Starting phenix.real_space_refine on Sun Feb 18 00:42:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e59_27907/02_2024/8e59_27907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e59_27907/02_2024/8e59_27907.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/8e59_27907/02_2024/8e59_27907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e59_27907/02_2024/8e59_27907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e59_27907/02_2024/8e59_27907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e59_27907/02_2024/8e59_27907_updated.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= 0.005 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 I 2 10.91 5 Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13097 2.51 5 N 3350 2.21 5 O 3745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 516": "OD1" <-> "OD2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D GLU 646": "OE1" <-> "OE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D ASP 849": "OD1" <-> "OD2" Residue "D ASP 866": "OD1" <-> "OD2" Residue "D PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20309 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {' CA': 1, '3PE': 1, 'BBI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.88, per 1000 atoms: 0.54 Number of scatterers: 20309 At special positions: 0 Unit cell: (172.67, 170.442, 182.696, 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) I 2 52.95 Ca 2 19.99 S 112 16.00 P 1 15.00 O 3745 8.00 N 3350 7.00 C 13097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.87 Conformation dependent library (CDL) restraints added in 3.9 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 13 sheets defined 49.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 127 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.636A pdb=" N LYS A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.790A pdb=" N ALA A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 243 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 245 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 255 through 292 removed outlier: 3.643A pdb=" N MET A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.818A pdb=" N HIS A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.654A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 419 removed outlier: 3.962A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.876A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 542 Processing helix chain 'A' and resid 549 through 574 Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.936A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.501A pdb=" N PHE A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 630 removed outlier: 3.621A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 624 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 626 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 629 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 647 through 672 Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.633A pdb=" N TYR A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 771 removed outlier: 4.248A pdb=" N MET A 726 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 728 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 733 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 734 " --> pdb=" O TYR A 731 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 737 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS A 738 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 740 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 741 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE A 747 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 748 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 749 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE A 750 " --> pdb=" O PHE A 747 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 753 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN A 754 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 755 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 756 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 757 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 770 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 771 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 removed outlier: 4.371A pdb=" N LEU A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.613A pdb=" N ALA A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 941 removed outlier: 3.588A pdb=" N TYR A 924 " --> pdb=" O GLY A 920 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 968 removed outlier: 3.506A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 966 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 removed outlier: 4.276A pdb=" N VAL