Starting phenix.real_space_refine on Mon Feb 19 11:58:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6c_30119/02_2024/6m6c_30119.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6c_30119/02_2024/6m6c_30119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6c_30119/02_2024/6m6c_30119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6c_30119/02_2024/6m6c_30119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6c_30119/02_2024/6m6c_30119.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m6c_30119/02_2024/6m6c_30119.pdb" } resolution = 3.1 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 58 5.49 5 Mg 1 5.21 5 S 64 5.16 5 C 15380 2.51 5 N 4362 2.21 5 O 4716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 426": "OD1" <-> "OD2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C ASP 553": "OD1" <-> "OD2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ASP 653": "OD1" <-> "OD2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 698": "OD1" <-> "OD2" Residue "C TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 711": "OE1" <-> "OE2" Residue "C ASP 725": "OD1" <-> "OD2" Residue "C GLU 739": "OE1" <-> "OE2" Residue "C PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 787": "OD1" <-> "OD2" Residue "C ARG 808": "NH1" <-> "NH2" Residue "C ASP 837": "OD1" <-> "OD2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 913": "OE1" <-> "OE2" Residue "C GLU 916": "OE1" <-> "OE2" Residue "C TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 932": "OE1" <-> "OE2" Residue "C PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 942": "OE1" <-> "OE2" Residue "C PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "C GLU 1036": "OE1" <-> "OE2" Residue "C ASP 1058": "OD1" <-> "OD2" Residue "C GLU 1061": "OE1" <-> "OE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1091": "OE1" <-> "OE2" Residue "C PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ASP 430": "OD1" <-> "OD2" Residue "D ARG 441": "NH1" <-> "NH2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D ASP 579": "OD1" <-> "OD2" Residue "D ARG 587": "NH1" <-> "NH2" Residue "D ASP 597": "OD1" <-> "OD2" Residue "D ASP 605": "OD1" <-> "OD2" Residue "D TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D GLU 693": "OE1" <-> "OE2" Residue "D GLU 734": "OE1" <-> "OE2" Residue "D GLU 758": "OE1" <-> "OE2" Residue "D PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 832": "NH1" <-> "NH2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "D ASP 859": "OD1" <-> "OD2" Residue "D ARG 867": "NH1" <-> "NH2" Residue "D TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 872": "NH1" <-> "NH2" Residue "D GLU 888": "OE1" <-> "OE2" Residue "D GLU 898": "OE1" <-> "OE2" Residue "D ASP 903": "OD1" <-> "OD2" Residue "D GLU 907": "OE1" <-> "OE2" Residue "D TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 952": "OD1" <-> "OD2" Residue "D TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 979": "OE1" <-> "OE2" Residue "D PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 985": "OD1" <-> "OD2" Residue "D GLU 987": "OE1" <-> "OE2" Residue "D PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1051": "OE1" <-> "OE2" Residue "D PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1054": "OE1" <-> "OE2" Residue "D PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1087": "NH1" <-> "NH2" Residue "D TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1104": "OE1" <-> "OE2" Residue "D ARG 1108": "NH1" <-> "NH2" Residue "D GLU 1127": "OE1" <-> "OE2" Residue "D ARG 1133": "NH1" <-> "NH2" Residue "D GLU 1141": "OE1" <-> "OE2" Residue "D TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1151": "NH1" <-> "NH2" Residue "D GLU 1152": "OE1" <-> "OE2" Residue "D GLU 1185": "OE1" <-> "OE2" Residue "D TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1288": "OE1" <-> "OE2" Residue "D GLU 1297": "OE1" <-> "OE2" Residue "D TYR 1303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1308": "OE1" <-> "OE2" Residue "D ASP 1315": "OD1" <-> "OD2" Residue "D TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1380": "OE1" <-> "OE2" Residue "D ASP 1383": "OD1" <-> "OD2" Residue "D GLU 1405": "OE1" <-> "OE2" Residue "D ARG 1406": "NH1" <-> "NH2" Residue "D PHE 1440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1449": "OE1" <-> "OE2" Residue "D PHE 1483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1497": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E TYR 93": "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: 24583 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1782 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1750 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 207} Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8770 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1038} Chain breaks: 1 Chain: "D" Number of atoms: 10300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10300 Classifications: {'peptide': 1305} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1240} Chain breaks: 2 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "N" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19686 SG CYS D1112 84.043 65.037 103.462 1.00116.18 S ATOM 20330 SG CYS D1194 83.244 65.269 99.635 1.00113.44 S ATOM 20386 SG CYS D1201 82.157 62.149 101.536 1.00109.81 S ATOM 20410 SG CYS D1204 80.510 65.312 102.376 1.00109.29 S ATOM 12771 SG CYS D 58 112.562 45.724 44.929 1.00182.15 S ATOM 12782 SG CYS D 60 114.388 47.085 42.144 1.00185.70 S ATOM 12893 SG CYS D 73 116.459 47.364 44.938 1.00180.59 S ATOM 12919 SG CYS D 76 113.687 49.792 44.980 1.00177.15 S Time building chain proxies: 14.17, per 1000 atoms: 0.58 Number of scatterers: 24583 At special positions: 0 Unit cell: (159.454, 138.542, 138.542, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 64 16.00 P 58 15.00 Mg 1 11.99 O 4716 8.00 N 4362 7.00 C 15380 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: 11.31 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 58 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 76 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 48 sheets defined 40.6% alpha, 19.1% beta 27 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 9.49 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.620A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.635A pdb=" N HIS A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.793A pdb=" N TYR A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.748A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Proline residue: B 39 - end of helix removed outlier: 4.351A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.715A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.718A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.970A pdb=" N SER C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.591A pdb=" N ARG C 39 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.644A pdb=" N VAL C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.927A pdb=" N MET C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.516A pdb=" N ALA C 315 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 359 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.530A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.827A pdb=" N ARG C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.023A pdb=" N TYR C 435 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.963A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 854 through 858 removed outlier: 3.536A pdb=" N MET C 858 " --> pdb=" O VAL C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 874 No H-bonds generated for 'chain 'C' and resid 872 through 874' Processing helix chain 'C' and resid 875 through 880 removed outlier: 3.562A pdb=" N ARG C 879 " --> pdb=" O GLY C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.722A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG C 929 " --> pdb=" O TYR C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 949 Processing helix chain 'C' and resid 958 through 968 Processing helix chain 'C' and resid 1000 through 1004 Processing helix chain 'C' and resid 1033 through 1043 Processing helix chain 'C' and resid 1045 through 1054 removed outlier: 3.684A