Starting phenix.real_space_refine on Fri Jul 3 18:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.cif" model { file = "/net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niu_12365/07_2026/7niu_12365.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 9889 2.51 5 N 2601 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15495 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8780 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 27, 'TRANS': 1105} Chain breaks: 2 Chain: "D" Number of atoms: 1584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1578 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Conformer: "B" Number of residues, atoms: 208, 1575 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1598 Chain: "E" Number of atoms: 1702 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 229, 1702 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.90, per 1000 atoms: 0.25 Number of scatterers: 15495 At special positions: 0 Unit cell: (158.4, 132, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2952 8.00 N 2601 7.00 C 9889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.02 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.02 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 773.4 milliseconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 33 sheets defined 38.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 50 through 92 removed outlier: 4.781A pdb=" N LEU A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 108 through 160 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.631A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 260 removed outlier: 4.069A pdb=" N VAL A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 5.029A pdb=" N LYS A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 271 through 325 removed outlier: 4.286A pdb=" N GLU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.607A pdb=" N ALA A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 350 through 372 removed outlier: 3.620A pdb=" N ILE A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 471 removed outlier: 4.292A pdb=" N GLU A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 498 through 507 removed outlier: 4.014A pdb=" N ALA A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.542A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.541A pdb=" N MET A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.584A pdb=" N VAL A 628 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.232A pdb=" N ASN A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 740 removed outlier: 3.788A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.507A pdb=" N ALA A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 750 through 798 removed outlier: 3.652A pdb=" N PHE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 803 removed outlier: 3.785A pdb=" N TRP A 802 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 853 removed outlier: 3.743A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 828 " --> pdb=" O VAL A 824 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 853 " --> pdb=" O SER A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.676A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 909 removed outlier: 4.417A pdb=" N ILE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 904 " --> pdb=" O ILE A 900 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 966 removed outlier: 4.480A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 3.603A pdb=" N TYR A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 984 Processing helix chain 'A' and resid 985 through 987 No H-bonds generated for 'chain 'A' and resid 985 through 987' Processing helix chain 'A' and resid 994 through 1013 removed outlier: 3.925A pdb=" N ARG A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1082 removed outlier: 3.709A pdb=" N LEU A1081 " --> pdb=" O VAL A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 Processing helix chain 'A' and resid 1104 through 1112 Processing helix chain 'A' and resid 1125 through 1132 removed outlier: 3.799A pdb=" N ASN A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 removed outlier: 4.307A pdb=" N VAL A1145 " --> pdb=" O GLN A1141 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.522A pdb=" N ILE A1157 " --> pdb=" O ILE A1153 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' Processing helix chain 'A' and resid 1168 through 1173 removed outlier: 4.350A pdb=" N GLY A1172 " --> pdb=" O VAL A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1183 Processing helix chain 'A' and resid 1184 through 1192 removed outlier: 3.837A pdb=" N LEU A1189 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A1190 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1211 removed outlier: 3.688A pdb=" N LYS A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 4.057A pdb=" N LEU A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A1219 " --> pdb=" O