A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ARG A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) Proline residue: A 991 - end of helix removed outlier: 4.650A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1036 removed outlier: 3.560A pdb=" N GLY A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1087 through 1098 Processing helix chain 'A' and resid 1103 through 1111 Processing helix chain 'A' and resid 1126 through 1139 Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 3.524A pdb=" N PHE A1147 " --> pdb=" O MET A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1173 No H-bonds generated for 'chain 'A' and resid 1171 through 1173' Processing helix chain 'A' and resid 1176 through 1180 Processing helix chain 'A' and resid 1193 through 1202 removed outlier: 4.245A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1224 removed outlier: 3.707A pdb=" N MET A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1259 removed outlier: 3.763A pdb=" N VAL A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1286 removed outlier: 3.571A pdb=" N PHE A1272 " --> pdb=" O ALA A1268 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1273 " --> pdb=" O TRP A1269 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A1285 " --> pdb=" O ILE A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1330 removed outlier: 3.766A pdb=" N ARG A1319 " --> pdb=" O ILE A1315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A1323 " --> pdb=" O ARG A1319 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N MET A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG A1325 " --> pdb=" O PHE A1321 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A1326 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A1327 " --> pdb=" O VAL A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1349 Processing helix chain 'A' and resid 1353 through 1372 Processing helix chain 'A' and resid 1392 through 1404 Processing helix chain 'A' and resid 1408 through 1414 Processing helix chain 'A' and resid 1438 through 1470 removed outlier: 3.729A pdb=" N ILE A1441 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A1446 " --> pdb=" O TYR A1443 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A1467 " --> pdb=" O MET A1464 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A1468 " --> pdb=" O ASP A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1491 Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1527 through 1533 removed outlier: 3.868A pdb=" N VAL A1532 " --> pdb=" O CYS A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1557 removed outlier: 4.347A pdb=" N LEU A1550 " --> pdb=" O PHE A1546 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1575 Processing helix chain 'A' and resid 1584 through 1588 Processing helix chain 'D' and resid 30 through 52 Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.966A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 109 removed outlier: 3.552A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 199 removed outlier: 3.590A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 189 " --> pdb=" O TRP D 185 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.563A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.512A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.781A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.633A pdb=" N PHE D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 406 removed outlier: 3.801A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.642A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.601A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.755A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.589A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.821A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 653 Processing helix chain 'D' and resid 678 through 687 removed outlier: 3.535A pdb=" N PHE D 686 " --> pdb=" O ASN D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 718 removed outlier: 3.599A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'D' and resid 818 through 826 Processing helix chain 'D' and resid 866 through 869 No H-bonds generated for 'chain 'D' and resid 866 through 869' Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 880 through 888 removed outlier: 3.540A pdb=" N HIS D 885 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 57 removed outlier: 4.878A pdb=" N HIS C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 191 through 207 removed outlier: 4.263A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 247 through 263 removed outlier: 3.722A pdb=" N GLU C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.851A pdb=" N ARG C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 326 removed outlier: 4.244A pdb=" N LYS