pdb=" N LEU C1049 " --> pdb=" O ALA C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1073 Processing helix chain 'C' and resid 1082 through 1094 removed outlier: 3.697A pdb=" N ARG C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.704A pdb=" N PHE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.684A pdb=" N ASP D 107 " --> pdb=" O TRP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 423 through 426 Processing helix chain 'D' and resid 457 through 467 removed outlier: 3.531A pdb=" N GLU D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 481 removed outlier: 3.540A pdb=" N LEU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS D 475 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.782A pdb=" N ARG D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 506 " --> pdb=" O PHE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 538 through 561 removed outlier: 3.759A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 583 Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 612 through 618 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 678 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.561A pdb=" N ASP D 682 " --> pdb=" O ARG D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.569A pdb=" N ASP D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 732 through 737 Processing helix chain 'D' and resid 752 through 762 Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 793 Processing helix chain 'D' and resid 808 through 819 removed outlier: 3.664A pdb=" N ALA D 812 " --> pdb=" O THR D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 841 Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.664A pdb=" N ALA D 896 " --> pdb=" O ASP D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 923 Processing helix chain 'D' and resid 923 through 944 removed outlier: 3.729A pdb=" N THR D 944 " --> pdb=" O THR D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 removed outlier: 3.855A pdb=" N ALA D 954 " --> pdb=" O ILE D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.027A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1026 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1102 removed outlier: 3.982A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1179 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1220 through 1231 removed outlier: 3.811A pdb=" N VAL D1224 " --> pdb=" O ALA D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1232 through 1236 Processing helix chain 'D' and resid 1255 through 1264 Processing helix chain 'D' and resid 1331 through 1340 Processing helix chain 'D' and resid 1340 through 1359 removed outlier: 3.531A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D1355 " --> pdb=" O GLU D1351 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D1356 " --> pdb=" O ILE D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1364 through 1376 removed outlier: 4.355A pdb=" N ILE D1368 " --> pdb=" O HIS D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1408 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.625A pdb=" N ALA D1437 " --> pdb=" O SER D1433 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 Processing helix chain 'D' and resid 1462 through 1468 Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1501 Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.873A pdb=" N VAL E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 41 through 45 removed outlier: 3.760A pdb=" N ARG E 45 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.623A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.644A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.462A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.635A pdb=" N ALA A 130 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 5.797A pdb=" N TYR B 20 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 201 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU B 22 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 199 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL B 24 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 197 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU B 26 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 195 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 186 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 104 removed outlier: 7.533A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.885A pdb=" N ALA B 130 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 73 removed outlier: 7.033A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 3.844A pdb=" N SER C 138 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.413A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 3.527A pdb=" N ARG C 473 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU C 482 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 475 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR C 480 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.717A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 7.009A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 7.042A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.519A pdb=" N ASP C 714 " --> pdb=" O VAL C 819 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 819 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 802 " --> pdb=" O TYR C 826 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA C 828 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL C 800 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N LYS C 830 " --> pdb=" O GLY C 798 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N GLY C 798 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AC9, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.730A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 7.909A pdb=" N ILE D 726 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 630 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU D 728 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 632 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AD3, first strand: chain 'C' and resid 1097 through 1102 Processing sheet with id=AD4, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.818A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 152 through 153 removed outlier: 7.012A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 170 Processing sheet with id=AD8, first strand: chain 'D' and resid 190 through 192 Processing sheet with id=AD9, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AE1, first strand: chain 'D' and resid 420 through 422 removed outlier: 7.125A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AE3, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AE4, first strand: chain 'D' and resid 842 through 843 Processing sheet with id=AE5, first strand: chain 'D' and resid 1106 through 1109 Processing sheet with id=AE6, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE7, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AE8, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AE9, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 4.110A pdb=" N LEU D1290 " --> pdb=" O LEU D1305 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 6.830A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1485 through 1488 Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 49 1053 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 14.59 Time building geometry restraints manager: 12.