GLU A1215 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 397 removed outlier: 3.641A pdb=" N GLU A 395 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 454 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 455 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 458 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.860A pdb=" N LEU A 412 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 475 removed outlier: 4.344A pdb=" N ASP A 557 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ILE A 587 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 556 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1058 through 1059 removed outlier: 3.519A pdb=" N VAL A1059 " --> pdb=" O ILE A1034 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A1034 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1035 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1094 " --> pdb=" O THR A1035 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1065 through 1067 Processing sheet with id=AA7, first strand: chain 'A' and resid 1113 through 1115 removed outlier: 6.652A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASP A1199 " --> pdb=" O GLY A1113 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A1115 " --> pdb=" O ASP A1199 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A1229 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A1198 " --> pdb=" O ILE A1229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 20 through 25 Processing sheet with id=AA9, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.526A pdb=" N LEU D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS D 89 " --> pdb=" O GLY D 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.526A pdb=" N LEU D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.411A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 146 through 151 Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AB5, first strand: chain 'E' and resid 21 through 25 removed outlier: 3.823A pdb=" N ALA E 82 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 53 removed outlier: 3.569A pdb=" N VAL E 51 " --> pdb=" O TRP E 39 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TRP E 39 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS E 38 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 133 through 136 Processing sheet with id=AB8, first strand: chain 'E' and resid 164 through 167 removed outlier: 4.007A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC1, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC2, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AC5, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AC6, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AC7, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.808A pdb=" N GLN B 161 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 154 through 155 removed outlier: 3.594A pdb=" N PHE B 210 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 197 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 206 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.764A pdb=" N SER C 24 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 14 through 15 removed outlier: 3.611A pdb=" N VAL C 15 " --> pdb=" O THR C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.732A pdb=" N GLY C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 100 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR C 122 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD4, first strand: chain 'C' and resid 140 through 142 removed outlier: 5.000A pdb=" N ALA C 157 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY C 159 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 202 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU C 161 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER C 200 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS C 163 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU C 198 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL C 201 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS C 184 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 140 through 142 removed outlier: 5.000A pdb=" N ALA C 157 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY C 159 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 202 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU C 161 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER C 200 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS C 163 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU C 198 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 170 through 174 717 hydrogen bonds defined for protein. 