076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3759 0.058 - 0.115: 910 0.115 - 0.173: 115 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 4788 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 2.08e+00 chirality pdb=" CA PHE B 939 " pdb=" N PHE B 939 " pdb=" C PHE B 939 " pdb=" CB PHE B 939 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU B 422 " pdb=" CB LEU B 422 " pdb=" CD1 LEU B 422 " pdb=" CD2 LEU B 422 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4785 not shown) Planarity restraints: 5346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 85 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 73 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 675 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 676 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.033 5.00e-02 4.00e+02 ... (remaining 5343 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 292 2.51 - 3.11: 24661 3.11 - 3.70: 47054 3.70 - 4.30: 65632 4.30 - 4.90: 106496 Nonbonded interactions: 244135 Sorted by model distance: nonbonded pdb=" CB CYS J 10 " pdb="ZN ZN J 101 " model vdw 1.910 2.630 nonbonded pdb=" O VAL A 491 " pdb=" OG1 THR A 629 " model vdw 1.974 2.440 nonbonded pdb=" O LEU A1036 " pdb=" OG SER A1199 " model vdw 1.999 2.440 nonbonded pdb=" OE2 GLU A 893 " pdb=" OG SER B 617 " model vdw 2.064 2.440 nonbonded pdb=" O ALA E 61 " pdb=" OG1 THR E 71 " model vdw 2.065 2.440 ... (remaining 244130 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 5.740 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 98.310 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.097 31539 Z= 0.492 Angle : 0.922 14.277 42816 Z= 0.524 Chirality : 0.048 0.289 4788 Planarity : 0.006 0.075 5346 Dihedral : 16.033 90.097 12017 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.38 % Favored : 88.30 % Rotamer: Outliers : 0.57 % Allowed : 11.04 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.39 % 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: -4.07 (0.11), residues: 3718 helix: -2.20 (0.12), residues: 1208 sheet: -2.67 (0.19), residues: 526 loop : -3.09 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 15 HIS 0.012 0.002 HIS B 618 PHE 0.030 0.003 PHE A 786 TYR 0.031 0.002 TYR A1063 ARG 0.012 0.001 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 669 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5504 (ttm) cc_final: 0.5021 (ttp) REVERT: A 12 LYS cc_start: 0.8068 (mttm) cc_final: 0.7817 (mttp) REVERT: A 362 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7824 (pp) REVERT: A 700 ASP cc_start: 0.7480 (t70) cc_final: 0.7152 (t70) REVERT: A 894 GLU cc_start: 0.7795 (tt0) cc_final: 0.7377 (tp30) REVERT: A 1016 ARG cc_start: 0.7577 (tmm160) cc_final: 0.7050 (tmm160) REVERT: A 1049 HIS cc_start: 0.7614 (t70) cc_final: 0.7323 (t-170) REVERT: A 1078 GLN cc_start: 0.8001 (mm110) cc_final: 0.7738 (tp40) REVERT: A 1179 MET cc_start: 0.7732 (mmp) cc_final: 0.7280 (mmp) REVERT: A 1185 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7049 (tm-30) REVERT: A 1209 MET cc_start: 0.5031 (tpp) cc_final: 0.4828 (tpp) REVERT: A 1247 MET cc_start: 0.8112 (mtm) cc_final: 0.7291 (mtp) REVERT: B 190 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7475 (mtm180) REVERT: B 216 ARG cc_start: 0.8443 (ttt-90) cc_final: 0.8112 (ttt-90) REVERT: B 244 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7831 (tpp-160) REVERT: B 332 GLN cc_start: 0.7622 (tt0) cc_final: 0.7364 (tm-30) REVERT: B 466 LYS cc_start: 0.8766 (tttt) cc_final: 0.8546 (ttpt) REVERT: B 645 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6476 (mm-30) REVERT: B 1024 MET cc_start: 0.7001 (pmm) cc_final: 0.6666 (pmm) REVERT: B 1114 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7700 (mmt-90) REVERT: C 29 TYR cc_start: 0.7159 (t80) cc_final: 0.6574 (p90) REVERT: C 141 PHE cc_start: 0.8575 (m-80) cc_final: 0.8211 (m-80) REVERT: C 323 LEU cc_start: 0.8045 (mm) cc_final: 0.7769 (mp) REVERT: F 113 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8314 (mttt) REVERT: H 125 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7232 (mtp180) REVERT: K 69 HIS cc_start: 0.7812 (t-90) cc_final: 0.7486 (t-90) outliers start: 19 outliers final: 8 residues processed: 683 average time/residue: 0.4666 time to fit residues: 489.7648 Evaluate side-chains 494 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 485 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain K residue 22 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 108 HIS ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 255 ASN A 257 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 497 ASN A 543 HIS A 545 GLN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 655 GLN A 735 GLN A 860 GLN A 891 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS A1078 GLN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1317 GLN A1345 GLN A1486 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 83 GLN B 98 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 300 GLN B 305 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 HIS B 562 GLN B 619 ASN B 680 ASN ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 