C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N HIS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 342 through 359 removed outlier: 3.538A pdb=" N GLU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 300 through 303 removed outlier: 3.891A pdb=" N THR A 300 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 334 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id= C, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= D, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.695A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 410 through 413 removed outlier: 8.315A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN D 290 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL D 258 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA D 292 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= G, first strand: chain 'D' and resid 658 through 661 removed outlier: 4.227A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 736 " --> pdb=" O ILE D 740 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS D 815 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG D 732 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY D 813 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL D 734 " --> pdb=" O VAL D 811 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 811 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 848 through 854 removed outlier: 3.520A pdb=" N VAL D 851 " --> pdb=" O ILE D1016 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 892 through 899 removed outlier: 4.308A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 902 through 905 removed outlier: 3.616A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 62 through 65 Processing sheet with id= L, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.912A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.576A pdb=" N LEU C 266 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR C 215 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 268 " --> pdb=" O THR C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 854 hydrogen bonds defined for protein. 2286 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 8.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 6574 1.37 - 1.52: 10168 1.52 - 1.68: 3822 1.68 - 1.84: 176 1.84 - 1.99: 2 Bond restraints: 20742 Sorted by residual: bond pdb=" CBC BBI A2201 " pdb=" IBD BBI A2201 " ideal model delta sigma weight residual 2.097 1.988 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CAR BBI A2201 " pdb=" IAS BBI A2201 " ideal model delta sigma weight residual 2.098 1.991 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" CAV BBI A2201 " pdb=" CAW BBI A2201 " ideal model delta sigma weight residual 1.510 1.614 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CAW BBI A2201 " pdb=" NAX BBI A2201 " ideal model delta sigma weight residual 1.449 1.534 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG F 3 " pdb=" O5 NAG F 3 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 20737 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.48: 649 107.48 - 115.01: 12371 115.01 - 122.54: 12836 122.54 - 130.06: 2123 130.06 - 137.59: 111 Bond angle restraints: 28090 Sorted by residual: angle pdb=" C TYR D 744 " pdb=" N PRO D 745 " pdb=" CA PRO D 745 " ideal model delta sigma weight residual 119.84 114.19 5.65 1.25e+00 6.40e-01 2.04e+01 angle pdb=" CAM BBI A2201 " pdb=" CAN BBI A2201 " pdb=" CAP BBI A2201 " ideal model delta sigma weight residual 118.51 131.39 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" N SER A 252 " pdb=" CA SER A 252 " pdb=" C SER A 252 " ideal model delta sigma weight residual 111.07 106.91 4.16 1.07e+00 8.73e-01 1.51e+01 angle pdb=" CA TYR D 744 " pdb=" C TYR D 744 " pdb=" N PRO D 745 " ideal model delta sigma weight residual 120.52 117.36 3.16 8.30e-01 1.45e+00 1.45e+01 angle pdb=" CAC BBI A2201 " pdb=" CAD BBI A2201 " pdb=" CAE BBI A2201 " ideal model delta sigma weight residual 112.57 123.57 -11.00 3.00e+00 1.11e-01 1.35e+01 ... (remaining 28085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 11509 23.11 - 46.22: 934 46.22 - 69.33: 112 69.33 - 92.44: 36 92.44 - 115.55: 33 Dihedral angle restraints: 12624 sinusoidal: 5307 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 167.62 -74.62 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -149.51 63.51 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS A1421 " pdb=" SG CYS A1421 " pdb=" SG CYS A1435 " pdb=" CB CYS A1435 " ideal model delta sinusoidal sigma weight residual -86.00 -141.43 55.43 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 12621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3187 0.138 - 0.276: 9 0.276 - 0.414: 2 0.414 - 0.552: 0 0.552 - 0.690: 1 Chirality restraints: 