1998 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: 3.46 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2514 1.28 - 1.42: 4127 1.42 - 1.55: 9084 1.55 - 1.69: 17 1.69 - 1.82: 79 Bond restraints: 15821 Sorted by residual: bond pdb=" C LEU A1217 " pdb=" O LEU A1217 " ideal model delta sigma weight residual 1.235 1.150 0.084 1.40e-02 5.10e+03 3.62e+01 bond pdb=" N GLU A1023 " pdb=" CA GLU A1023 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.87e+00 bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 7.70e+00 bond pdb=" N VAL A 985 " pdb=" CA VAL A 985 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.68e+00 bond pdb=" N ILE A1017 " pdb=" CA ILE A1017 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.23e-02 6.61e+03 7.25e+00 ... (remaining 15816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 20602 2.26 - 4.53: 745 4.53 - 6.79: 81 6.79 - 9.06: 21 9.06 - 11.32: 9 Bond angle restraints: 21458 Sorted by residual: angle pdb=" N VAL A 746 " pdb=" CA VAL A 746 " pdb=" C VAL A 746 " ideal model delta sigma weight residual 110.36 120.49 -10.13 1.05e+00 9.07e-01 9.30e+01 angle pdb=" C TRP A 214 " pdb=" N LYS A 215 " pdb=" CA LYS A 215 " ideal model delta sigma weight residual 122.17 114.16 8.01 1.54e+00 4.22e-01 2.70e+01 angle pdb=" N ILE A1236 " pdb=" CA ILE A1236 " pdb=" C ILE A1236 " ideal model delta sigma weight residual 111.90 107.98 3.92 8.10e-01 1.52e+00 2.35e+01 angle pdb=" N ILE A1153 " pdb=" CA ILE A1153 " pdb=" C ILE A1153 " ideal model delta sigma weight residual 113.71 109.44 4.27 9.50e-01 1.11e+00 2.02e+01 angle pdb=" N ASP A1218 " pdb=" CA ASP A1218 " pdb=" C ASP A1218 " ideal model delta sigma weight residual 110.80 119.97 -9.17 2.13e+00 2.20e-01 1.85e+01 ... (remaining 21453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8237 17.87 - 35.74: 942 35.74 - 53.62: 185 53.62 - 71.49: 40 71.49 - 89.36: 15 Dihedral angle restraints: 9419 sinusoidal: 3601 harmonic: 5818 Sorted by residual: dihedral pdb=" CB CYS D 24 " pdb=" SG CYS D 24 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 160.17 -67.17 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CA VAL A 964 " pdb=" C VAL A 964 " pdb=" N ASN A 965 " pdb=" CA ASN A 965 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ALA D 85 " pdb=" C ALA D 85 " pdb=" N THR D 86 " pdb=" CA THR D 86 " ideal model delta harmonic sigma weight residual 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 9416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1893 0.062 - 0.123: 476 0.123 - 0.185: 70 0.185 - 0.247: 8 0.247 - 0.309: 4 Chirality restraints: 2451 Sorted by residual: chirality pdb=" CA TYR A 328 " pdb=" N TYR A 328 " pdb=" C TYR A 328 " pdb=" CB TYR A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C14 CLR A1301 " pdb=" C13 CLR A1301 " pdb=" C15 CLR A1301 " pdb=" C8 CLR A1301 " both_signs ideal model delta sigma weight residual False -2.32 -2.60 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C17 CLR A1302 " pdb=" C13 CLR A1302 " pdb=" C16 CLR A1302 " pdb=" C20 CLR A1302 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2448 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " -0.027 2.00e-02 2.50e+03 2.28e-02 9.08e+00 pdb=" CG PHE A 305 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 154 " -0.008 2.00e-02 2.50e+03 1.83e-02 5.83e+00 pdb=" CG PHE A 154 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 154 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 154 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 154 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 154 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 154 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 827 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ALA A 827 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 827 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 828 " -0.012 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 604 2.67 - 3.23: 16490 3.23 - 3.78: 24303 3.78 - 4.34: 32792 4.34 - 4.90: 51734 Nonbonded interactions: 125923 Sorted by model distance: nonbonded pdb=" N GLU A1023 " pdb=" OE1 GLU A1023 " model vdw 2.110 3.120 nonbonded pdb=" OG1 THR A 706 " pdb=" OE1 GLU A 707 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR A 857 " pdb=" N LEU A 858 " model vdw 2.198 3.120 nonbonded pdb=" O ALA A 840 " pdb=" OG1 THR A 844 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 275 " pdb=" NH1 ARG A 278 " model vdw 2.199 3.120 ... (remaining 125918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) selection = (chain 'D' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) } ncs_group { reference = (chain 'C' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 109 or resid 111 throug \ h 112 or resid 115 or resid 121 through 236)) selection = (chain 'E' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 103 or resid 105 throug \ h 106 or resid 108 or resid 114 through 229)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.910 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 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 : 0.008 0.084 15829 Z= 0.382 Angle : 1.014 11.321 21474 Z= 0.575 Chirality : 0.055 0.309 2451 Planarity : 0.006 0.050 2716 Dihedral : 15.899 89.361 5671 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 34.