742 HIS B 752 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1005 GLN ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS B1039 ASN ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 223 HIS C 292 HIS C 300 GLN D 27 ASN E 124 GLN E 138 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN G 167 GLN H 45 GLN H 58 GLN H 118 HIS I 15 ASN J 63 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31539 Z= 0.217 Angle : 0.724 13.553 42816 Z= 0.377 Chirality : 0.044 0.275 4788 Planarity : 0.005 0.081 5346 Dihedral : 12.115 88.651 4650 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.31 % Favored : 90.59 % Rotamer: Outliers : 3.50 % Allowed : 17.13 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.36 % 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: -2.70 (0.13), residues: 3718 helix: -0.65 (0.14), residues: 1209 sheet: -2.11 (0.20), residues: 529 loop : -2.49 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 395 HIS 0.014 0.001 HIS B 779 PHE 0.031 0.002 PHE C 31 TYR 0.032 0.002 TYR A 896 ARG 0.008 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 599 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7440 (mm110) REVERT: A 12 LYS cc_start: 0.7967 (mttm) cc_final: 0.7727 (mttp) REVERT: A 362 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7880 (pp) REVERT: A 894 GLU cc_start: 0.7711 (tt0) cc_final: 0.7282 (tp30) REVERT: A 1016 ARG cc_start: 0.7400 (tmm160) cc_final: 0.6700 (tmm160) REVERT: A 1078 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7445 (tp40) REVERT: A 1179 MET cc_start: 0.7509 (mmp) cc_final: 0.7049 (mmt) REVERT: A 1572 ILE cc_start: 0.8659 (pt) cc_final: 0.8215 (mt) REVERT: A 1576 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.3295 (t80) REVERT: A 1645 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8079 (tt) REVERT: B 190 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7600 (mtm180) REVERT: B 238 MET cc_start: 0.7374 (mmt) cc_final: 0.6845 (mmt) REVERT: B 332 GLN cc_start: 0.7717 (tt0) cc_final: 0.7498 (tm-30) REVERT: B 418 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6957 (t0) REVERT: B 645 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6240 (mm-30) REVERT: B 662 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: B 1024 MET cc_start: 0.6798 (pmm) cc_final: 0.6350 (pmm) REVERT: B 1076 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: B 1104 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.4290 (ptm) REVERT: B 1114 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.7669 (mmt-90) REVERT: B 1161 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8020 (mm-30) REVERT: C 29 TYR cc_start: 0.6910 (t80) cc_final: 0.6372 (p90) REVERT: H 47 TYR cc_start: 0.7136 (t80) cc_final: 0.6338 (t80) REVERT: L 31 ASN cc_start: 0.7762 (m-40) cc_final: 0.7480 (m-40) outliers start: 116 outliers final: 68 residues processed: 672 average time/residue: 0.4694 time to fit residues: 504.8023 Evaluate side-chains 571 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 497 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1645 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1027 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain L residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 367 optimal weight: 6.9990 chunk 303 optimal weight: 0.6980 chunk 337 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 chunk 272 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS B 373 GLN B 374 HIS B 508 HIS B 619 ASN B 621 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** 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: 0.7765 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 31539 Z= 0.404 Angle : 0.790 13.702 42816 Z= 0.408 Chirality : 0.047 0.285 4788 Planarity : 0.006 0.084 5346 Dihedral : 12.179 85.313 4650 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.65 % Favored : 89.21 % Rotamer: Outliers : 5.94 % Allowed : 19.93 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % 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: -2.53 (0.13), residues: 3718 helix: -0.47 (0.14), residues: 1215 sheet: -2.11 (0.21), residues: 505 loop : -2.39 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 395 HIS 0.012 0.002 HIS C 223 PHE 0.030 0.002 PHE A1680 TYR 0.030 0.002 TYR A 896 ARG 0.006 0.001 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 500 time to evaluate : 3.562 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 12 LYS cc_start: 0.8047 (mttm) cc_final: 0.7757 (mttp) REVERT: A 23 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7237 (p0) REVERT: A 136 MET cc_start: -0.0481 (ttt) cc_final: -0.1250 (ptm) REVERT: A 179 MET cc_start: 0.4030 (mmp) cc_final: 0.3417 (mmt) REVERT: A 327 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: A 362 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7771 (pp) REVERT: A 467 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7183 (pt) REVERT: A 533 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8359 (m-40) REVERT: A 723 MET cc_start: 0.6631 (ptm) cc_final: 0.6411 (ptt) REVERT: A 894 GLU cc_start: 0.7827 (tt0) cc_final: 0.7402 (tp30) REVERT: A 