3199 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3196 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 743 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C VAL D 743 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL D 743 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR D 744 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 140 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO C 141 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1416 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A1417 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1417 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1417 " -0.023 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.67: 293 2.67 - 3.24: 20004 3.24 - 3.82: 34144 3.82 - 4.39: 42428 4.39 - 4.96: 72627 Nonbonded interactions: 169496 Sorted by model distance: nonbonded pdb=" OD1 ASN D 895 " pdb=" O3 NAG H 1 " model vdw 2.098 2.440 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.247 2.440 nonbonded pdb=" OG SER D 594 " pdb=" O ASP D 596 " model vdw 2.267 2.440 nonbonded pdb=" O THR D 32 " pdb=" OG SER D 35 " model vdw 2.272 2.440 nonbonded pdb=" OD1 ASN D 668 " pdb=" OG SER D 696 " model vdw 2.272 2.440 ... (remaining 169491 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 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.060 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: 6.190 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 56.450 Find NCS groups from input model: 0.560 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 0.109 20742 Z= 0.211 Angle : 0.535 12.885 28090 Z= 0.265 Chirality : 0.042 0.690 3199 Planarity : 0.003 0.051 3554 Dihedral : 17.557 115.546 7858 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 0.54 % Allowed : 12.76 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.04 (0.17), residues: 2472 helix: 1.02 (0.15), residues: 1184 sheet: 0.14 (0.36), residues: 217 loop : -1.25 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1199 HIS 0.002 0.000 HIS A 886 PHE 0.022 0.001 PHE D 686 TYR 0.014 0.001 TYR D1068 ARG 0.003 0.000 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 269 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: A 606 GLU cc_start: 0.6617 (mm-30) cc_final: 0.5366 (mp0) REVERT: D 745 PRO cc_start: 0.7176 (Cg_exo) cc_final: 0.6883 (Cg_endo) outliers start: 12 outliers final: 0 residues processed: 274 average time/residue: 0.3227 time to fit residues: 138.4729 Evaluate side-chains 255 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 226 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN D 652 ASN D 751 ASN D 824 ASN C 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20742 Z= 0.154 Angle : 0.524 10.307 28090 Z= 0.260 Chirality : 0.042 0.512 3199 Planarity : 0.004 0.052 3554 Dihedral : 11.164 106.054 3043 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 1.49 % Allowed : 13.21 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.02 (0.17), residues: 2472 helix: 1.06 (0.15), residues: 1195 sheet: -0.01 (0.33), residues: 255 loop : -1.30 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.003 0.000 HIS C 94 PHE 0.021 0.001 PHE A1147 TYR 0.013 0.001 TYR A 921 ARG 0.003 0.000 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.6847 (mmt) REVERT: A 890 ASN cc_start: 0.6905 (m110) cc_final: 0.6420 (m110) REVERT: A 1028 MET cc_start: 0.8235 (mtm) cc_final: 0.8018 (mtm) REVERT: A 1143 MET cc_start: 0.8529 (mtp) cc_final: 0.8319 (mmt) REVERT: A 1378 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7951 (mtp180) REVERT: D 745 PRO cc_start: 0.7051 (Cg_exo) cc_final: 0.6744 (Cg_endo) REVERT: D 747 GLU cc_start: 0.6940 (mp0) cc_final: 0.5727 (tt0) REVERT: C 195 MET cc_start: 0.4429 (mpp) cc_final: 0.4011 (mpp) outliers start: 33 outliers final: 16 residues processed: 288 average time/residue: 0.3108 time to fit residues: 140.2471 Evaluate side-chains 276 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 chunk 188 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 226 optimal weight: 0.0000 chunk 244 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.7946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20742 Z= 0.147 Angle : 0.502 13.092 28090 Z= 0.245 Chirality : 0.041 0.342 3199 Planarity : 0.004 0.048 3554 Dihedral : 9.459 103.744 3043 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 1.90 % Allowed : 13.98 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.06 (0.17), residues: 2472 helix: 1.12 (0.15), residues: 1192 sheet: 0.11 (0.33), residues: 248 loop : -1.27 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.002 0.000 HIS C 94 PHE 0.018 0.001 PHE A1147 TYR 0.013 0.001 TYR D1068 ARG 0.004 0.000 ARG D 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 