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7864 1.34 - 1.45: 3186 1.45 - 1.57: 13865 1.57 - 1.69: 113 1.69 - 1.81: 115 Bond restraints: 25143 Sorted by residual: bond pdb=" N THR C 335 " pdb=" CA THR C 335 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.20e+00 bond pdb=" N ALA D 830 " pdb=" CA ALA D 830 " ideal model delta sigma weight residual 1.458 1.476 -0.017 1.23e-02 6.61e+03 1.96e+00 bond pdb=" C THR C 335 " pdb=" O THR C 335 " ideal model delta sigma weight residual 1.234 1.251 -0.017 1.35e-02 5.49e+03 1.64e+00 bond pdb=" C THR D 875 " pdb=" N SER D 876 " ideal model delta sigma weight residual 1.327 1.291 0.036 2.86e-02 1.22e+03 1.62e+00 bond pdb=" C3' DG T 12 " pdb=" O3' DG T 12 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.10e+00 ... (remaining 25138 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.68: 903 105.68 - 112.76: 13437 112.76 - 119.83: 8031 119.83 - 126.91: 11506 126.91 - 133.98: 389 Bond angle restraints: 34266 Sorted by residual: angle pdb=" C VAL D 829 " pdb=" N ALA D 830 " pdb=" CA ALA D 830 " ideal model delta sigma weight residual 120.82 126.00 -5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" N GLY C 215 " pdb=" CA GLY C 215 " pdb=" C GLY C 215 " ideal model delta sigma weight residual 112.50 116.37 -3.87 1.16e+00 7.43e-01 1.12e+01 angle pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" C SER A 47 " ideal model delta sigma weight residual 110.44 114.31 -3.87 1.20e+00 6.94e-01 1.04e+01 angle pdb=" C ALA D 830 " pdb=" CA ALA D 830 " pdb=" CB ALA D 830 " ideal model delta sigma weight residual 110.74 115.38 -4.64 1.66e+00 3.63e-01 7.83e+00 angle pdb=" C ASN D1014 " pdb=" N TYR D1015 " pdb=" CA TYR D1015 " ideal model delta sigma weight residual 122.85 119.85 3.00 1.10e+00 8.26e-01 7.44e+00 ... (remaining 34261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 14718 30.78 - 61.56: 537 61.56 - 92.34: 61 92.34 - 123.12: 0 123.12 - 153.90: 1 Dihedral angle restraints: 15317 sinusoidal: 6820 harmonic: 8497 Sorted by residual: dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N SER B 47 " pdb=" CA SER B 47 " ideal model delta harmonic sigma weight residual -180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DG T 12 " pdb=" C3' DG T 12 " pdb=" O3' DG T 12 " pdb=" P DT T 13 " ideal model delta sinusoidal sigma weight residual 220.00 66.10 153.90 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA GLY D 831 " pdb=" C GLY D 831 " pdb=" N ARG D 832 " pdb=" CA ARG D 832 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 15314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2458 0.029 - 0.059: 884 0.059 - 0.088: 270 0.088 - 0.118: 226 0.118 - 0.147: 35 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA VAL D 864 " pdb=" N VAL D 864 " pdb=" C VAL D 864 " pdb=" CB VAL D 864 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE C 159 " pdb=" N ILE C 159 " pdb=" C ILE C 159 " pdb=" CB ILE C 159 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL C 317 " pdb=" N VAL C 317 " pdb=" C VAL C 317 " pdb=" CB VAL C 317 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 3870 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 634 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO D 635 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 635 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 635 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 469 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C 470 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 865 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO C 866 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 866 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 866 " -0.020 5.00e-02 4.00e+02 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 214 2.59 - 3.17: 19943 3.17 - 3.75: 37228 3.75 - 4.32: 51727 4.32 - 4.90: 85777 Nonbonded interactions: 194889 Sorted by model distance: nonbonded pdb=" OD1 ASP D 739 " pdb="MG MG D2003 " model vdw 2.016 2.170 nonbonded pdb=" O3' A R 20 " pdb="MG MG D2003 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP D 741 " pdb="MG MG D2003 " model vdw 2.080 2.170 nonbonded pdb=" OG SER D1190 " pdb=" OE1 GLU D1369 " model vdw 2.215 2.440 nonbonded pdb=" NE2 GLN E 49 " pdb=" O THR E 50 " model vdw 2.240 2.520 ... (remaining 194884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 228) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.280 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 86.210 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 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 : 0.003 0.036 25143 Z= 0.179 Angle : 0.559 5.341 34266 Z= 0.348 Chirality : 0.041 0.147 3873 Planarity : 0.004 0.047 4287 Dihedral : 15.309 153.902 9855 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 2942 helix: -0.22 (0.15), residues: 1039 sheet: -1.40 (0.21), residues: 451 loop : -1.40 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS C 552 PHE 0.010 0.001 PHE C 896 TYR 0.013 0.001 TYR D1207 ARG 0.005 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 3.075 Fit side-chains revert: symmetry clash REVERT: A 47 SER cc_start: 0.8254 (t) cc_final: 0.8045 (p) REVERT: A 57 TYR cc_start: 0.7859 (t80) cc_final: 0.7525 (t80) REVERT: A 66 SER cc_start: 0.7946 (t) cc_final: 0.7709 (p) REVERT: A 102 LYS cc_start: 0.8332 (mttp) cc_final: 0.7920 (mtpp) REVERT: A 113 ASP cc_start: 0.8684 (m-30) cc_final: 0.8452 (m-30) REVERT: A 175 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6542 (mmt90) REVERT: B 29 GLU cc_start: 0.6650 (tp30) cc_final: 0.6307 (mp0) REVERT: B 47 SER cc_start: 0.8277 (m) cc_final: 0.7967 (p) REVERT: B 137 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7978 (ttm110) REVERT: B 160 ASP cc_start: 0.7961 (t0) cc_final: 0.7619 (t0) REVERT: B 220 GLU cc_start: 0.7425 (tt0) cc_final: 0.7074 (tp30) REVERT: C 24 GLU cc_start: 0.6566 (tp30) cc_final: 0.5786 (mm-30) REVERT: C 27 ARG cc_start: 0.7218 (ttp80) cc_final: 0.6781 (ttm170) REVERT: C 64 LEU cc_start: 0.7605 (mp) cc_final: 0.7088 (tt) REVERT: C 229 MET cc_start: 0.8116 (ptt) cc_final: 0.7573 (ptp) REVERT: C 288 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6519 (mtp-110) REVERT: C 384 GLU cc_start: 0.6123 (tp30) cc_final: 0.5761 (tt0) REVERT: C 426 ASP cc_start: 0.6858 (p0) cc_final: 0.6561 (m-30) REVERT: C 504 GLU cc_start: 0.6474 (pt0) cc_final: 0.6071 (pt0) REVERT: C 512 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7608 (ptm-80) REVERT: C 599 GLU cc_start: 0.7201 (tp30) cc_final: 0.6598 (mt-10) REVERT: C 605 LYS cc_start: 0.7246 (mttt) cc_final: 0.6735 (mtmt) REVERT: C 626 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7004 (ttp-170) REVERT: C 677 MET cc_start: 0.8033 (ptm) cc_final: 0.7707 (ptp) REVERT: C 706 GLU cc_start: 0.7100 (tp30) cc_final: 0.6819 (tp30) REVERT: C 736 ASP cc_start: 0.7442 (p0) cc_final: 0.7233 (p0) REVERT: C 754 ILE cc_start: 0.8219 (mt) cc_final: 0.7999 (mp) REVERT: C 821 GLU cc_start: 0.6407 (pt0) cc_final: 0.6205 (pt0) REVERT: C 916 GLU cc_start: 0.5807 (tp30) cc_final: 0.5582 (pt0) REVERT: C 1000 MET cc_start: 0.8266 (mtm) cc_final: 0.8058 (mtm) REVERT: C 1005 MET cc_start: 0.8108 (ttp) cc_final: 0.7875 (ttt) REVERT: C 1106 ASP cc_start: 0.7033 (m-30) cc_final: 0.6340 (t0) REVERT: C 1107 ASN cc_start: 0.6360 (m-40) cc_final: 0.6152 (m-40) REVERT: D 27 GLU cc_start: 0.8183 (pt0) cc_final: 0.7862 (pt0) REVERT: D 38 LYS cc_start: 0.6524 (mmtp) cc_final: 0.6171 (mtmm) REVERT: D 40 GLU cc_start: 0.6433 (tp30) cc_final: 0.6103 (mt-10) REVERT: D 46 ASP cc_start: 0.8971 (t0) cc_final: 0.8212 (t70) REVERT: D 54 LYS cc_start: 0.6900 (mttp) cc_final: 0.6384 (mtpp) REVERT: D 464 LEU cc_start: 0.6366 (mt) cc_final: 0.6152 (mt) REVERT: D 476 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6900 (tm-30) REVERT: D 491 LYS cc_start: 0.6391 (tmmt) cc_final: 0.5839 (mtmm) REVERT: D 512 MET cc_start: 0.8333 (mtm) cc_final: 0.8019 (mtm) REVERT: D 601 ARG cc_start: 0.6366 (ttt-90) cc_final: 0.6152 (mmm-85) REVERT: D 797 LYS cc_start: 0.7808 (tptt) cc_final: 0.6892 (mttp) REVERT: D 799 LYS cc_start: 0.8156 (mttt) cc_final: 0.7887 (mttp) REVERT: D 845 ASN cc_start: 0.7171 (p0) cc_final: 0.6809 (p0) REVERT: D 847 ASP cc_start: 0.6034 (m-30) cc_final: 0.5650 (m-30) REVERT: D 871 LYS cc_start: 0.7010 (pttt) cc_final: 0.6579 (pttt) REVERT: D 1012 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6231 (mt-10) REVERT: D 1046 GLN cc_start: 0.7011 (pm20) cc_final: 0.5865 (mp10) REVERT: D 1079 LYS cc_start: 0.6163 (tptt) cc_final: 0.5655 (tppt) REVERT: D 1159 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7455 (ttm170) REVERT: D 1184 GLN cc_start: 0.7970 (mt0) cc_final: 0.7573 (mt0) REVERT: D 1211 MET cc_start: 0.7073 (mtm) cc_final: 0.6818 (mtp) REVERT: D 1269 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7649 (mttt) REVERT: D 1301 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7475 (mmtm) REVERT: D 1327 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7838 (mtp85) REVERT: D 1350 GLU cc_start: 0.6454 (tp30) cc_final: 0.6016 (tt0) REVERT: D 1455 LYS cc_start: 0.7437 (mtpp) cc_final: 0.6998 (mttt) REVERT: D 1490 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7735 (ttmm) REVERT: E 32 ARG cc_start: 0.7093 (ttp-110) cc_final: 0.6869 (ttp-110) REVERT: E 48 MET cc_start: 0.6977 (ttt) cc_final: 0.5650 (ttp) REVERT: E 56 ASP cc_start: 0.8450 (m-30) cc_final: 0.8198 (m-30) REVERT: E 59 ASN cc_start: 0.7788 (t0) cc_final: 0.7343 (t0) REVERT: E 86 GLN cc_start: 0.8467 (tp40) cc_final: 0.8185 (tp40) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.4831 time to fit residues: 302.6248 Evaluate side-chains 287 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 0.1980 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 187 ASN C 390 GLN C 434 HIS C 543 ASN C 860 HIS D 507 ASN D 552 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN ** D1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25143 Z= 0.241 Angle : 0.519 8.170 34266 Z= 0.273 Chirality : 0.043 0.149 3873 Planarity : 0.005 0.043 4287 Dihedral : 12.999 149.772 3948 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.11 % Allowed : 7.95 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2942 helix: 0.78 (0.16), residues: 1056 sheet: -0.74 (0.23), residues: 429 loop : -0.73 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 200 HIS 0.008 0.001 HIS C 434 PHE 0.012 0.001 PHE C 239 TYR 0.020 0.001 TYR C1043 ARG 0.007 0.000 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 294 time to evaluate : 3.095 Fit side-chains revert: symmetry clash REVERT: A 47 SER cc_start: 0.8126 (t) cc_final: 0.7609 (p) REVERT: A 57 TYR cc_start: 0.7793 (t80) cc_final: 0.7471 (t80) REVERT: A 159 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7571 (mtmt) REVERT: A 175 ARG cc_start: 0.7260 (mtt-85) cc_final: 0.6759 (mmt90) REVERT: A 202 ASP cc_start: 0.7928 (p0) cc_final: 0.7649 (p0) REVERT: B 29 GLU cc_start: 0.6693 (tp30) cc_final: 0.6246 (mp0) REVERT: B 137 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8049 (ttm110) REVERT: B 220 GLU cc_start: 0.7456 (tt0) cc_final: 0.7085 (tp30) REVERT: C 24 GLU cc_start: 0.6262 (tp30) cc_final: 0.6033 (mm-30) REVERT: C 229 MET cc_start: 0.8279 (ptt) cc_final: 0.8001 (ptp) REVERT: C 288 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6477 (mtp-110) REVERT: C 384 GLU cc_start: 0.6158 (tp30) cc_final: 0.5766 (tt0) REVERT: C 426 ASP cc_start: 0.6833 (p0) cc_final: 0.6490 (m-30) REVERT: C 429 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6874 (t0) REVERT: C 504 GLU cc_start: 0.6234 (pt0) cc_final: 0.5812 (pt0) REVERT: C 512 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7706 (ptm-80) REVERT: C 599 GLU cc_start: 0.7079 (tp30) cc_final: 0.6682 (mt-10) REVERT: C 605 LYS cc_start: 0.7354 (mttt) cc_final: 0.6824 (mtmt) REVERT: C 626 ARG cc_start: 0.7440 (ttm110) cc_final: 0.6987 (ttp-170) REVERT: C 677 MET cc_start: 0.7918 (ptm) cc_final: 0.7652 (ptp) REVERT: C 706 GLU cc_start: 0.7286 (tp30) cc_final: 0.6902 (tp30) REVERT: C 754 ILE cc_start: 0.8091 (mt) cc_final: 0.7796 (mp) REVERT: C 916 GLU cc_start: 0.5647 (tp30) cc_final: 0.5435 (pt0) REVERT: C 960 GLU cc_start: 0.6376 (tt0) cc_final: 0.5888 (mp0) REVERT: C 1005 MET cc_start: 0.8624 (ttp) cc_final: 0.8355 (ttt) REVERT: C 1106 ASP cc_start: 0.7160 (m-30) cc_final: 0.6413 (t0) REVERT: D 38 LYS cc_start: 0.6526 (mmtp) cc_final: 0.6151 (mtmm) REVERT: D 40 GLU cc_start: 0.6426 (tp30) cc_final: 0.6141 (mt-10) REVERT: D 46 ASP cc_start: 0.8774 (t0) cc_final: 0.8010 (t70) REVERT: D 54 LYS cc_start: 0.6961 (mttp) cc_final: 0.6431 (mtpp) REVERT: D 453 ASP cc_start: 0.7790 (t0) cc_final: 0.7318 (t0) REVERT: D 464 LEU cc_start: 0.6262 (mt) cc_final: 0.6062 (mt) REVERT: D 476 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6875 (tm-30) REVERT: D 491 LYS cc_start: 0.6606 (tmmt) cc_final: 0.6027 (mtmm) REVERT: D 512 MET cc_start: 0.8443 (mtm) cc_final: 0.8191 (mtm) REVERT: D 553 ARG cc_start: 0.6370 (ttm110) cc_final: 0.6111 (ttp-110) REVERT: D 601 ARG cc_start: 0.6416 (ttt-90) cc_final: 0.6198 (mmm-85) REVERT: D 662 GLU cc_start: 0.6819 (tp30) cc_final: 0.6590 (tp30) REVERT: D 797 LYS cc_start: 0.7847 (tptt) cc_final: 0.6930 (mttt) REVERT: D 799 LYS cc_start: 0.8188 (mttt) cc_final: 0.7921 (mttp) REVERT: D 828 LYS cc_start: 0.7607 (mttt) cc_final: 0.7399 (mttm) REVERT: D 845 ASN cc_start: 0.5948 (p0) cc_final: 0.5561 (p0) REVERT: D 847 ASP cc_start: 0.6288 (m-30) cc_final: 0.5854 (m-30) REVERT: D 871 LYS cc_start: 0.6834 (pttt) cc_final: 0.6508 (pttt) REVERT: D 1012 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6266 (mt-10) REVERT: D 1046 GLN cc_start: 0.7094 (pm20) cc_final: 0.6188 (mp10) REVERT: D 1079 LYS cc_start: 0.6221 (tptt) cc_final: 0.5560 (tppt) REVERT: D 1159 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7545 (ttm170) REVERT: D 1184 GLN cc_start: 0.8024 (mt0) cc_final: 0.7697 (mt0) REVERT: D 1188 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6450 (m) REVERT: D 1211 MET cc_start: 0.7064 (mtm) cc_final: 0.6864 (mtp) REVERT: D 1327 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7767 (mtp85) REVERT: D 1350 GLU cc_start: 0.6208 (tp30) cc_final: 0.5705 (tt0) REVERT: D 1455 LYS cc_start: 0.7579 (mtpp) cc_final: 0.7152 (mttt) REVERT: D 1456 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7684 (ttmt) REVERT: D 1490 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7774 (ttmm) REVERT: E 32 ARG cc_start: 0.7088 (ttp-110) cc_final: 0.6851 (ttp-110) REVERT: E 48 MET cc_start: 0.6804 (ttt) cc_final: 0.5733 (ttp) REVERT: E 56 ASP cc_start: 0.8324 (m-30) cc_final: 0.8000 (m-30) REVERT: E 59 ASN cc_start: 0.7795 (t160) cc_final: 0.7424 (t0) REVERT: E 72 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7538 (mtt180) outliers start: 28 outliers final: 19 residues processed: 307 average time/residue: 0.4866 time to fit residues: 215.9375 Evaluate side-chains 293 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 272 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 269 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1359 GLN E 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25143 Z= 0.279 Angle : 0.524 7.769 34266 Z= 0.274 Chirality : 0.044 0.148 3873 Planarity : 0.005 0.043 4287 Dihedral : 12.856 147.328 3948 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.59 % Allowed : 9.42 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 2942 helix: 1.03 (0.16), residues: 1061 sheet: -0.36 (0.23), residues: 426 loop : -0.43 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.006 0.001 HIS A 156 PHE 0.014 0.001 PHE C 239 TYR 0.017 0.001 TYR C1043 ARG 0.005 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 287 time to evaluate : 3.522 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6007 (tt0) REVERT: A 175 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.6679 (mmt90) REVERT: B 137 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8038 (ttm110) REVERT: B 220 GLU cc_start: 0.7537 (tt0) cc_final: 0.7146 (tp30) REVERT: C 24 GLU cc_start: 0.6403 (tp30) cc_final: 0.6177 (mm-30) REVERT: C 191 PHE cc_start: 0.6842 (p90) cc_final: 0.6439 (p90) REVERT: C 229 MET cc_start: 0.8329 (ptt) cc_final: 0.8118 (ptp) REVERT: C 288 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.6504 (mtp180) REVERT: C 361 MET cc_start: 0.7221 (mmp) cc_final: 0.6810 (mmm) REVERT: C 372 LEU cc_start: 0.7873 (mp) cc_final: 0.7601 (mt) REVERT: C 384 GLU cc_start: 0.6191 (tp30) cc_final: 0.5833 (tt0) REVERT: C 426 ASP cc_start: 0.6819 (p0) cc_final: 0.6447 (m-30) REVERT: C 429 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6938 (t0) REVERT: C 504 GLU cc_start: 0.6207 (pt0) cc_final: 0.5801 (pt0) REVERT: C 512 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7725 (ptm-80) REVERT: C 599 GLU cc_start: 0.6962 (tp30) cc_final: 0.6712 (mt-10) REVERT: C 605 LYS cc_start: 0.7473 (mttt) cc_final: 0.6878 (mtmt) REVERT: C 626 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6770 (ttp-170) REVERT: C 677 MET cc_start: 0.7825 (ptm) cc_final: 0.7587 (ptp) REVERT: C 706 GLU cc_start: 0.7197 (tp30) cc_final: 0.6792 (tp30) REVERT: C 754 ILE cc_start: 0.8071 (mt) cc_final: 0.7781 (mp) REVERT: C 788 THR