1016 ARG cc_start: 0.7272 (tmm160) cc_final: 0.6515 (tmm160) REVERT: A 1576 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.3598 (t80) REVERT: B 190 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7814 (mtm180) REVERT: B 238 MET cc_start: 0.7682 (mmt) cc_final: 0.7136 (mmt) REVERT: B 332 GLN cc_start: 0.7707 (tt0) cc_final: 0.7397 (tm-30) REVERT: B 504 MET cc_start: 0.7260 (ptp) cc_final: 0.6903 (mtm) REVERT: B 645 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6470 (mm-30) REVERT: B 662 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: B 688 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7176 (mtm) REVERT: B 1007 MET cc_start: 0.7653 (mmm) cc_final: 0.7115 (mtt) REVERT: B 1076 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7851 (mmm-85) REVERT: B 1104 MET cc_start: 0.4532 (OUTLIER) cc_final: 0.4310 (ptm) REVERT: B 1114 ARG cc_start: 0.8284 (mmt-90) cc_final: 0.7580 (mmt-90) REVERT: C 41 LYS cc_start: 0.7059 (tptt) cc_final: 0.6844 (tppt) REVERT: C 323 LEU cc_start: 0.8075 (mm) cc_final: 0.7833 (mp) REVERT: E 186 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7334 (mmtm) REVERT: F 79 GLU cc_start: 0.7912 (mp0) cc_final: 0.7490 (mp0) REVERT: H 47 TYR cc_start: 0.7201 (t80) cc_final: 0.6581 (t80) REVERT: J 59 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9033 (tt) outliers start: 197 outliers final: 140 residues processed: 630 average time/residue: 0.4269 time to fit residues: 428.3881 Evaluate side-chains 611 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 461 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1223 ASN Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1481 ASP Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1557 ASN Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1608 ILE Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 876 ASN 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 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1027 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1104 MET Chi-restraints excluded: chain B residue 1134 ASP Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 69 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 51 THR 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 81 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1548 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN B 619 ASN ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31539 Z= 0.262 Angle : 0.710 13.723 42816 Z= 0.365 Chirality : 0.045 0.320 4788 Planarity : 0.005 0.086 5346 Dihedral : 11.989 85.203 4649 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.63 % Favored : 90.29 % Rotamer: Outliers : 6.00 % Allowed : 21.53 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % 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: -2.23 (0.13), residues: 3718 helix: -0.13 (0.14), residues: 1222 sheet: -2.05 (0.22), residues: 500 loop : -2.26 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 395 HIS 0.009 0.001 HIS B 779 PHE 0.023 0.002 PHE B 939 TYR 0.026 0.002 TYR A 896 ARG 0.010 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 525 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7628 (mm-40) REVERT: A 12 LYS cc_start: 0.8040 (mttm) cc_final: 0.7776 (mttp) REVERT: A 23 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7107 (p0) REVERT: A 179 MET cc_start: 0.3976 (mmp) cc_final: 0.3514 (mmt) REVERT: A 327 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5247 (tm-30) REVERT: A 362 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7644 (pp) REVERT: A 893 GLU cc_start: 0.6586 (tt0) cc_final: 0.6380 (tt0) REVERT: A 894 GLU cc_start: 0.7849 (tt0) cc_final: 0.7445 (tp30) REVERT: A 1078 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7592 (tp40) REVERT: A 1576 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.3570 (t80) REVERT: B 190 ARG cc_start: 0.8288 (mtt-85) cc_final: 0.7908 (mtm180) REVERT: B 238 MET cc_start: 0.7413 (mmt) cc_final: 0.7015 (mmt) REVERT: B 332 GLN cc_start: 0.7557 (tt0) cc_final: 0.7276 (tm-30) REVERT: B 504 MET cc_start: 0.7191 (ptp) cc_final: 0.6825 (mtm) REVERT: B 662 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7434 (m-10) REVERT: B 688 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7122 (mtm) REVERT: B 877 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.5593 (p0) REVERT: B 1007 MET cc_start: 0.7685 (mmm) cc_final: 0.7237 (mtt) REVERT: B 1076 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7877 (mmm-85) REVERT: B 1114 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.7679 (mmt-90) REVERT: C 323 LEU cc_start: 0.7950 (mm) cc_final: 0.7708 (mp) REVERT: E 186 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7289 (mmtm) REVERT: F 79 GLU cc_start: 0.7766 (mp0) cc_final: 0.7485 (mp0) REVERT: G 9 GLN cc_start: 0.6039 (pm20) cc_final: 0.5568 (mm110) REVERT: H 47 TYR cc_start: 0.7029 (t80) cc_final: 0.6733 (t80) REVERT: J 59 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8980 (tt) outliers start: 199 outliers final: 136 residues processed: 653 average time/residue: 0.4117 time to fit residues: 434.5399 Evaluate side-chains 626 