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.74 % Favored : 85.01 % Rotamer: Outliers : 1.67 % Allowed : 12.57 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.18 (0.14), residues: 2005 helix: -3.56 (0.13), residues: 682 sheet: -2.80 (0.23), residues: 368 loop : -3.58 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1191 TYR 0.030 0.003 TYR A 919 PHE 0.052 0.003 PHE A 305 TRP 0.024 0.002 TRP A 164 HIS 0.006 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.38 (15821) covalent geometry : angle 1.01385 / 0.58 (21458) SS BOND : bond 0.00426 / 0.19 ( 8) SS BOND : angle 1.27953 / 0.75 ( 16) hydrogen bonds : bond 0.17214 / 11.74 ( 701) hydrogen bonds : angle 8.46769 / 6.06 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ARG cc_start: 0.6126 (mtm180) cc_final: 0.5846 (mtp180) REVERT: A 469 ARG cc_start: 0.6506 (mtt90) cc_final: 0.3938 (ptp-110) REVERT: A 577 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.5779 (pttt) REVERT: A 618 MET cc_start: 0.2222 (ttt) cc_final: 0.1460 (mtp) REVERT: A 704 ASN cc_start: 0.6941 (p0) cc_final: 0.6604 (p0) REVERT: A 975 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6112 (tp) REVERT: E 97 TYR cc_start: 0.4188 (m-10) cc_final: 0.3518 (m-10) REVERT: E 108 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.5837 (tp40) REVERT: B 5 MET cc_start: 0.3819 (tpp) cc_final: 0.2851 (pmm) outliers start: 27 outliers final: 13 residues processed: 211 average time/residue: 0.1471 time to fit residues: 44.6365 Evaluate side-chains 137 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 332 ASN A 393 ASN A 539 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 823 GLN ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN A 965 ASN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS A1238 ASN D 7 GLN D 91 GLN E 108 GLN E 184 GLN B 28 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 161 GLN B 167 GLN B 211 ASN C 31 ASN C 87 ASN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.171249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.147063 restraints weight = 63447.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.150466 restraints weight = 114573.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.150937 restraints weight = 45094.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.151625 restraints weight = 35840.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.152330 restraints weight = 26890.946| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4469 r_free = 0.4469 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4468 r_free = 0.4468 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.4468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15829 Z= 0.159 Angle : 0.695 10.801 21474 Z= 0.367 Chirality : 0.045 0.236 2451 Planarity : 0.005 0.051 2716 Dihedral : 6.516 104.035 2188 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.42 % Allowed : 5.96 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.16), residues: 2005 helix: -1.63 (0.17), residues: 684 sheet: -2.25 (0.24), residues: 388 loop : -2.81 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 70 TYR 0.025 0.002 TYR A 937 PHE 0.021 0.002 PHE A 774 TRP 0.018 0.002 TRP A 164 HIS 0.010 0.002 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (15821) covalent geometry : angle 0.69462 / 0.37 (21458) SS BOND : bond 0.00305 / 0.17 ( 8) SS BOND : angle 0.75317 / 0.46 ( 16) hydrogen bonds : bond 0.05578 / 3.74 ( 701) hydrogen bonds : angle 6.09556 / 4.38 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8038 (tpp) cc_final: 0.7811 (tpp) REVERT: A 113 MET cc_start: 0.7082 (mmm) cc_final: 0.6293 (mmm) REVERT: A 116 TYR cc_start: 0.5479 (m-80) cc_final: 0.5057 (m-80) REVERT: A 194 MET cc_start: 0.7586 (tpp) cc_final: 0.6771 (tpt) REVERT: A 406 ARG cc_start: 0.6099 (mtm180) cc_final: 0.5695 (mtp180) REVERT: A 515 ILE cc_start: 0.4687 (mt) cc_final: 0.4473 (mt) REVERT: A 549 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6697 (tpp-160) REVERT: A 618 MET cc_start: 0.2987 (ttt) cc_final: 0.2395 (mtp) REVERT: A 704 ASN cc_start: 0.6693 (p0) cc_final: 0.6483 (p0) REVERT: A 756 LEU cc_start: 0.7141 (mm) cc_final: 0.6934 (mm) REVERT: A 975 LEU cc_start: 0.5512 (tp) cc_final: 0.5143 (tp) REVERT: D 193 TYR cc_start: 0.3497 (m-80) cc_final: 0.3262 (m-10) REVERT: E 73 ILE cc_start: 0.4975 (tp) cc_final: 0.4676 (tt) REVERT: B 5 MET cc_start: 0.3467 (tpp) cc_final: 0.2722 (pmm) outliers start: 6 outliers final: 0 residues processed: 193 average time/residue: 0.1380 time to fit residues: 38.7796 Evaluate side-chains 136 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 147 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN A 748 GLN A 841 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.164987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.134261 restraints weight = 64834.