cc_start: 0.6277 (p) cc_final: 0.5910 (p) REVERT: C 960 GLU cc_start: 0.6402 (tt0) cc_final: 0.5875 (mp0) REVERT: C 1106 ASP cc_start: 0.7172 (m-30) cc_final: 0.6438 (t0) REVERT: D 38 LYS cc_start: 0.6554 (mmtp) cc_final: 0.6187 (mtmm) REVERT: D 54 LYS cc_start: 0.7049 (mttp) cc_final: 0.6512 (mtpp) REVERT: D 121 THR cc_start: 0.6502 (p) cc_final: 0.6302 (m) REVERT: D 453 ASP cc_start: 0.7412 (t0) cc_final: 0.6982 (t0) REVERT: D 491 LYS cc_start: 0.6638 (tmmt) cc_final: 0.6034 (mtmm) REVERT: D 512 MET cc_start: 0.8466 (mtm) cc_final: 0.8218 (mtm) REVERT: D 662 GLU cc_start: 0.6831 (tp30) cc_final: 0.6569 (tp30) REVERT: D 797 LYS cc_start: 0.7940 (tptt) cc_final: 0.6995 (mttt) REVERT: D 799 LYS cc_start: 0.8212 (mttt) cc_final: 0.7929 (mttp) REVERT: D 845 ASN cc_start: 0.6163 (p0) cc_final: 0.5769 (p0) REVERT: D 847 ASP cc_start: 0.6202 (m-30) cc_final: 0.5779 (m-30) REVERT: D 871 LYS cc_start: 0.6732 (pttt) cc_final: 0.6468 (pttt) REVERT: D 1005 GLN cc_start: 0.6514 (mm-40) cc_final: 0.6080 (mt0) REVERT: D 1012 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6308 (mt-10) REVERT: D 1046 GLN cc_start: 0.7389 (pm20) cc_final: 0.6844 (mt0) REVERT: D 1079 LYS cc_start: 0.6359 (tptt) cc_final: 0.5760 (tppt) REVERT: D 1100 ASP cc_start: 0.6768 (t0) cc_final: 0.6232 (m-30) REVERT: D 1159 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7457 (ttm170) REVERT: D 1184 GLN cc_start: 0.7952 (mt0) cc_final: 0.7635 (mt0) REVERT: D 1188 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6488 (m) REVERT: D 1269 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7547 (mttt) REVERT: D 1327 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7881 (mtp85) REVERT: D 1346 ARG cc_start: 0.6645 (ttm110) cc_final: 0.6247 (mtm-85) REVERT: D 1350 GLU cc_start: 0.5941 (tp30) cc_final: 0.5386 (tt0) REVERT: D 1455 LYS cc_start: 0.7336 (mtpp) cc_final: 0.6762 (mttt) REVERT: D 1456 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7702 (ttmt) REVERT: D 1490 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7768 (ttmm) REVERT: E 12 MET cc_start: 0.7334 (mtm) cc_final: 0.7028 (mtp) REVERT: E 32 ARG cc_start: 0.7076 (ttp-110) cc_final: 0.6779 (ttp-110) REVERT: E 48 MET cc_start: 0.6921 (ttt) cc_final: 0.5860 (ttp) REVERT: E 56 ASP cc_start: 0.8280 (m-30) cc_final: 0.7961 (m-30) REVERT: E 59 ASN cc_start: 0.7848 (t160) cc_final: 0.7286 (t0) outliers start: 40 outliers final: 32 residues processed: 310 average time/residue: 0.4623 time to fit residues: 209.9432 Evaluate side-chains 302 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 267 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 272 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN D 762 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25143 Z= 0.410 Angle : 0.589 10.015 34266 Z= 0.306 Chirality : 0.046 0.161 3873 Planarity : 0.005 0.043 4287 Dihedral : 12.891 143.987 3948 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.99 % Allowed : 10.41 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2942 helix: 0.93 (0.16), residues: 1055 sheet: -0.27 (0.24), residues: 434 loop : -0.39 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.010 0.002 HIS D 709 PHE 0.015 0.002 PHE C 896 TYR 0.021 0.002 TYR C 925 ARG 0.007 0.001 ARG C 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 275 time to evaluate : 2.629 Fit side-chains REVERT: A 64 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6049 (tt0) REVERT: A 175 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.6718 (mtt180) REVERT: A 202 ASP cc_start: 0.7998 (p0) cc_final: 0.7679 (p0) REVERT: B 137 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8051 (ttm110) REVERT: C 24 GLU cc_start: 0.6339 (tp30) cc_final: 0.6127 (mm-30) REVERT: C 167 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8235 (mptt) REVERT: C 191 PHE cc_start: 0.6901 (p90) cc_final: 0.6587 (p90) REVERT: C 288 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7345 (mtp180) REVERT: C 384 GLU cc_start: 0.6293 (tp30) cc_final: 0.5758 (tt0) REVERT: C 512 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7770 (ptm-80) REVERT: C 605 LYS cc_start: 0.7514 (mttt) cc_final: 0.6959 (mtmt) REVERT: C 626 ARG cc_start: 0.7098 (ttm110) cc_final: 0.6661 (ttp-170) REVERT: C 677 MET cc_start: 0.7867 (ptm) cc_final: 0.7639 (ptp) REVERT: C 706 GLU cc_start: 0.7291 (tp30) cc_final: 0.6889 (tp30) REVERT: C 1106 ASP cc_start: 0.7201 (m-30) cc_final: 0.6498 (t0) REVERT: D 38 LYS cc_start: 0.6611 (mmtp) cc_final: 0.6265 (mtmm) REVERT: D 54 LYS cc_start: 0.7072 (mttp) cc_final: 0.6527 (mtpp) REVERT: D 453 ASP cc_start: 0.7316 (t0) cc_final: 0.6918 (t0) REVERT: D 491 LYS cc_start: 0.6687 (tmmt) cc_final: 0.6060 (mtmm) REVERT: D 662 GLU cc_start: 0.6817 (tp30) cc_final: 0.6487 (tp30) REVERT: D 797 LYS cc_start: 0.7953 (tptt) cc_final: 0.7030 (mttt) REVERT: D 799 LYS cc_start: 0.8159 (mttt) cc_final: 0.7876 (mttp) REVERT: D 847 ASP cc_start: 0.6163 (m-30) cc_final: 0.5747 (m-30) REVERT: D 871 LYS cc_start: 0.6645 (pttt) cc_final: 0.6405 (pttt) REVERT: D 1005 GLN cc_start: 0.6409 (mm-40) cc_final: 0.5956 (mt0) REVERT: D 1012 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6273 (mt-10) REVERT: D 1046 GLN cc_start: 0.7191 (pm20) cc_final: 0.6745 (mt0) REVERT: D 1079 LYS cc_start: 0.6387 (tptt) cc_final: 0.5805 (tppt) REVERT: D 1159 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7576 (ttm170) REVERT: D 1184 GLN cc_start: 0.8113 (mt0) cc_final: 0.7673 (mt0) REVERT: D 1188 VAL cc_start: 0.6815 (OUTLIER) cc_final: 0.6469 (m) REVERT: D 1269 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7552 (mttt) REVERT: D 1327 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7883 (mtp85) REVERT: D 1350 GLU cc_start: 0.6203 (tp30) cc_final: 0.5655 (tt0) REVERT: D 1455 LYS cc_start: 0.7449 (mtpp) cc_final: 0.6875 (mttt) REVERT: D 1456 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7683 (ttmt) REVERT: D 1479 ASP cc_start: 0.8191 (m-30) cc_final: 0.7941 (m-30) REVERT: D 1490 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7736 (ttmm) REVERT: E 12 MET cc_start: 0.7254 (mtm) cc_final: 0.6997 (mtp) REVERT: E 48 MET cc_start: 0.6923 (ttt) cc_final: 0.5860 (ttp) REVERT: E 59 ASN cc_start: 0.7620 (t160) cc_final: 0.7023 (t0) outliers start: 50 outliers final: 41 residues processed: 312 average time/residue: 0.4457 time to fit residues: 203.8853 Evaluate side-chains 301 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 258 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 940 THR Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1261 GLU Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 246 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25143 Z= 0.157 Angle : 0.463 6.578 34266 Z= 0.244 Chirality : 0.041 0.149 3873 Planarity : 0.004 0.045 4287 Dihedral : 12.727 149.750 3948 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.39 % Allowed : 11.96 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 2942 helix: 1.32 (0.16), residues: 1062 sheet: -0.04 (0.24), residues: 420 loop : -0.16 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.004 0.001 HIS D 709 PHE 0.015 0.001 PHE C 239 TYR 0.012 0.001 TYR C 925 ARG 0.005 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 266 time to evaluate : 3.098 Fit side-chains REVERT: A 66 SER cc_start: 0.8206 (t) cc_final: 0.7766 (p) REVERT: A 175 ARG cc_start: 0.7231 (mtt-85) cc_final: 0.6639 (mmt90) REVERT: B 137 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8132 (ttm110) REVERT: C 24 GLU cc_start: 0.6359 (tp30) cc_final: 0.6128 (mm-30) REVERT: C 191 PHE cc_start: 0.6856 (p90) cc_final: 0.6558 (p90) REVERT: C 229 MET cc_start: 0.7675 (ptp) cc_final: 0.7460 (ptt) REVERT: C 384 GLU cc_start: 0.6323 (tp30) cc_final: 0.5788 (tt0) REVERT: C 429 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6936 (t0) REVERT: C 504 GLU cc_start: 0.6014 (pt0) cc_final: 0.5706 (pt0) REVERT: C 512 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7834 (ptm-80) REVERT: C 605 LYS cc_start: 0.7618 (mttt) cc_final: 0.6963 (mtmt) REVERT: C 626 ARG cc_start: 0.7153 (ttm110) cc_final: 0.6733 (ttp-170) REVERT: C 677 MET cc_start: 0.7718 (ptm) cc_final: 0.7469 (ptp) REVERT: C 706 GLU cc_start: 0.7208 (tp30) cc_final: 0.6767 (tp30) REVERT: C 1106 ASP cc_start: 0.7141 (m-30) cc_final: 0.6550 (t0) REVERT: D 38 LYS cc_start: 0.6517 (mmtp) cc_final: 0.6221 (mtmm) REVERT: D 54 LYS cc_start: 0.7024 (mttp) cc_final: 0.6494 (mtpp) REVERT: D 453 ASP cc_start: 0.7258 (t0) cc_final: 0.6874 (t0) REVERT: D 491 LYS cc_start: 0.6606 (tmmt) cc_final: 0.6011 (mtmm) REVERT: D 553 ARG cc_start: 0.6435 (ttp80) cc_final: 0.6169 (ttp-110) REVERT: D 662 GLU cc_start: 0.6751 (tp30) cc_final: 0.6343 (tp30) REVERT: D 797 LYS cc_start: 0.7924 (tptt) cc_final: 0.7059 (mttt) REVERT: D 799 LYS cc_start: 0.8114 (mttt) cc_final: 0.7750 (mttp) REVERT: D 845 ASN cc_start: 0.5822 (p0) cc_final: 0.5470 (p0) REVERT: D 847 ASP cc_start: 0.6200 (m-30) cc_final: 0.5771 (m-30) REVERT: D 871 LYS cc_start: 0.6407 (pttt) cc_final: 0.6198 (pttt) REVERT: D 1005 GLN cc_start: 0.6514 (mm-40) cc_final: 0.6064 (mt0) REVERT: D 1012 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6301 (mt-10) REVERT: D 1046 GLN cc_start: 0.7375 (pm20) cc_final: 0.6816 (mp10) REVERT: D 1079 LYS cc_start: 0.6354 (tptt) cc_final: 0.5803 (ttmt) REVERT: D 1100 ASP cc_start: 0.6787 (t0) cc_final: 0.6184 (m-30) REVERT: D 1159 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7455 (ttm170) REVERT: D 1184 GLN cc_start: 0.8019 (mt0) cc_final: 0.7585 (mt0) REVERT: D 1269 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7631 (mttt) REVERT: D 1327 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7941 (mtp85) REVERT: D 1350 GLU cc_start: 0.5992 (tp30) cc_final: 0.5441 (tt0) REVERT: D 1455 LYS cc_start: 0.7545 (mtpp) cc_final: 0.7078 (mttt) REVERT: D 1456 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7670 (ttmt) REVERT: D 1479 ASP cc_start: 0.8265 (m-30) cc_final: 0.8015 (m-30) REVERT: D 1490 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7740 (ttmm) REVERT: E 12 MET cc_start: 0.7193 (mtm) cc_final: 0.6877 (mtp) REVERT: E 28 GLN cc_start: 0.5309 (mt0) cc_final: 0.4969 (mt0) REVERT: E 48 MET cc_start: 0.6980 (ttt) cc_final: 0.5971 (ttp) REVERT: E 59 ASN cc_start: 0.7564 (t160) cc_final: 0.7024 (t0) REVERT: E 88 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7197 (tp30) outliers start: 35 outliers final: 29 residues processed: 289 average time/residue: 0.4844 time to fit residues: 205.6874 Evaluate side-chains 291 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 0.9980 chunk 260 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25143 Z= 0.206 Angle : 0.483 7.249 34266 Z= 0.253 Chirality : 0.042 0.143 3873 Planarity : 0.004 0.047 4287 Dihedral : 12.664 147.343 3948 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.63 % Allowed : 12.32 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2942 helix: 1.40 (0.16), residues: 1067 sheet: 0.10 (0.25), residues: 420 loop : -0.06 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 PHE 0.012 0.001 PHE C 239 TYR 0.017 0.001 TYR B 224 ARG 0.006 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 2.821 Fit side-chains REVERT: A 64 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5963 (tt0) REVERT: A 175 ARG cc_start: 0.7278 (mtt-85) cc_final: 0.6697 (mmt90) REVERT: A 202 ASP cc_start: 0.7940 (p0) cc_final: 0.7649 (p0) REVERT: B 134 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8602 (tp30) REVERT: B 137 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8090 (ttm110) REVERT: C 167 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8157 (mptt) REVERT: C 191 PHE cc_start: 0.6702 (p90) cc_final: 0.6414 (p90) REVERT: C 321 GLU cc_start: 0.7931 (pm20) cc_final: 0.7681 (pm20) REVERT: C 361 MET cc_start: 0.7055 (mmp) cc_final: 0.6384 (mtt) REVERT: C 384 GLU cc_start: 0.6329 (tp30) cc_final: 0.5793 (tt0) REVERT: C 429 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6945 (t0) REVERT: C 504 GLU cc_start: 0.6130 (pt0) cc_final: 0.5849 (pt0) REVERT: C 512 ARG cc_start: 0.8164 (ptm160) cc_final: 0.7870 (ptm-80) REVERT: C 605 LYS cc_start: 0.7479 (mttt) cc_final: 0.7107 (mtmt) REVERT: C 626 ARG cc_start: 0.7169 (ttm110) cc_final: 0.6746 (ttp-170) REVERT: C 677 MET cc_start: 0.7721 (ptm) cc_final: 0.7462 (ptp) REVERT: C 706 GLU cc_start: 0.7290 (tp30) cc_final: 0.6852 (tp30) REVERT: C 1106 ASP cc_start: 0.7145 (m-30) cc_final: 0.6557 (t0) REVERT: D 38 LYS cc_start: 0.6532 (mmtp) cc_final: 0.6233 (mtmm) REVERT: D 54 LYS cc_start: 0.7008 (mttp) cc_final: 0.6486 (mtpp) REVERT: D 131 LYS cc_start: 0.8141 (mttm) cc_final: 0.7847 (mttt) REVERT: D 453 ASP cc_start: 0.7244 (t0) cc_final: 0.6854 (t0) REVERT: D 491 LYS cc_start: 0.6623 (tmmt) cc_final: 0.6024 (mtmm) REVERT: D 662 GLU cc_start: 0.6789 (tp30) cc_final: 0.6356 (tp30) REVERT: D 797 LYS cc_start: 0.7913 (tptt) cc_final: 0.6989 (mttt) REVERT: D 799 LYS cc_start: 0.8128 (mttt) cc_final: 0.7747 (mttp) REVERT: D 847 ASP cc_start: 0.6206 (m-30) cc_final: 0.5789 (m-30) REVERT: D 871 LYS cc_start: 0.6417 (pttt) cc_final: 0.6215 (pttt) REVERT: D 1005 GLN cc_start: 0.6445 (mm-40) cc_final: 0.5968 (mt0) REVERT: D 1012 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6260 (mt-10) REVERT: D 1046 GLN cc_start: 0.7386 (pm20) cc_final: 0.6824 (mp10) REVERT: D 1079 LYS cc_start: 0.6362 (tptt) cc_final: 0.5803 (ttmt) REVERT: D 1159 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7455 (ttm170) REVERT: D 1184 GLN cc_start: 0.8024 (mt0) cc_final: 0.7587 (mt0) REVERT: D 1188 VAL cc_start: 0.6800 (OUTLIER) cc_final: 0.6524 (m) REVERT: D 1269 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7635 (mttt) REVERT: D 1327 ARG cc_start: 0.8232 (mtt90) cc_final: 0.7943 (mtp85) REVERT: D 1346 ARG cc_start: 0.6608 (ttm110) cc_final: 0.6227 (mtm-85) REVERT: D 1350 GLU cc_start: 0.5920 (tp30) cc_final: 0.5327 (tt0) REVERT: D 1455 LYS cc_start: 0.7522 (mtpp) cc_final: 0.7017 (mttt) REVERT: D 1456 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7666 (ttmt) REVERT: D 1479 ASP cc_start: 0.8248 (m-30) cc_final: 0.7997 (m-30) REVERT: D 1490 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7726 (ttmm) REVERT: E 12 MET cc_start: 0.7236 (mtm) cc_final: 0.6940 (mtp) REVERT: E 48 MET cc_start: 0.6840 (ttt) cc_final: 0.6558 (ptm) REVERT: E 59 ASN cc_start: 0.7563 (t160) cc_final: 0.7004 (t0) REVERT: E 88 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7142 (tp30) outliers start: 41 outliers final: 32 residues processed: 291 average time/residue: 0.4731 time to fit residues: 200.9512 Evaluate side-chains 293 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 258 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 164 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 288 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 175 optimal weight: 40.0000 chunk 133 optimal weight: 3.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25143 Z= 0.339 Angle : 0.545 8.944 34266 Z= 0.284 Chirality : 0.045 0.206 3873 Planarity : 0.005 0.048 4287 Dihedral : 12.702 144.441 3948 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.99 % Allowed : 12.48 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 2942 helix: 1.31 (0.16), residues: 1055 sheet: 0.11 (0.25), residues: 423 loop : -0.10 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 200 HIS 0.007 0.001 HIS D 709 PHE 0.013 0.002 PHE C 896 TYR 0.022 0.001 TYR B 224 ARG 0.007 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 2.961 Fit side-chains REVERT: A 64 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6053 (tt0) REVERT: A 175 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.6859 (mmt90) REVERT: A 202 ASP cc_start: 0.8012 (p0) cc_final: 0.7655 (p0) REVERT: B 134 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8683 (tp30) REVERT: B 137 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8097 (ttm110) REVERT: C 167 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8165 (mptt) REVERT: C 191 PHE cc_start: 0.6723 (p90) cc_final: 0.6455 (p90) REVERT: C 229 MET cc_start: 0.7787 (ptp) cc_final: 0.7459 (ptp) REVERT: C 321 GLU cc_start: 0.7930 (pm20) cc_final: 0.7648 (pm20) REVERT: C 384 GLU cc_start: 0.6319 (tp30) cc_final: 0.5781 (tt0) REVERT: C 426 ASP cc_start: 0.6783 (p0) cc_final: 0.6455 (m-30) REVERT: C 429 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6870 (t0) REVERT: C 504 GLU cc_start: 