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 482 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1481 ASP Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 69 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 51 THR 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 34 SER Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31539 Z= 0.292 Angle : 0.719 13.729 42816 Z= 0.369 Chirality : 0.045 0.279 4788 Planarity : 0.005 0.086 5346 Dihedral : 11.918 84.181 4647 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.95 % Favored : 89.94 % Rotamer: Outliers : 6.60 % Allowed : 22.77 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % 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: -2.15 (0.13), residues: 3718 helix: -0.05 (0.14), residues: 1242 sheet: -2.05 (0.21), residues: 526 loop : -2.22 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 395 HIS 0.007 0.001 HIS B 779 PHE 0.025 0.002 PHE B 329 TYR 0.025 0.002 TYR G 65 ARG 0.009 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 503 time to evaluate : 3.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8055 (mttm) cc_final: 0.7737 (mttp) REVERT: A 23 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7155 (p0) REVERT: A 179 MET cc_start: 0.4018 (mmp) cc_final: 0.3588 (mmt) REVERT: A 359 MET cc_start: 0.7900 (mtm) cc_final: 0.7510 (mtp) REVERT: A 362 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7663 (pp) REVERT: A 486 TYR cc_start: 0.8357 (m-80) cc_final: 0.8026 (m-80) REVERT: A 624 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7487 (mt) REVERT: A 847 ASP cc_start: 0.8050 (m-30) cc_final: 0.7524 (t0) REVERT: A 894 GLU cc_start: 0.7878 (tt0) cc_final: 0.7451 (tp30) REVERT: A 900 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6380 (mt-10) REVERT: A 1003 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8509 (pt) REVERT: A 1068 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7319 (tt) REVERT: A 1078 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7553 (tp40) REVERT: A 1572 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 1576 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.3538 (t80) REVERT: B 238 MET cc_start: 0.7624 (mmt) cc_final: 0.7091 (mmt) REVERT: B 332 GLN cc_start: 0.7472 (tt0) cc_final: 0.7235 (tm-30) REVERT: B 478 MET cc_start: 0.8566 (ptt) cc_final: 0.8138 (ptm) REVERT: B 504 MET cc_start: 0.7269 (ptp) cc_final: 0.6912 (mtm) REVERT: B 662 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 688 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7130 (mtm) REVERT: B 838 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 877 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5600 (p0) REVERT: B 1007 MET cc_start: 0.7711 (mmm) cc_final: 0.7179 (mtt) REVERT: B 1114 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.7799 (mmt-90) REVERT: E 186 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7269 (mmtm) REVERT: E 206 TYR cc_start: 0.8638 (m-80) cc_final: 0.8209 (m-10) REVERT: F 79 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: G 9 GLN cc_start: 0.6185 (pm20) cc_final: 0.5461 (mm110) REVERT: H 47 TYR cc_start: 0.6895 (t80) cc_final: 0.6644 (t80) REVERT: J 59 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8938 (tt) outliers start: 219 outliers final: 166 residues processed: 643 average time/residue: 0.4164 time to fit residues: 435.3226 Evaluate side-chains 654 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 475 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1481 ASP Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1661 SER Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 69 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 51 THR 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 59 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 5.9990 chunk 325 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 361 optimal weight: 2.9990 chunk 300 optimal weight: 40.0000 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 619 ASN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 45 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31539 Z= 0.249 Angle : 0.695 13.742 42816 Z= 0.356 Chirality : 0.044 0.277 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.802 84.958 4647 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.44 % Favored : 90.48 % Rotamer: Outliers : 6.27 % Allowed : 24.03 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3718 helix: 0.14 (0.15), residues: 1239 sheet: -1.95 (0.21), residues: 529 loop : -2.11 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 395 HIS 0.011 0.001 HIS B 779 PHE 0.028 0.002 PHE B 484 TYR 0.024 0.002 TYR G 65 ARG 0.009 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 528 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8006 (mttm) cc_final: 0.7720 (mttp) REVERT: A 23 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7183 (p0) REVERT: A 38 LEU cc_start: 0.6209 (mm) cc_final: 0.5704 (mm) REVERT: A 80 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7496 (pt) REVERT: A 179 MET cc_start: 0.4023 (mmp) cc_final: 0.3591 (mmt) REVERT: A 362 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7634 (pp) REVERT: A 384 GLU cc_start: 0.6705 (pm20) cc_final: 0.6499 (pm20) REVERT: A 486 TYR cc_start: 0.8385 (m-80) cc_final: 0.8029 (m-80) REVERT: A 522 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6699 (p90) REVERT: A 624 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7017 (mp) REVERT: A 847 ASP cc_start: 0.8045 (m-30) cc_final: 0.7552 (t0) REVERT: A 894 GLU cc_start: 0.7811 (tt0) cc_final: 0.7350 (tp30) REVERT: A 896 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.5675 (p90) REVERT: A 898 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6562 (p0) REVERT: A 1003 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (pt) REVERT: A 1078 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7632 (tp40) REVERT: A 1561 MET cc_start: 0.6823 (mmp) cc_final: 0.6607 (mmt) REVERT: A 1572 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8284 (mt) REVERT: A 1576 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.3543 (t80) REVERT: B 190 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7646 (mtm180) REVERT: B 238 MET cc_start: 0.7506 (mmt) cc_final: 0.6972 (mmt) REVERT: B 332 GLN cc_start: 0.7500 (tt0) cc_final: 0.7187 (tm-30) REVERT: B 376 GLU cc_start: 0.7803 (pt0) cc_final: 0.7310 (pt0) REVERT: B 478 MET cc_start: 0.8526 (ptt) cc_final: 0.7974 (ptm) REVERT: B 504 MET cc_start: 0.7170 (ptp) cc_final: 0.6855 (mtm) REVERT: B 662 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: B 688 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7041 (mtm) REVERT: B 770 ASP cc_start: 0.8611 (t70) cc_final: 0.7737 (t0) REVERT: B 838 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 877 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5572 (p0) REVERT: B 1007 MET cc_start: 0.7684 (mmm) cc_final: 0.7196 (mtt) REVERT: E 186 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7370 (mmtm) REVERT: E 206 TYR cc_start: 0.8641 (m-80) cc_final: 0.8275 (m-10) REVERT: F 79 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: G 9 GLN cc_start: 0.6169 (pm20) cc_final: 0.5617 (mm110) REVERT: J 48 MET cc_start: 0.8223 (mmm) cc_final: 0.7717 (tpt) REVERT: J 59 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8892 (tt) outliers start: 208 outliers final: 156 residues processed: 665 average time/residue: 0.4130 time to fit residues: 443.1936 Evaluate side-chains 661 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 489 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1328 PHE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1481 ASP Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1557 ASN Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 838 LEU 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 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 51 THR 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 34 SER Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 360 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1479 HIS ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31539 Z= 0.309 Angle : 0.725 13.745 42816 Z= 0.372 Chirality : 0.045 0.297 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.828 84.080 4647 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.06 % Favored : 89.83 % Rotamer: Outliers : 6.45 % Allowed : 24.46 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % 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: -1.96 (0.13), residues: 3718 helix: 0.15 (0.15), residues: 1236 sheet: -1.97 (0.21), residues: 540 loop : -2.12 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 916 HIS 0.009 0.001 HIS B 779 PHE 0.023 0.002 PHE B 329 TYR 0.029 0.002 TYR E 203 ARG 0.009 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 501 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7174 (p0) REVERT: A 38 LEU cc_start: 0.6316 (mm) cc_final: 0.5825 (mm) REVERT: A 80 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7618 (pt) REVERT: A 179 MET cc_start: 0.4092 (mmp) cc_final: 0.3667 (mmt) REVERT: A 247 PHE cc_start: 0.5412 (m-10) cc_final: 0.5100 (m-10) REVERT: A 327 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6243 (pp20) REVERT: A 362 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7656 (pp) REVERT: A 482 LYS cc_start: 0.7875 (pttm) cc_final: 0.7465 (pttm) REVERT: A 522 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6589 (p90) REVERT: A 602 MET cc_start: 0.8268 (tpp) cc_final: 0.8016 (tpp) REVERT: A 894 GLU cc_start: 0.7918 (tt0) cc_final: 0.7453 (tp30) REVERT: A 896 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.5978 (p90) REVERT: A 1003 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8491 (pt) REVERT: A 1078 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7652 (tp40) REVERT: A 1185 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 1572 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8226 (mt) REVERT: A 1576 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.3690 (t80) REVERT: B 238 MET cc_start: 0.7549 (mmt) cc_final: 0.7030 (mmt) REVERT: B 332 GLN cc_start: 0.7572 (tt0) cc_final: 0.7247 (tm-30) REVERT: B 478 MET cc_start: 0.8616 (ptt) cc_final: 0.8231 (ptm) REVERT: B 504 MET cc_start: 0.7229 (ptp) cc_final: 0.6939 (mtm) REVERT: B 