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.135266 restraints weight = 87733.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.137299 restraints weight = 53219.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.137437 restraints weight = 33417.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.138146 restraints weight = 30504.013| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15829 Z= 0.278 Angle : 0.834 12.001 21474 Z= 0.437 Chirality : 0.050 0.247 2451 Planarity : 0.006 0.066 2716 Dihedral : 6.931 100.364 2188 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.54 % Allowed : 6.37 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.17), residues: 2005 helix: -1.70 (0.17), residues: 687 sheet: -2.04 (0.25), residues: 378 loop : -2.61 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 831 TYR 0.034 0.003 TYR A 927 PHE 0.028 0.003 PHE A 728 TRP 0.025 0.002 TRP A 164 HIS 0.006 0.002 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.28 (15821) covalent geometry : angle 0.83350 / 0.44 (21458) SS BOND : bond 0.00398 / 0.23 ( 8) SS BOND : angle 1.15632 / 0.58 ( 16) hydrogen bonds : bond 0.06721 / 4.46 ( 701) hydrogen bonds : angle 6.58103 / 4.74 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7061 (mmm) cc_final: 0.6476 (mmm) REVERT: A 147 ARG cc_start: 0.7148 (ppt170) cc_final: 0.6716 (ttt180) REVERT: A 406 ARG cc_start: 0.6210 (mtm180) cc_final: 0.5838 (mtp180) REVERT: A 446 TYR cc_start: 0.7373 (m-80) cc_final: 0.7071 (m-80) REVERT: A 469 ARG cc_start: 0.6963 (mtt90) cc_final: 0.6667 (mtt90) REVERT: A 517 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7454 (pptt) REVERT: A 618 MET cc_start: 0.2506 (ttt) cc_final: 0.1841 (mtp) REVERT: A 704 ASN cc_start: 0.6966 (p0) cc_final: 0.6630 (p0) REVERT: A 975 LEU cc_start: 0.5982 (tp) cc_final: 0.5664 (tp) REVERT: E 73 ILE cc_start: 0.5095 (tp) cc_final: 0.4668 (tt) REVERT: E 113 MET cc_start: 0.4920 (mmt) cc_final: 0.4719 (mmt) REVERT: B 5 MET cc_start: 0.3755 (tpp) cc_final: 0.2980 (pmm) outliers start: 8 outliers final: 4 residues processed: 165 average time/residue: 0.1221 time to fit residues: 30.3882 Evaluate side-chains 122 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 154 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 423 GLN A 539 GLN A 806 HIS ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.168284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.141217 restraints weight = 71442.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.142829 restraints weight = 102381.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.143222 restraints weight = 55232.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.143442 restraints weight = 37822.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.143797 restraints weight = 33321.398| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15829 Z= 0.194 Angle : 0.720 10.924 21474 Z= 0.378 Chirality : 0.046 0.240 2451 Planarity : 0.005 0.059 2716 Dihedral : 6.505 102.181 2188 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.24 % Allowed : 4.53 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.17), residues: 2005 helix: -1.16 (0.18), residues: 689 sheet: -1.86 (0.25), residues: 394 loop : -2.42 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 444 TYR 0.025 0.002 TYR A 927 PHE 0.030 0.002 PHE A 305 TRP 0.023 0.002 TRP A 164 HIS 0.006 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (15821) covalent geometry : angle 0.72030 / 0.38 (21458) SS BOND : bond 0.00264 / 0.13 ( 8) SS BOND : angle 0.82901 / 0.41 ( 16) hydrogen bonds : bond 0.05810 / 3.86 ( 701) hydrogen bonds : angle 6.07100 / 4.37 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7769 (tpp) cc_final: 0.7322 (tpt) REVERT: A 406 ARG cc_start: 0.6114 (mtm180) cc_final: 0.5773 (mtp180) REVERT: A 446 TYR cc_start: 0.7334 (m-80) cc_final: 0.7102 (m-80) REVERT: A 618 MET cc_start: 0.2250 (ttt) cc_final: 0.1574 (mtp) REVERT: A 884 ARG cc_start: 0.5832 (ptp-170) cc_final: 0.5596 (ptp-170) REVERT: A 965 ASN cc_start: 0.4625 (m-40) cc_final: 0.4338 (t0) REVERT: A 975 LEU cc_start: 0.5703 (tp) cc_final: 0.5336 (tp) REVERT: E 73 ILE cc_start: 0.5033 (tp) cc_final: 0.4539 (tt) REVERT: B 5 MET cc_start: 0.3636 (tpp) cc_final: 0.2908 (pmm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1143 time to fit residues: 29.4495 Evaluate side-chains 129 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 272 GLN A 423 GLN A 539 GLN A 806 HIS ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.171814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.146657 restraints weight = 60514.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.149681 restraints weight = 105202.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.150395 restraints weight = 47693.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.150816 restraints weight = 36906.