0.6206 (pt0) cc_final: 0.5935 (pt0) REVERT: C 512 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7893 (ptm-80) REVERT: C 543 ASN cc_start: 0.7491 (m110) cc_final: 0.7099 (m-40) REVERT: C 605 LYS cc_start: 0.7254 (mttt) cc_final: 0.6893 (mtmt) REVERT: C 677 MET cc_start: 0.7869 (ptm) cc_final: 0.7647 (ptp) REVERT: C 706 GLU cc_start: 0.7287 (tp30) cc_final: 0.6882 (tp30) REVERT: C 1106 ASP cc_start: 0.7151 (m-30) cc_final: 0.6594 (t0) REVERT: D 38 LYS cc_start: 0.6591 (mmtp) cc_final: 0.6258 (mtmm) REVERT: D 54 LYS cc_start: 0.7022 (mttp) cc_final: 0.6494 (mtpp) REVERT: D 131 LYS cc_start: 0.8139 (mttm) cc_final: 0.7825 (mttt) REVERT: D 453 ASP cc_start: 0.7257 (t0) cc_final: 0.6944 (t0) REVERT: D 491 LYS cc_start: 0.6675 (tmmt) cc_final: 0.6049 (mtmm) REVERT: D 587 ARG cc_start: 0.7427 (ttt90) cc_final: 0.6820 (ttt180) REVERT: D 662 GLU cc_start: 0.6705 (tp30) cc_final: 0.6211 (tp30) REVERT: D 797 LYS cc_start: 0.8014 (tptt) cc_final: 0.7157 (mttt) REVERT: D 799 LYS cc_start: 0.8105 (mttt) cc_final: 0.7718 (mttp) REVERT: D 847 ASP cc_start: 0.6214 (m-30) cc_final: 0.5793 (m-30) REVERT: D 871 LYS cc_start: 0.6370 (pttt) cc_final: 0.6164 (pttt) REVERT: D 976 GLN cc_start: 0.6853 (tm-30) cc_final: 0.6584 (tm-30) REVERT: D 1005 GLN cc_start: 0.6524 (mm-40) cc_final: 0.6058 (mt0) REVERT: D 1012 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6272 (mt-10) REVERT: D 1046 GLN cc_start: 0.7174 (pm20) cc_final: 0.6765 (mp10) REVERT: D 1079 LYS cc_start: 0.6364 (tptt) cc_final: 0.5788 (tppt) REVERT: D 1159 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7411 (ttm170) REVERT: D 1184 GLN cc_start: 0.8076 (mt0) cc_final: 0.7644 (mt0) REVERT: D 1188 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6525 (m) REVERT: D 1269 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7645 (mttt) REVERT: D 1327 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7947 (mtp85) REVERT: D 1346 ARG cc_start: 0.6613 (ttm110) cc_final: 0.5908 (mtp180) REVERT: D 1350 GLU cc_start: 0.6023 (tp30) cc_final: 0.5485 (tt0) REVERT: D 1455 LYS cc_start: 0.7459 (mtpp) cc_final: 0.6959 (mttt) REVERT: D 1456 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7677 (ttmt) REVERT: D 1479 ASP cc_start: 0.8253 (m-30) cc_final: 0.7998 (m-30) REVERT: D 1490 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7715 (ttmm) REVERT: E 12 MET cc_start: 0.7263 (mtm) cc_final: 0.6926 (mtp) REVERT: E 48 MET cc_start: 0.6853 (ttt) cc_final: 0.5890 (ttp) REVERT: E 59 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.6986 (t0) REVERT: E 88 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7073 (tp30) outliers start: 50 outliers final: 42 residues processed: 298 average time/residue: 0.4579 time to fit residues: 201.1016 Evaluate side-chains 306 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1086 LEU Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1261 GLU Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 172 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25143 Z= 0.139 Angle : 0.448 6.977 34266 Z= 0.235 Chirality : 0.041 0.226 3873 Planarity : 0.004 0.048 4287 Dihedral : 12.568 148.935 3948 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.59 % Allowed : 13.24 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 2942 helix: 1.58 (0.16), residues: 1061 sheet: 0.31 (0.25), residues: 423 loop : 0.09 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.004 0.001 HIS D 709 PHE 0.013 0.001 PHE C 114 TYR 0.014 0.001 TYR B 224 ARG 0.007 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 3.121 Fit side-chains REVERT: A 47 SER cc_start: 0.8085 (t) cc_final: 0.7566 (p) REVERT: A 66 SER cc_start: 0.8216 (t) cc_final: 0.7769 (p) REVERT: A 102 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7934 (mtpp) REVERT: A 175 ARG cc_start: 0.7220 (mtt-85) cc_final: 0.6620 (mmt90) REVERT: A 202 ASP cc_start: 0.7986 (p0) cc_final: 0.7684 (p0) REVERT: B 134 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8643 (tp30) REVERT: B 137 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8114 (ttm110) REVERT: C 167 LYS cc_start: 0.8557 (mmtt) cc_final: 0.7990 (mptt) REVERT: C 191 PHE cc_start: 0.6713 (p90) cc_final: 0.6442 (p90) REVERT: C 229 MET cc_start: 0.7870 (ptp) cc_final: 0.7588 (ptp) REVERT: C 321 GLU cc_start: 0.7995 (pm20) cc_final: 0.7690 (pm20) REVERT: C 361 MET cc_start: 0.6969 (mmp) cc_final: 0.6258 (mtt) REVERT: C 384 GLU cc_start: 0.6355 (tp30) cc_final: 0.5846 (tt0) REVERT: C 429 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6985 (t0) REVERT: C 512 ARG cc_start: 0.8185 (ptm160) cc_final: 0.7876 (ptm-80) REVERT: C 605 LYS cc_start: 0.7433 (mttt) cc_final: 0.6931 (mtmt) REVERT: C 706 GLU cc_start: 0.7289 (tp30) cc_final: 0.6849 (tp30) REVERT: C 1106 ASP cc_start: 0.7088 (m-30) cc_final: 0.6584 (t0) REVERT: D 30 GLU cc_start: 0.7365 (mp0) cc_final: 0.7072 (mp0) REVERT: D 38 LYS cc_start: 0.6454 (mmtp) cc_final: 0.6150 (mtmm) REVERT: D 40 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5462 (mm-30) REVERT: D 54 LYS cc_start: 0.7139 (mttp) cc_final: 0.6640 (mtpp) REVERT: D 453 ASP cc_start: 0.7199 (t0) cc_final: 0.6913 (t0) REVERT: D 491 LYS cc_start: 0.6565 (tmmt) cc_final: 0.5973 (mtmm) REVERT: D 662 GLU cc_start: 0.6845 (tp30) cc_final: 0.6332 (tp30) REVERT: D 797 LYS cc_start: 0.8001 (tptt) cc_final: 0.7193 (mttt) REVERT: D 845 ASN cc_start: 0.5812 (p0) cc_final: 0.5397 (p0) REVERT: D 847 ASP cc_start: 0.6294 (m-30) cc_final: 0.5850 (m-30) REVERT: D 976 GLN cc_start: 0.6747 (tm-30) cc_final: 0.6541 (tm-30) REVERT: D 1005 GLN cc_start: 0.6593 (mm-40) cc_final: 0.6165 (mt0) REVERT: D 1012 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6246 (mt-10) REVERT: D 1046 GLN cc_start: 0.7360 (pm20) cc_final: 0.6890 (mp10) REVERT: D 1079 LYS cc_start: 0.6298 (tptt) cc_final: 0.5744 (ttmt) REVERT: D 1100 ASP cc_start: 0.6472 (t0) cc_final: 0.6091 (m-30) REVERT: D 1159 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7398 (ttm170) REVERT: D 1184 GLN cc_start: 0.7983 (mt0) cc_final: 0.7556 (mt0) REVERT: D 1188 VAL cc_start: 0.6807 (OUTLIER) cc_final: 0.6560 (m) REVERT: D 1327 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7916 (mtp85) REVERT: D 1346 ARG cc_start: 0.6533 (ttm110) cc_final: 0.6192 (mtm-85) REVERT: D 1350 GLU cc_start: 0.6064 (tp30) cc_final: 0.5481 (tt0) REVERT: D 1455 LYS cc_start: 0.7572 (mtpp) cc_final: 0.7168 (mttt) REVERT: D 1479 ASP cc_start: 0.8273 (m-30) cc_final: 0.8021 (m-30) REVERT: D 1490 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7706 (ttmm) REVERT: E 12 MET cc_start: 0.7082 (mtm) cc_final: 0.6684 (mtp) REVERT: E 28 GLN cc_start: 0.5317 (mt0) cc_final: 0.4956 (mt0) REVERT: E 48 MET cc_start: 0.6867 (ttt) cc_final: 0.6642 (ptm) REVERT: E 59 ASN cc_start: 0.7518 (t160) cc_final: 0.6947 (t0) outliers start: 40 outliers final: 32 residues processed: 300 average time/residue: 0.4621 time to fit residues: 202.8548 Evaluate side-chains 293 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1090 ASP Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1261 GLU Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 251 optimal weight: 0.3980 chunk 268 optimal weight: 4.9990 chunk 161 optimal weight: 0.0970 chunk 116 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25143 Z= 0.210 Angle : 0.481 8.134 34266 Z= 0.251 Chirality : 0.042 0.139 3873 Planarity : 0.004 0.049 4287 Dihedral : 12.564 146.189 3948 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.51 % Allowed : 13.79 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 2942 helix: 1.54 (0.16), residues: 1067 sheet: 0.36 (0.25), residues: 423 loop : 0.12 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS A 156 PHE 0.011 0.001 PHE C 114 TYR 0.011 0.001 TYR C 925 ARG 0.008 0.000 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 3.201 Fit side-chains REVERT: A 64 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6017 (tt0) REVERT: A 102 LYS cc_start: 0.8344 (mtmm) cc_final: 0.7948 (mtpp) REVERT: A 175 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6645 (mmt90) REVERT: A 202 ASP cc_start: 0.7991 (p0) cc_final: 0.7671 (p0) REVERT: B 84 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 134 