645 GLU cc_start: 0.6247 (mm-30) cc_final: 0.6016 (mm-30) REVERT: B 662 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: B 688 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7088 (mtm) REVERT: B 768 MET cc_start: 0.7571 (tpp) cc_final: 0.7277 (mmm) REVERT: B 838 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8575 (mp) REVERT: B 877 ASP cc_start: 0.6132 (OUTLIER) cc_final: 0.5590 (p0) REVERT: B 885 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: B 1114 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7440 (mmt-90) REVERT: B 1161 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8004 (mm-30) REVERT: E 186 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7265 (mmtm) REVERT: E 206 TYR cc_start: 0.8733 (m-80) cc_final: 0.8338 (m-10) REVERT: F 79 GLU cc_start: 0.7799 (mp0) cc_final: 0.7404 (mp0) REVERT: G 9 GLN cc_start: 0.6115 (pm20) cc_final: 0.5560 (mm110) REVERT: J 48 MET cc_start: 0.8270 (mmm) cc_final: 0.7743 (tpt) REVERT: J 59 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8914 (tt) outliers start: 214 outliers final: 180 residues processed: 641 average time/residue: 0.3985 time to fit residues: 418.4644 Evaluate side-chains 675 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 480 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1122 ASP Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1557 ASN Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1572 ILE Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1633 PHE Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 838 LEU 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 885 GLN Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 903 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1010 ASP Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1072 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1170 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 69 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 51 THR 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 34 SER Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 0.0870 chunk 143 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 466 GLN A 606 ASN A 952 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1062 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 HIS A1519 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 700 ASN ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 HIS ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN L 31 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31539 Z= 0.177 Angle : 0.676 13.628 42816 Z= 0.343 Chirality : 0.043 0.270 4788 Planarity : 0.005 0.088 5346 Dihedral : 11.608 85.826 4647 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.45 % Favored : 91.47 % Rotamer: Outliers : 4.64 % Allowed : 26.63 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.17 % 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: -1.65 (0.14), residues: 3718 helix: 0.46 (0.15), residues: 1224 sheet: -1.75 (0.21), residues: 556 loop : -1.96 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 73 HIS 0.009 0.001 HIS B 779 PHE 0.029 0.001 PHE A1175 TYR 0.028 0.001 TYR E 203 ARG 0.008 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 559 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7810 (mttm) cc_final: 0.7604 (mttp) REVERT: A 38 LEU cc_start: 0.6246 (mm) cc_final: 0.5813 (mm) REVERT: A 179 MET cc_start: 0.3970 (mmp) cc_final: 0.3550 (mmt) REVERT: A 362 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 482 LYS cc_start: 0.7801 (pttm) cc_final: 0.7401 (pttp) REVERT: A 522 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6433 (p90) REVERT: A 602 MET cc_start: 0.8228 (tpp) cc_final: 0.7971 (tpp) REVERT: A 608 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: A 624 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.6822 (mp) REVERT: A 847 ASP cc_start: 0.7900 (m-30) cc_final: 0.7415 (t0) REVERT: A 894 GLU cc_start: 0.7902 (tt0) cc_final: 0.7402 (tp30) REVERT: A 1185 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7379 (tm-30) REVERT: A 1572 ILE cc_start: 0.8540 (pt) cc_final: 0.8302 (mt) REVERT: A 1576 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.3813 (t80) REVERT: B 238 MET cc_start: 0.7203 (mmt) cc_final: 0.6794 (mmm) REVERT: B 478 MET cc_start: 0.8435 (ptt) cc_final: 0.7900 (ptm) REVERT: B 504 MET cc_start: 0.7084 (ptp) cc_final: 0.6768 (mtm) REVERT: B 662 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: B 688 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6629 (mtm) REVERT: B 877 ASP cc_start: 0.5755 (OUTLIER) cc_final: 0.5533 (p0) REVERT: B 998 MET cc_start: 0.8141 (mtp) cc_final: 0.7807 (mtt) REVERT: B 1114 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.7404 (mmt-90) REVERT: B 1161 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7832 (mm-30) REVERT: C 99 GLN cc_start: 0.7871 (mp10) cc_final: 0.7585 (mp10) REVERT: E 186 LYS cc_start: 0.7476 (mmtt) cc_final: 0.7083 (mmtm) REVERT: E 206 TYR cc_start: 0.8638 (m-80) cc_final: 0.8217 (m-10) REVERT: F 126 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7269 (mtm110) REVERT: G 9 GLN cc_start: 0.6081 (pm20) cc_final: 0.5518 (mm110) REVERT: G 32 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.5959 (m170) REVERT: G 33 MET cc_start: 0.8438 (mmm) cc_final: 0.8010 (mmm) REVERT: H 23 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7672 (mtt90) REVERT: J 48 MET cc_start: 0.8042 (mmm) cc_final: 0.7779 (tpt) REVERT: J 59 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8785 (tt) outliers start: 154 outliers final: 107 residues processed: 655 average time/residue: 0.4221 time to fit residues: 447.0814 Evaluate side-chains 631 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 514 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1557 ASN Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 51 THR 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 34 SER Chi-restraints excluded: chain K residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 7.9990 chunk 345 optimal weight: 0.3980 chunk 315 optimal weight: 8.9990 chunk 335 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 103 optimal weight: 0.4980 chunk 303 optimal weight: 6.9990 chunk 317 optimal weight: 0.9980 chunk 334 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN A1317 GLN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 700 ASN ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31539 Z= 0.180 Angle : 0.679 13.981 42816 Z= 0.342 Chirality : 0.043 0.276 4788 Planarity : 0.005 0.089 5346 Dihedral : 11.532 87.118 4647 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 27.50 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.20 % 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: -1.54 (0.14), residues: 3718 helix: 0.52 (0.15), residues: 1226 sheet: -1.66 (0.21), residues: 571 loop : -1.88 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 822 HIS 0.006 0.001 HIS E 23 PHE 0.038 0.002 PHE C 31 TYR 0.034 0.001 TYR E 203 ARG 0.012 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 544 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.6317 (mm) cc_final: 0.5832 (mm) REVERT: A 179 MET cc_start: 0.4068 (mmp) cc_final: 0.3605 (mmt) REVERT: A 362 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7655 (pp) REVERT: A 436 GLN cc_start: 0.7762 (tt0) cc_final: 0.7468 (tm-30) REVERT: A 480 MET cc_start: 0.7644 (mmt) cc_final: 0.7418 (mmm) REVERT: A 482 LYS cc_start: 0.7763 (pttm) cc_final: 0.7323 (pttm) REVERT: A 486 TYR cc_start: 0.8390 (m-80) cc_final: 0.8109 (m-80) REVERT: A 522 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6628 (p90) REVERT: A 602 MET cc_start: 0.8260 (tpp) cc_final: 0.7981 (tpp) REVERT: A 624 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6595 (mp) REVERT: A 688 ASP cc_start: 0.7302 (m-30) cc_final: 0.6593 (m-30) REVERT: A 847 ASP cc_start: 0.7875 (m-30) cc_final: 0.7384 (t0) REVERT: A 896 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6109 (p90) REVERT: A 1515 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5784 (tt0) REVERT: A 1561 MET cc_start: 0.7173 (mmp) cc_final: 0.6944 (mmp) REVERT: A 1576 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.3575 (t80) REVERT: B 190 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7966 (mtt90) REVERT: B 238 MET cc_start: 0.7230 (mmt) cc_final: 0.6924 (mmm) REVERT: B 478 MET cc_start: 0.8445 (ptt) cc_final: 0.7925 (ptm) REVERT: B 504 MET cc_start: 0.7104 (ptp) cc_final: 0.6790 (mtm) REVERT: B 662 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: B 688 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6611 (mtm) REVERT: B 998 MET cc_start: 0.8143 (mtp) cc_final: 0.7870 (mtt) REVERT: B 1114 ARG cc_start: 0.8280 (mmt-90) cc_final: 0.7338 (mmt-90) REVERT: C 323 LEU cc_start: 0.7813 (mm) cc_final: 0.7596 (mp) REVERT: E 186 LYS cc_start: 0.7393 (mmtt) cc_final: 0.6965 (mmtm) REVERT: E 206 TYR cc_start: 0.8610 (m-80) cc_final: 0.8188 (m-10) REVERT: F 79 GLU cc_start: 0.7525 (mp0) cc_final: 0.7217 (mp0) REVERT: F 126 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7086 (mtm110) REVERT: G 32 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.6064 (m170) REVERT: G 33 MET cc_start: 0.8495 (mmm) cc_final: 0.8205 (mmm) REVERT: G 64 MET cc_start: 0.6840 (tpp) cc_final: 0.6357 (ttp) REVERT: J 48 MET cc_start: 0.7997 (mmm) cc_final: 0.7782 (tpt) REVERT: J 59 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8770 (tt) REVERT: K 60 VAL cc_start: 0.9000 (t) cc_final: 0.8780 (t) outliers start: 134 outliers final: 109 residues processed: 630 average time/residue: 0.4250 time to fit residues: 432.0291 Evaluate side-chains 627 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 508 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1557 ASN Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 51 THR 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 34 SER Chi-restraints excluded: chain K residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 9.9990 chunk 355 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 342 optimal weight: 0.7980 chunk 296 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 220 HIS A 255 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31539 Z= 0.271 Angle : 0.719 13.642 42816 Z= 0.366 Chirality : 0.044 0.270 