272 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 890 ASN cc_start: 0.6886 (m110) cc_final: 0.6410 (m110) REVERT: A 1028 MET cc_start: 0.8271 (mtm) cc_final: 0.8051 (mtm) REVERT: A 1464 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6800 (ptm) REVERT: D 646 GLU cc_start: 0.7271 (mp0) cc_final: 0.7063 (mp0) REVERT: D 704 ARG cc_start: 0.8466 (tpt90) cc_final: 0.8060 (tpt90) REVERT: D 708 ASP cc_start: 0.6900 (m-30) cc_final: 0.6066 (m-30) REVERT: D 745 PRO cc_start: 0.6901 (Cg_exo) cc_final: 0.6617 (Cg_endo) REVERT: D 1003 PHE cc_start: 0.8368 (p90) cc_final: 0.8124 (p90) REVERT: C 195 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3998 (mpp) outliers start: 42 outliers final: 21 residues processed: 300 average time/residue: 0.3058 time to fit residues: 144.1978 Evaluate side-chains 284 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20742 Z= 0.198 Angle : 0.509 9.522 28090 Z= 0.252 Chirality : 0.041 0.253 3199 Planarity : 0.004 0.046 3554 Dihedral : 8.530 102.669 3043 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 2.08 % Allowed : 15.07 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.02 (0.17), residues: 2472 helix: 1.03 (0.15), residues: 1207 sheet: 0.03 (0.33), residues: 250 loop : -1.29 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1103 HIS 0.002 0.000 HIS A 886 PHE 0.021 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.005 0.000 ARG A1378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8656 (tt) REVERT: A 890 ASN cc_start: 0.7130 (m110) cc_final: 0.6670 (m110) REVERT: A 1464 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6854 (ptm) REVERT: D 745 PRO cc_start: 0.7144 (Cg_exo) cc_final: 0.6873 (Cg_endo) REVERT: C 195 MET cc_start: 0.4432 (mpp) cc_final: 0.4017 (mpp) outliers start: 46 outliers final: 33 residues processed: 297 average time/residue: 0.3059 time to fit residues: 144.9737 Evaluate side-chains 295 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.0010 chunk 216 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 443 GLN D 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20742 Z= 0.197 Angle : 0.509 9.557 28090 Z= 0.254 Chirality : 0.042 0.253 3199 Planarity : 0.004 0.042 3554 Dihedral : 8.165 102.104 3043 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 2.58 % Allowed : 15.52 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.00 (0.17), residues: 2472 helix: 1.05 (0.15), residues: 1207 sheet: -0.01 (0.33), residues: 253 loop : -1.29 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1103 HIS 0.003 0.000 HIS A 886 PHE 0.020 0.001 PHE A1147 TYR 0.013 0.001 TYR D1068 ARG 0.004 0.000 ARG A1378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 264 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8655 (tt) REVERT: A 408 GLU cc_start: 0.7550 (tp30) cc_final: 0.7338 (mm-30) REVERT: A 607 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5675 (mm) REVERT: A 890 ASN cc_start: 0.7146 (m110) cc_final: 0.6677 (m110) REVERT: A 1464 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6870 (ptm) REVERT: D 704 ARG cc_start: 0.8542 (tpt90) cc_final: 0.7976 (tpt90) REVERT: D 708 ASP cc_start: 0.6946 (m-30) cc_final: 0.6329 (m-30) REVERT: D 745 PRO cc_start: 0.7070 (Cg_exo) cc_final: 0.6792 (Cg_endo) REVERT: D 1003 PHE cc_start: 0.8418 (p90) cc_final: 0.8063 (p90) REVERT: C 195 MET cc_start: 0.4455 (OUTLIER) cc_final: 0.4044 (mpp) outliers start: 57 outliers final: 39 residues processed: 302 average time/residue: 0.2955 time to fit residues: 142.2235 Evaluate side-chains 298 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 255 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 111 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20742 Z= 0.157 Angle : 0.506 10.413 28090 Z= 0.249 Chirality : 0.041 0.258 3199 Planarity : 0.004 0.051 3554 Dihedral : 7.842 100.924 3043 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 2.17 % Allowed : 16.74 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.07 (0.17), residues: 2472 helix: 1.12 (0.15), residues: 1207 sheet: 0.05 (0.33), residues: 253 loop : -1.26 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1103 HIS 0.002 0.000 HIS A 886 PHE 0.020 0.001 PHE A1147 TYR 0.012 0.001 TYR D1068 ARG 0.004 0.000 ARG A1378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 269 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8642 (tt) REVERT: A 408 GLU cc_start: 0.7544 (tp30) cc_final: 0.7333 (mm-30) REVERT: A 607 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5933 (mm) REVERT: A 890 ASN cc_start: 0.7265 (m110) cc_final: 0.6908 (m110) REVERT: A 1464 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6891 (ptm) REVERT: D 506 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7312 (pp) REVERT: D 