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8647 (tp30) REVERT: B 137 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8121 (ttm110) REVERT: C 167 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8180 (mptt) REVERT: C 229 MET cc_start: 0.7558 (ptp) cc_final: 0.7309 (ptp) REVERT: C 361 MET cc_start: 0.7298 (mmp) cc_final: 0.6649 (mtt) REVERT: C 384 GLU cc_start: 0.6168 (tp30) cc_final: 0.5752 (tt0) REVERT: C 429 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6969 (t0) REVERT: C 512 ARG cc_start: 0.8209 (ptm160) cc_final: 0.7905 (ptm-80) REVERT: C 605 LYS cc_start: 0.7381 (mttt) cc_final: 0.6900 (mtmt) REVERT: C 677 MET cc_start: 0.7993 (ptp) cc_final: 0.7773 (ptt) REVERT: C 706 GLU cc_start: 0.7285 (tp30) cc_final: 0.6850 (tp30) REVERT: C 1106 ASP cc_start: 0.7071 (m-30) cc_final: 0.6595 (t0) REVERT: D 38 LYS cc_start: 0.6527 (mmtp) cc_final: 0.6186 (mtmm) REVERT: D 40 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5536 (mm-30) REVERT: D 54 LYS cc_start: 0.7144 (mttp) cc_final: 0.6643 (mtpp) REVERT: D 453 ASP cc_start: 0.7211 (t0) cc_final: 0.6921 (t0) REVERT: D 491 LYS cc_start: 0.6651 (tmmt) cc_final: 0.6061 (mtmm) REVERT: D 662 GLU cc_start: 0.6858 (tp30) cc_final: 0.6337 (tp30) REVERT: D 797 LYS cc_start: 0.8016 (tptt) cc_final: 0.7209 (mttt) REVERT: D 847 ASP cc_start: 0.6295 (m-30) cc_final: 0.5869 (m-30) REVERT: D 976 GLN cc_start: 0.6818 (tm-30) cc_final: 0.6541 (tm-30) REVERT: D 1002 LYS cc_start: 0.6905 (mttt) cc_final: 0.6685 (mtmt) REVERT: D 1005 GLN cc_start: 0.6476 (mm-40) cc_final: 0.6015 (mt0) REVERT: D 1012 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6246 (mt-10) REVERT: D 1046 GLN cc_start: 0.7377 (pm20) cc_final: 0.6888 (mp10) REVERT: D 1079 LYS cc_start: 0.6325 (tptt) cc_final: 0.5836 (ttmt) REVERT: D 1100 ASP cc_start: 0.6473 (t0) cc_final: 0.6053 (m-30) REVERT: D 1159 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7396 (ttm170) REVERT: D 1184 GLN cc_start: 0.8010 (mt0) cc_final: 0.7577 (mt0) REVERT: D 1188 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6525 (m) REVERT: D 1327 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7924 (mtp85) REVERT: D 1346 ARG cc_start: 0.6564 (ttm110) cc_final: 0.6223 (mtm-85) REVERT: D 1350 GLU cc_start: 0.5912 (tp30) cc_final: 0.5311 (tt0) REVERT: D 1388 ARG cc_start: 0.7640 (mmp80) cc_final: 0.7199 (mtm110) REVERT: D 1455 LYS cc_start: 0.7514 (mtpp) cc_final: 0.6994 (mttt) REVERT: D 1479 ASP cc_start: 0.8257 (m-30) cc_final: 0.7997 (m-30) REVERT: D 1490 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7705 (ttmm) REVERT: E 12 MET cc_start: 0.7101 (mtm) cc_final: 0.6696 (mtp) REVERT: E 28 GLN cc_start: 0.5316 (mt0) cc_final: 0.4961 (mt0) REVERT: E 59 ASN cc_start: 0.7571 (t160) cc_final: 0.6991 (t0) outliers start: 38 outliers final: 33 residues processed: 285 average time/residue: 0.4688 time to fit residues: 195.6770 Evaluate side-chains 295 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1261 GLU Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 50.0000 chunk 283 optimal weight: 4.9990 chunk 173 optimal weight: 50.0000 chunk 134 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 297 optimal weight: 20.0000 chunk 274 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25143 Z= 0.313 Angle : 0.539 8.735 34266 Z= 0.280 Chirality : 0.044 0.151 3873 Planarity : 0.005 0.050 4287 Dihedral : 12.629 144.217 3948 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.47 % Allowed : 13.83 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 2942 helix: 1.44 (0.16), residues: 1057 sheet: 0.31 (0.25), residues: 429 loop : 0.04 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.007 0.001 HIS D 709 PHE 0.012 0.001 PHE A 179 TYR 0.013 0.001 TYR D1198 ARG 0.008 0.000 ARG C 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 255 time to evaluate : 2.636 Fit side-chains REVERT: A 102 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7955 (mtpp) REVERT: A 175 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.6767 (mtt180) REVERT: A 202 ASP cc_start: 0.7972 (p0) cc_final: 0.7613 (p0) REVERT: B 134 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8655 (tp30) REVERT: B 137 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8132 (ttm110) REVERT: C 167 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8398 (mmtm) REVERT: C 229 MET cc_start: 0.7555 (ptp) cc_final: 0.7341 (ptp) REVERT: C 384 GLU cc_start: 0.6149 (tp30) cc_final: 0.5722 (tt0) REVERT: C 426 ASP cc_start: 0.6788 (p0) cc_final: 0.6456 (m-30) REVERT: C 429 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6933 (t0) REVERT: C 512 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7904 (ptm-80) REVERT: C 605 LYS cc_start: 0.7261 (mttt) cc_final: 0.6891 (mtmt) REVERT: C 706 GLU cc_start: 0.7283 (tp30) cc_final: 0.6874 (tp30) REVERT: C 1106 ASP cc_start: 0.7163 (m-30) cc_final: 0.6786 (t0) REVERT: D 38 LYS cc_start: 0.6560 (mmtp) cc_final: 0.6245 (mtmm) REVERT: D 40 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5547 (mm-30) REVERT: D 54 LYS cc_start: 0.7000 (mttp) cc_final: 0.6479 (mtpp) REVERT: D 453 ASP cc_start: 0.7238 (t0) cc_final: 0.6983 (t0) REVERT: D 491 LYS cc_start: 0.6693 (tmmt) cc_final: 0.6082 (mtmm) REVERT: D 662 GLU cc_start: 0.6772 (tp30) cc_final: 0.6252 (tp30) REVERT: D 797 LYS cc_start: 0.8045 (tptt) cc_final: 0.7247 (mttt) REVERT: D 847 ASP cc_start: 0.6213 (m-30) cc_final: 0.5792 (m-30) REVERT: D 976 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6724 (tm-30) REVERT: D 1005 GLN cc_start: 0.6443 (mm-40) cc_final: 0.6019 (mt0) REVERT: D 1012 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6285 (mt-10) REVERT: D 1046 GLN cc_start: 0.7213 (pm20) cc_final: 0.6831 (mp10) REVERT: D 1079 LYS cc_start: 0.6355 (tptt) cc_final: 0.5858 (ttmt) REVERT: D 1100 ASP cc_start: 0.6768 (t0) cc_final: 0.6140 (m-30) REVERT: D 1159 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7395 (ttm170) REVERT: D 1184 GLN cc_start: 0.8078 (mt0) cc_final: 0.7641 (mt0) REVERT: D 1188 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6521 (m) REVERT: D 1327 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7930 (mtp85) REVERT: D 1346 ARG cc_start: 0.6593 (ttm110) cc_final: 0.5910 (mtp180) REVERT: D 1350 GLU cc_start: 0.6020 (tp30) cc_final: 0.5456 (tt0) REVERT: D 1388 ARG cc_start: 0.7407 (mmp80) cc_final: 0.7061 (mtm110) REVERT: D 1455 LYS cc_start: 0.7489 (mtpp) cc_final: 0.6936 (mttt) REVERT: D 1479 ASP cc_start: 0.8263 (m-30) cc_final: 0.8000 (m-30) REVERT: D 1490 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7751 (ttmm) REVERT: E 12 MET cc_start: 0.7232 (mtm) cc_final: 0.6772 (mtp) REVERT: E 48 MET cc_start: 0.6379 (ptm) cc_final: 0.6101 (ptm) REVERT: E 59 ASN cc_start: 0.7571 (t160) cc_final: 0.6970 (t0) outliers start: 37 outliers final: 35 residues processed: 280 average time/residue: 0.4868 time to fit residues: 199.6043 Evaluate side-chains 291 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 684 LYS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 875 THR Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1188 VAL Chi-restraints excluded: chain D residue 1261 GLU Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1415 VAL Chi-restraints excluded: chain D residue 1488 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.9980 chunk 252 optimal weight: 0.0010 chunk 72 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119768 restraints weight = 27726.283| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.87 r_work: 0.2876 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25143 Z= 0.180 Angle : 0.476 8.062 34266 Z= 0.248 Chirality : 0.042 0.139 3873 Planarity : 0.004 0.050 4287 Dihedral : 12.556 146.967 3948 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.59 % Allowed : 13.75 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 2942 helix: 1.55 (0.16), residues: 1068 sheet: 0.41 (0.25), residues: 423 loop : 0.14 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.005 0.001 HIS D 709 PHE 0.011 0.001 PHE C 114 TYR 0.010 0.001 TYR C 629 ARG 0.009 0.000 ARG C 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5361.76 seconds wall clock time: 97 minutes 36.24 seconds (5856.24 seconds total)