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.151573 restraints weight = 30181.047| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4467 r_free = 0.4467 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4467 r_free = 0.4467 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.4467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15829 Z= 0.131 Angle : 0.635 10.979 21474 Z= 0.329 Chirality : 0.043 0.189 2451 Planarity : 0.005 0.070 2716 Dihedral : 5.910 103.520 2188 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.18), residues: 2005 helix: -0.38 (0.19), residues: 694 sheet: -1.55 (0.25), residues: 392 loop : -2.16 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 444 TYR 0.024 0.001 TYR A 132 PHE 0.022 0.002 PHE A 970 TRP 0.016 0.001 TRP A 164 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (15821) covalent geometry : angle 0.63476 / 0.33 (21458) SS BOND : bond 0.00257 / 0.13 ( 8) SS BOND : angle 0.64080 / 0.36 ( 16) hydrogen bonds : bond 0.04926 / 3.29 ( 701) hydrogen bonds : angle 5.47028 / 3.92 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.5725 (t80) cc_final: 0.5038 (t80) REVERT: A 194 MET cc_start: 0.7576 (tpp) cc_final: 0.7000 (tpt) REVERT: A 406 ARG cc_start: 0.5959 (mtm180) cc_final: 0.5576 (mtp180) REVERT: A 446 TYR cc_start: 0.7185 (m-80) cc_final: 0.6813 (m-80) REVERT: A 469 ARG cc_start: 0.6227 (mtt180) cc_final: 0.2537 (ptp-110) REVERT: A 618 MET cc_start: 0.2300 (ttt) cc_final: 0.1616 (mtp) REVERT: A 809 SER cc_start: 0.8288 (t) cc_final: 0.8044 (p) REVERT: A 975 LEU cc_start: 0.5622 (tp) cc_final: 0.5417 (tp) REVERT: E 31 ASN cc_start: 0.6999 (m-40) cc_final: 0.6793 (m-40) REVERT: E 73 ILE cc_start: 0.4922 (tp) cc_final: 0.4658 (tt) REVERT: E 110 ARG cc_start: 0.6731 (ttm110) cc_final: 0.6463 (ttm170) REVERT: B 5 MET cc_start: 0.3373 (tpp) cc_final: 0.2795 (pmm) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1065 time to fit residues: 29.4529 Evaluate side-chains 138 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 187 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 385 HIS A 423 GLN A 539 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN B 90 GLN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.144976 restraints weight = 77349.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.146605 restraints weight = 105974.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.148089 restraints weight = 58097.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.148714 restraints weight = 38288.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.148956 restraints weight = 34884.500| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4440 r_free = 0.4440 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4440 r_free = 0.4440 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15829 Z= 0.148 Angle : 0.650 12.427 21474 Z= 0.337 Chirality : 0.044 0.263 2451 Planarity : 0.004 0.049 2716 Dihedral : 5.826 102.993 2188 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.18), residues: 2005 helix: -0.24 (0.19), residues: 681 sheet: -1.36 (0.26), residues: 392 loop : -2.03 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.023 0.002 TYR A 937 PHE 0.042 0.002 PHE A 970 TRP 0.017 0.001 TRP A 164 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15821) covalent geometry : angle 0.64963 / 0.34 (21458) SS BOND : bond 0.00196 / 0.10 ( 8) SS BOND : angle 0.63031 / 0.36 ( 16) hydrogen bonds : bond 0.05056 / 3.38 ( 701) hydrogen bonds : angle 5.46498 / 3.92 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7648 (tpp) cc_final: 0.7097 (tpt) REVERT: A 295 ILE cc_start: 0.7199 (mt) cc_final: 0.6739 (mt) REVERT: A 301 MET cc_start: 0.7300 (tpt) cc_final: 0.7070 (tpp) REVERT: A 406 ARG cc_start: 0.5928 (mtm180) cc_final: 0.5498 (mtp180) REVERT: A 469 ARG cc_start: 0.6232 (mtt180) cc_final: 0.2561 (ptp-110) REVERT: A 618 MET cc_start: 0.2363 (ttt) cc_final: 0.1556 (mtp) REVERT: A 884 ARG cc_start: 0.5619 (ptp-170) cc_final: 0.5344 (ptp-170) REVERT: A 975 LEU cc_start: 0.5901 (tp) cc_final: 0.5492 (tp) REVERT: E 31 ASN cc_start: 0.7064 (m-40) cc_final: 0.6793 (m-40) REVERT: E 73 ILE cc_start: 0.5002 (tp) cc_final: 0.4685 (tt) REVERT: B 5 MET cc_start: 0.3266 (tpp) cc_final: 0.2738 (pmm) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1032 time to fit residues: 28.2052 Evaluate side-chains 135 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 196 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 159 optimal weight: 50.0000 chunk 12 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.171623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.146049 restraints weight = 80133.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.148302 restraints weight = 111988.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.149007 restraints weight = 54986.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.149596 restraints weight = 37513.