4788 Planarity : 0.005 0.087 5346 Dihedral : 11.597 86.473 4647 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.52 % Favored : 90.42 % Rotamer: Outliers : 3.92 % Allowed : 27.86 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.17 % 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: -1.58 (0.14), residues: 3718 helix: 0.46 (0.15), residues: 1229 sheet: -1.67 (0.21), residues: 558 loop : -1.90 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 916 HIS 0.008 0.001 HIS B 779 PHE 0.032 0.002 PHE B1056 TYR 0.035 0.002 TYR E 203 ARG 0.012 0.000 ARG F 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 494 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.6227 (mm) cc_final: 0.5759 (mm) REVERT: A 179 MET cc_start: 0.4076 (mmp) cc_final: 0.3647 (mmt) REVERT: A 362 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7611 (pp) REVERT: A 482 LYS cc_start: 0.7835 (pttm) cc_final: 0.7505 (pttp) REVERT: A 522 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6618 (p90) REVERT: A 624 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6615 (mp) REVERT: A 847 ASP cc_start: 0.7936 (m-30) cc_final: 0.7396 (t0) REVERT: A 896 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.5993 (p90) REVERT: A 972 LEU cc_start: 0.8149 (mm) cc_final: 0.7886 (mm) REVERT: A 1016 ARG cc_start: 0.7550 (tmm160) cc_final: 0.6480 (tmm160) REVERT: A 1561 MET cc_start: 0.7152 (mmp) cc_final: 0.6865 (mmp) REVERT: A 1576 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.3690 (t80) REVERT: B 190 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7965 (mtt90) REVERT: B 238 MET cc_start: 0.7278 (mmt) cc_final: 0.6622 (mmt) REVERT: B 478 MET cc_start: 0.8569 (ptt) cc_final: 0.8181 (ptm) REVERT: B 504 MET cc_start: 0.7283 (ptp) cc_final: 0.6871 (mtm) REVERT: B 662 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: B 688 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7010 (mtm) REVERT: B 1114 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.7316 (mmt-90) REVERT: B 1161 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8070 (mm-30) REVERT: E 186 LYS cc_start: 0.7399 (mmtt) cc_final: 0.6989 (mmtm) REVERT: E 206 TYR cc_start: 0.8708 (m-80) cc_final: 0.8362 (m-10) REVERT: F 126 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7443 (mtm110) REVERT: G 32 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6066 (m170) REVERT: G 33 MET cc_start: 0.8569 (mmm) cc_final: 0.8263 (mmm) REVERT: G 64 MET cc_start: 0.7091 (tpp) cc_final: 0.6384 (ttt) REVERT: H 23 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7837 (mtt90) REVERT: J 48 MET cc_start: 0.8154 (mmm) cc_final: 0.7806 (tpt) REVERT: J 59 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8880 (tt) outliers start: 130 outliers final: 116 residues processed: 580 average time/residue: 0.4281 time to fit residues: 400.0105 Evaluate side-chains 611 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 486 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1228 ILE Chi-restraints excluded: chain A residue 1309 TYR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1494 LEU Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1538 THR Chi-restraints excluded: chain A residue 1557 ASN Chi-restraints excluded: chain A residue 1565 TYR Chi-restraints excluded: chain A residue 1576 TYR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1659 ASN Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 652 PHE Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 1018 TYR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1107 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1159 THR Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain E residue 15 TRP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 32 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 56 PHE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 51 THR 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 34 SER Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1479 HIS A1604 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.169976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139912 restraints weight = 52549.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140196 restraints weight = 44004.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140955 restraints weight = 35642.694| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31539 Z= 0.345 Angle : 0.769 13.782 42816 Z= 0.391 Chirality : 0.046 0.277 4788 Planarity : 0.005 0.088 5346 Dihedral : 11.780 85.669 4647 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.84 % Favored : 90.05 % Rotamer: Outliers : 4.58 % Allowed : 27.20 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.20 % 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: -1.79 (0.13), residues: 3718 helix: 0.22 (0.15), residues: 1242 sheet: -1.77 (0.22), residues: 537 loop : -1.99 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 916 HIS 0.007 0.001 HIS A 543 PHE 0.037 0.002 PHE C 31 TYR 0.036 0.002 TYR E 203 ARG 0.009 0.001 ARG F 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7550.24 seconds wall clock time: 137 minutes 42.03 seconds (8262.03 seconds total)