646 GLU cc_start: 0.7227 (mp0) cc_final: 0.7006 (mp0) REVERT: D 704 ARG cc_start: 0.8505 (tpt90) cc_final: 0.7859 (tpt90) REVERT: D 708 ASP cc_start: 0.6949 (m-30) cc_final: 0.6115 (m-30) REVERT: D 745 PRO cc_start: 0.6914 (Cg_exo) cc_final: 0.6643 (Cg_endo) REVERT: D 883 MET cc_start: 0.8794 (tpt) cc_final: 0.8545 (tpp) REVERT: D 1003 PHE cc_start: 0.8386 (p90) cc_final: 0.8106 (p90) REVERT: C 195 MET cc_start: 0.4460 (OUTLIER) cc_final: 0.4023 (mpp) outliers start: 48 outliers final: 37 residues processed: 299 average time/residue: 0.3382 time to fit residues: 162.8711 Evaluate side-chains 303 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1554 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 443 GLN ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 20742 Z= 0.349 Angle : 0.602 9.841 28090 Z= 0.300 Chirality : 0.045 0.248 3199 Planarity : 0.004 0.048 3554 Dihedral : 8.084 101.755 3043 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 2.76 % Allowed : 16.61 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.21 (0.17), residues: 2472 helix: 0.86 (0.15), residues: 1209 sheet: -0.02 (0.33), residues: 249 loop : -1.39 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1103 HIS 0.005 0.001 HIS A 886 PHE 0.026 0.002 PHE A1147 TYR 0.016 0.001 TYR D1068 ARG 0.004 0.000 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 268 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7356 (ptpt) cc_final: 0.6777 (pttp) REVERT: A 248 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8734 (tt) REVERT: A 607 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5734 (mm) REVERT: A 890 ASN cc_start: 0.7174 (m110) cc_final: 0.6811 (m110) REVERT: A 1464 MET cc_start: 0.7456 (ptt) cc_final: 0.7045 (ptm) REVERT: D 506 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7473 (pp) REVERT: D 595 GLN cc_start: 0.8162 (tp40) cc_final: 0.7797 (tp40) REVERT: D 646 GLU cc_start: 0.7193 (mp0) cc_final: 0.6813 (mp0) REVERT: D 708 ASP cc_start: 0.7014 (m-30) cc_final: 0.6237 (m-30) REVERT: D 745 PRO cc_start: 0.7200 (Cg_exo) cc_final: 0.6894 (Cg_endo) REVERT: C 195 MET cc_start: 0.4496 (OUTLIER) cc_final: 0.4050 (mpp) outliers start: 61 outliers final: 45 residues processed: 314 average time/residue: 0.3059 time to fit residues: 153.0194 Evaluate side-chains 313 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1554 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1016 ILE Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 301 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN D 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 20742 Z= 0.165 Angle : 0.523 9.416 28090 Z= 0.259 Chirality : 0.041 0.259 3199 Planarity : 0.004 0.052 3554 Dihedral : 7.698 102.287 3043 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 1.95 % Allowed : 17.87 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.04 (0.17), residues: 2472 helix: 1.02 (0.15), residues: 1210 sheet: 0.03 (0.33), residues: 251 loop : -1.33 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1103 HIS 0.002 0.000 HIS C 94 PHE 0.018 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.004 0.000 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7295 (ptpt) cc_final: 0.6737 (pttp) REVERT: A 248 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8644 (tt) REVERT: A 373 MET cc_start: 0.8698 (mmt) cc_final: 0.8393 (mmp) REVERT: A 607 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5967 (mm) REVERT: A 890 ASN cc_start: 0.7137 (m110) cc_final: 0.6784 (m110) REVERT: A 1464 MET cc_start: 0.7340 (ptt) cc_final: 0.6926 (ptm) REVERT: D 506 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7368 (pp) REVERT: D 595 GLN cc_start: 0.8135 (tp40) cc_final: 0.7915 (tp40) REVERT: D 646 GLU cc_start: 0.7323 (mp0) cc_final: 0.7077 (mp0) REVERT: D 704 ARG cc_start: 0.8566 (tpt90) cc_final: 0.7755 (tpt90) REVERT: D 708 ASP cc_start: 0.7044 (m-30) cc_final: 0.6433 (m-30) REVERT: D 883 MET cc_start: 0.8809 (tpt) cc_final: 0.8556 (tpp) REVERT: C 195 MET cc_start: 0.4460 (OUTLIER) cc_final: 0.3994 (mpp) outliers start: 43 outliers final: 37 residues processed: 297 average time/residue: 0.2979 time to fit residues: 140.8022 Evaluate side-chains 301 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 260 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1554 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 175 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 20742 Z= 0.204 Angle : 0.537 9.566 28090 Z= 0.265 Chirality : 0.042 0.255 3199 Planarity : 0.004 0.051 3554 Dihedral : 7.535 101.486 3043 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 2.31 % Allowed : 17.83 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.06 (0.17), residues: 2472 helix: 0.99 (0.15), residues: 1209 