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.150120 restraints weight = 32437.556| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15829 Z= 0.144 Angle : 0.638 11.768 21474 Z= 0.331 Chirality : 0.043 0.189 2451 Planarity : 0.004 0.049 2716 Dihedral : 5.715 103.298 2188 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 2005 helix: -0.08 (0.19), residues: 674 sheet: -1.32 (0.26), residues: 384 loop : -1.90 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.026 0.002 TYR C 58 PHE 0.028 0.002 PHE A 970 TRP 0.016 0.001 TRP A 164 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15821) covalent geometry : angle 0.63752 / 0.33 (21458) SS BOND : bond 0.00205 / 0.11 ( 8) SS BOND : angle 0.67463 / 0.37 ( 16) hydrogen bonds : bond 0.04945 / 3.31 ( 701) hydrogen bonds : angle 5.40849 / 3.88 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7683 (tpp) cc_final: 0.7147 (tpt) REVERT: A 406 ARG cc_start: 0.5830 (mtm180) cc_final: 0.5478 (mtp180) REVERT: A 469 ARG cc_start: 0.6268 (mtt180) cc_final: 0.2351 (ptp-110) REVERT: A 618 MET cc_start: 0.2412 (ttt) cc_final: 0.1816 (mpp) REVERT: A 809 SER cc_start: 0.8416 (t) cc_final: 0.8185 (p) REVERT: A 975 LEU cc_start: 0.5624 (tp) cc_final: 0.5286 (tp) REVERT: E 73 ILE cc_start: 0.5002 (tp) cc_final: 0.4702 (tt) REVERT: E 110 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6490 (mtp180) REVERT: B 5 MET cc_start: 0.3204 (tpp) cc_final: 0.2623 (pmm) REVERT: C 174 TRP cc_start: 0.3098 (m100) cc_final: 0.2791 (m-90) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1260 time to fit residues: 33.4398 Evaluate side-chains 132 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 24 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 chunk 166 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN C 42 GLN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.172861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.143638 restraints weight = 78825.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.146743 restraints weight = 92929.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.148122 restraints weight = 44025.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.148861 restraints weight = 29545.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.149327 restraints weight = 27059.096| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15829 Z= 0.122 Angle : 0.611 10.534 21474 Z= 0.316 Chirality : 0.042 0.180 2451 Planarity : 0.004 0.048 2716 Dihedral : 5.490 103.772 2188 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.18 % Allowed : 1.49 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.19), residues: 2005 helix: 0.11 (0.20), residues: 674 sheet: -1.17 (0.26), residues: 385 loop : -1.81 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.022 0.002 TYR A 120 PHE 0.021 0.001 PHE A 850 TRP 0.015 0.001 TRP C 112 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (15821) covalent geometry : angle 0.61098 / 0.32 (21458) SS BOND : bond 0.00248 / 0.12 ( 8) SS BOND : angle 0.71057 / 0.42 ( 16) hydrogen bonds : bond 0.04620 / 3.09 ( 701) hydrogen bonds : angle 5.15514 / 3.69 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7757 (tpp) cc_final: 0.7244 (tpt) REVERT: A 406 ARG cc_start: 0.5809 (mtm180) cc_final: 0.5381 (mtp180) REVERT: A 469 ARG cc_start: 0.6131 (mtt180) cc_final: 0.2083 (ptp-110) REVERT: A 558 GLU cc_start: 0.5078 (pt0) cc_final: 0.4589 (mm-30) REVERT: A 618 MET cc_start: 0.2246 (ttt) cc_final: 0.1677 (mpp) REVERT: A 809 SER cc_start: 0.8266 (t) cc_final: 0.8042 (m) REVERT: A 975 LEU cc_start: 0.5506 (tp) cc_final: 0.5179 (tp) REVERT: E 73 ILE cc_start: 0.4910 (tp) cc_final: 0.4585 (tt) REVERT: B 5 MET cc_start: 0.3064 (tpp) cc_final: 0.2512 (pmm) REVERT: C 174 TRP cc_start: 0.2931 (m100) cc_final: 0.2697 (m-90) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1179 time to fit residues: 32.3881 Evaluate side-chains 130 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.173090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.144751 restraints weight = 73245.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.147298 restraints weight = 88032.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.148207 restraints weight = 45754.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.148799 restraints weight = 30811.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.149257 restraints weight = 27612.470| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15829 Z= 0.125 Angle : 0.619 11.065 21474 Z= 0.321 Chirality : 0.042 0.170 2451 Planarity : 0.004 0.049 2716 Dihedral : 5.424 104.242 2188 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.12 % Allowed : 0.71 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 2005 helix: 0.28 (0.20), residues: 672 sheet: -1.02 (0.26), residues: 389 loop : -1.77 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 110 TYR 0.027 0.001 TYR A 952 PHE 0.024 0.002 PHE A 305 TRP 0.021 0.001 TRP C 112 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15821) covalent geometry : angle 0.61877 / 0.32 (21458) SS BOND : bond 0.00232 / 0.11 ( 8) SS BOND : angle 0.73981 / 0.42 ( 16) hydrogen bonds : bond 0.04682 / 3.12 ( 701) hydrogen bonds : angle 5.07085 / 3.63 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7771 (tpp) cc_final: 0.7218 (tpt) REVERT: A 301 MET cc_start: 0.7007 (tpt) cc_final: 0.6530 (tpt) REVERT: A 406 ARG cc_start: 0.5791 (mtm180) cc_final: 0.5581 (mtp180) REVERT: A 469 ARG cc_start: 0.6104 (mtt180) cc_final: 0.2139 (ptp-110) REVERT: A 558 GLU cc_start: 0.4967 (pt0) cc_final: 0.4506 (mm-30) REVERT: A 618 MET cc_start: 0.2375 (ttt) cc_final: 0.1678 (mpp) REVERT: A 809 SER cc_start: 0.8331 (t) cc_final: 0.8129 (m) REVERT: A 835 ILE cc_start: 0.7364 (mt) cc_final: 0.7151 (mt) REVERT: A 975 LEU cc_start: 0.5454 (tp) cc_final: 0.5130 (tp) REVERT: E 73 ILE cc_start: 0.4872 (tp) cc_final: 0.4583 (tt) REVERT: B 5 MET cc_start: 0.2950 (tpp) cc_final: 0.2475 (pmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1115 time to fit residues: 29.1644 Evaluate side-chains 133 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 30 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN B 90 GLN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.143100 restraints weight = 67104.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.142338 restraints weight = 71003.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.144193 restraints weight = 53073.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.145579 restraints weight = 32029.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.145990 restraints weight = 28064.037| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4401 r_free = 0.4401 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4401 r_free = 0.4401 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15829 Z= 0.131 Angle : 0.614 11.588 21474 Z= 0.316 Chirality : 0.042 0.156 2451 Planarity : 0.004 0.048 2716 Dihedral : 5.414 104.231 2188 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.24 % Allowed : 0.89 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.19), residues: 2005 helix: 0.22 (0.20), residues: 673 sheet: -0.98 (0.26), residues: 389 loop : -1.69 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 788 TYR 0.021 0.002 TYR A 952 PHE 0.024 0.002 PHE A 970 TRP 0.025 0.001 TRP E 106 HIS 0.006 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15821) covalent geometry : angle 0.61349 / 0.32 (21458) SS BOND : bond 0.00191 / 0.09 ( 8) SS BOND : angle 0.66798 / 0.38 ( 16) hydrogen bonds : bond 0.04710 / 3.14 ( 701) hydrogen bonds : angle 5.03811 / 3.62 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7745 (tpp) cc_final: 0.7138 (tpt) REVERT: A 301 MET cc_start: 0.6954 (tpt) cc_final: 0.6638 (tpt) REVERT: A 406 ARG cc_start: 0.5935 (mtm180) cc_final: 0.5460 (mtp180) REVERT: A 469 ARG cc_start: 0.6490 (mtt180) cc_final: 0.2328 (ptp-110) REVERT: A 558 GLU cc_start: 0.4990 (pt0) cc_final: 0.4474 (mm-30) REVERT: A 618 MET cc_start: 0.2321 (ttt) cc_final: 0.1526 (mpp) REVERT: A 866 ILE cc_start: 0.7833 (mm) cc_final: 0.7600 (mm) REVERT: A 947 PHE cc_start: 0.5515 (t80) cc_final: 0.5290 (t80) REVERT: A 975 LEU cc_start: 0.5448 (tp) cc_final: 0.5078 (tp) REVERT: E 73 ILE cc_start: 0.4946 (tp) cc_final: 0.4639 (tt) REVERT: B 5 MET cc_start: 0.3156 (tpp) cc_final: 0.2663 (pmm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1203 time to fit residues: 30.7415 Evaluate side-chains 130 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 91 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.171547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.141923 restraints weight = 85476.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.140304 restraints weight = 78704.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.138651 restraints weight = 51740.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.139747 restraints weight = 36840.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.140048 restraints weight = 26109.670| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.4330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15829 Z= 0.150 Angle : 0.641 12.431 21474 Z= 0.332 Chirality : 0.044 0.223 2451 Planarity : 0.004 0.049 2716 Dihedral : 5.497 103.732 2188 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.18 % Allowed : 0.42 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.19), residues: 2005 helix: 0.14 (0.20), residues: 668 sheet: -0.96 (0.26), residues: 395 loop : -1.65 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 788 TYR 0.019 0.002 TYR A 952 PHE 0.047 0.002 PHE A 774 TRP 0.022 0.002 TRP E 106 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15821) covalent geometry : angle 0.64068 / 0.33 (21458) SS BOND : bond 0.00192 / 0.10 ( 8) SS BOND : angle 0.69274 / 0.37 ( 16) hydrogen bonds : bond 0.04964 / 3.30 ( 701) hydrogen bonds : angle 5.14619 / 3.70 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.91 seconds wall clock time: 44 minutes 57.17 seconds (2697.17 seconds total)