sheet: 0.01 (0.32), residues: 251 loop : -1.31 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1103 HIS 0.002 0.000 HIS A 544 PHE 0.021 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.004 0.000 ARG A 993 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 258 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7308 (ptpt) cc_final: 0.6745 (pttp) REVERT: A 248 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8674 (tt) REVERT: A 606 GLU cc_start: 0.6662 (mm-30) cc_final: 0.5536 (mp0) REVERT: A 607 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5822 (mm) REVERT: A 890 ASN cc_start: 0.7097 (m110) cc_final: 0.6746 (m110) REVERT: A 1464 MET cc_start: 0.7343 (ptt) cc_final: 0.6914 (ptm) REVERT: D 506 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7398 (pp) REVERT: D 595 GLN cc_start: 0.8160 (tp40) cc_final: 0.7901 (tp40) REVERT: D 646 GLU cc_start: 0.7327 (mp0) cc_final: 0.7125 (mp0) REVERT: D 704 ARG cc_start: 0.8576 (tpt90) cc_final: 0.7753 (tpt90) REVERT: D 708 ASP cc_start: 0.6920 (m-30) cc_final: 0.6251 (m-30) REVERT: D 883 MET cc_start: 0.8825 (tpt) cc_final: 0.8567 (tpp) REVERT: C 195 MET cc_start: 0.4463 (OUTLIER) cc_final: 0.4006 (mpp) outliers start: 51 outliers final: 42 residues processed: 295 average time/residue: 0.3151 time to fit residues: 147.8027 Evaluate side-chains 304 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1554 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 228 optimal weight: 0.2980 chunk 197 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 20742 Z= 0.203 Angle : 0.537 9.571 28090 Z= 0.265 Chirality : 0.042 0.253 3199 Planarity : 0.004 0.053 3554 Dihedral : 7.348 101.248 3043 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 2.17 % Allowed : 18.01 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.09 (0.17), residues: 2472 helix: 0.97 (0.15), residues: 1209 sheet: -0.01 (0.32), residues: 251 loop : -1.34 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1103 HIS 0.002 0.000 HIS A 544 PHE 0.020 0.001 PHE A1147 TYR 0.014 0.001 TYR D1068 ARG 0.004 0.000 ARG A 993 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 259 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.7302 (ptpt) cc_final: 0.6739 (ptmm) REVERT: A 248 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 607 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6043 (mm) REVERT: A 890 ASN cc_start: 0.7104 (m110) cc_final: 0.6750 (m110) REVERT: D 506 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7405 (pp) REVERT: D 595 GLN cc_start: 0.8107 (tp40) cc_final: 0.7857 (tp40) REVERT: D 646 GLU cc_start: 0.7442 (mp0) cc_final: 0.7224 (mp0) REVERT: D 704 ARG cc_start: 0.8564 (tpt90) cc_final: 0.7794 (tpt90) REVERT: D 708 ASP cc_start: 0.7019 (m-30) cc_final: 0.6116 (m-30) REVERT: D 883 MET cc_start: 0.8814 (tpt) cc_final: 0.8576 (tpp) REVERT: D 1003 PHE cc_start: 0.8429 (p90) cc_final: 0.8164 (p90) REVERT: C 195 MET cc_start: 0.4473 (OUTLIER) cc_final: 0.4006 (mpp) outliers start: 48 outliers final: 40 residues processed: 294 average time/residue: 0.3038 time to fit residues: 142.4271 Evaluate side-chains 300 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 256 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1554 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 849 ASP Chi-restraints excluded: chain D residue 871 ILE Chi-restraints excluded: chain D residue 877 GLU Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain D residue 1071 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 182 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 203 optimal weight: 0.0170 chunk 25 optimal weight: 0.0670 chunk 36 optimal weight: 8.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 HIS ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN D 41 GLN D 443 GLN D 698 ASN D 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.209284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141952 restraints weight = 23254.823| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.75 r_work: 0.3179 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 20742 Z= 0.127 Angle : 0.499 9.680 28090 Z= 0.244 Chirality : 0.041 0.277 3199 Planarity : 0.004 0.052 3554 Dihedral : 6.822 98.230 3043 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 1.63 % Allowed : 18.46 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.16 (0.17), residues: 2472 helix: 1.23 (0.15), residues: 1192 sheet: 0.05 (0.31), residues: 266 loop : -1.24 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 185 HIS 0.002 0.000 HIS C 94 PHE 0.022 0.001 PHE A1150 TYR 0.016 0.001 TYR A1469 ARG 0.004 0.000 ARG A 993 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.47 seconds wall clock time: 92 minutes 45.82 seconds (5565.82 seconds total)