Starting phenix.real_space_refine on Wed Mar 4 18:50:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7niu_12365/03_2026/7niu_12365.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niu_12365/03_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_12365/03_2026/7niu_12365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niu_12365/03_2026/7niu_12365.map" model { file = "/net/cci-nas-00/data/ceres_data/7niu_12365/03_2026/7niu_12365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niu_12365/03_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-5986/lib/python3.9/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: 3.53, per 1000 atoms: 0.23 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: 1.33 Conformation dependent library (CDL) restraints added in 788.8 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: 0.46 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: 3.17 Time building geometry restraints manager: 1.64 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: 8302 17.87 - 35.74: 973 35.74 - 53.62: 198 53.62 - 71.49: 41 71.49 - 89.36: 17 Dihedral angle restraints: 9531 sinusoidal: 3713 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 9528 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: 8.340 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: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 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 : 16.083 89.361 5783 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 covalent geometry : bond 0.00804 (15821) covalent geometry : angle 1.01385 (21458) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.27953 ( 16) hydrogen bonds : bond 0.17214 ( 701) hydrogen bonds : angle 8.46769 ( 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 : 0.531 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: 0.1349 time to fit residues: 40.7936 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 : 0.527 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4747 r_free = 0.4747 target = 0.171252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.149665 restraints weight = 63448.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.151818 restraints weight = 113572.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.151785 restraints weight = 45363.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.152540 restraints weight = 36224.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.152971 restraints weight = 26533.192| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4486 r_free = 0.4486 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4484 r_free = 0.4484 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15829 Z= 0.159 Angle : 0.696 10.899 21474 Z= 0.368 Chirality : 0.045 0.235 2451 Planarity : 0.005 0.050 2716 Dihedral : 6.760 57.400 2300 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.42 % Allowed : 6.02 % Favored : 93.57 % 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: -3.45 (0.16), residues: 2005 helix: -1.61 (0.17), residues: 680 sheet: -2.25 (0.24), residues: 388 loop : -2.79 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 70 TYR 0.025 0.002 TYR A 937 PHE 0.022 0.002 PHE A 774 TRP 0.018 0.002 TRP A 164 HIS 0.011 0.002 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00341 (15821) covalent geometry : angle 0.69581 (21458) SS BOND : bond 0.00380 ( 8) SS BOND : angle 0.78699 ( 16) hydrogen bonds : bond 0.05610 ( 701) hydrogen bonds : angle 6.09604 ( 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 198 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8062 (tpp) cc_final: 0.7847 (tpp) REVERT: A 113 MET cc_start: 0.7094 (mmm) cc_final: 0.6294 (mmm) REVERT: A 116 TYR cc_start: 0.5516 (m-80) cc_final: 0.5118 (m-80) REVERT: A 194 MET cc_start: 0.7649 (tpp) cc_final: 0.6844 (tpt) REVERT: A 406 ARG cc_start: 0.6098 (mtm180) cc_final: 0.5711 (mtp180) REVERT: A 549 ARG cc_start: 0.7016 (ttm170) cc_final: 0.6683 (tpp-160) REVERT: A 618 MET cc_start: 0.3037 (ttt) cc_final: 0.2441 (mtp) REVERT: A 704 ASN cc_start: 0.6757 (p0) cc_final: 0.6480 (p0) REVERT: A 756 LEU cc_start: 0.7148 (mm) cc_final: 0.6942 (mm) REVERT: A 887 LYS cc_start: 0.7451 (tmmt) cc_final: 0.6387 (mttt) REVERT: A 975 LEU cc_start: 0.5550 (tp) cc_final: 0.5175 (tp) REVERT: E 73 ILE cc_start: 0.4946 (tp) cc_final: 0.4643 (tt) REVERT: B 5 MET cc_start: 0.3470 (tpp) cc_final: 0.2710 (pmm) outliers start: 6 outliers final: 0 residues processed: 195 average time/residue: 0.1273 time to fit residues: 36.1358 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 : 0.554 ------------------------------------------------------------------------------- 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: 0.6980 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 chunk 146 optimal weight: 0.1980 chunk 162 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN A 539 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.169679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.149975 restraints weight = 66167.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.151387 restraints weight = 115693.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.151482 restraints weight = 46270.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.152468 restraints weight = 34353.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.152603 restraints weight = 24573.478| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4477 r_free = 0.4477 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4477 r_free = 0.4477 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15829 Z= 0.171 Angle : 0.690 11.919 21474 Z= 0.359 Chirality : 0.045 0.214 2451 Planarity : 0.005 0.050 2716 Dihedral : 6.186 57.655 2300 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.36 % Allowed : 4.76 % Favored : 94.88 % 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: -2.76 (0.17), residues: 2005 helix: -0.92 (0.18), residues: 684 sheet: -1.91 (0.25), residues: 388 loop : -2.46 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 469 TYR 0.030 0.002 TYR A 949 PHE 0.025 0.002 PHE A 85 TRP 0.020 0.002 TRP A 164 HIS 0.007 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00381 (15821) covalent geometry : angle 0.68985 (21458) SS BOND : bond 0.00206 ( 8) SS BOND : angle 0.83685 ( 16) hydrogen bonds : bond 0.05488 ( 701) hydrogen bonds : angle 5.84810 ( 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 184 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6970 (mmm) cc_final: 0.6404 (mmm) REVERT: A 116 TYR cc_start: 0.5506 (m-80) cc_final: 0.5031 (m-80) REVERT: A 194 MET cc_start: 0.7708 (tpp) cc_final: 0.7057 (tpt) REVERT: A 406 ARG cc_start: 0.6002 (mtm180) cc_final: 0.5649 (mtp180) REVERT: A 469 ARG cc_start: 0.6604 (mtt90) cc_final: 0.3644 (ptp-110) REVERT: A 618 MET cc_start: 0.2806 (ttt) cc_final: 0.2102 (mtp) REVERT: A 704 ASN cc_start: 0.7090 (p0) cc_final: 0.6876 (p0) REVERT: A 820 ASP cc_start: 0.6903 (m-30) cc_final: 0.6533 (m-30) REVERT: A 975 LEU cc_start: 0.5693 (tp) cc_final: 0.5240 (tp) REVERT: E 73 ILE cc_start: 0.4921 (tp) cc_final: 0.4491 (tt) REVERT: B 5 MET cc_start: 0.3383 (tpp) cc_final: 0.2670 (pmm) REVERT: B 93 TYR cc_start: 0.6010 (t80) cc_final: 0.5742 (t80) outliers start: 5 outliers final: 1 residues processed: 183 average time/residue: 0.1234 time to fit residues: 33.5396 Evaluate side-chains 136 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 20.0000 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN A 539 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN A1152 ASN 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 = 0.4750 r_free = 0.4750 target = 0.171573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.145898 restraints weight = 71982.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.146751 restraints weight = 96925.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.145105 restraints weight = 49746.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.144933 restraints weight = 46925.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.145462 restraints weight = 33248.879| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4389 r_free = 0.4389 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4389 r_free = 0.4389 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.3436 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= 0.142 Angle : 0.639 10.463 21474 Z= 0.333 Chirality : 0.043 0.208 2451 Planarity : 0.004 0.059 2716 Dihedral : 5.710 58.247 2300 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % 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: -2.27 (0.18), residues: 2005 helix: -0.41 (0.19), residues: 701 sheet: -1.65 (0.24), residues: 403 loop : -2.30 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.022 0.002 TYR A 132 PHE 0.026 0.002 PHE A 956 TRP 0.016 0.001 TRP A 164 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00305 (15821) covalent geometry : angle 0.63915 (21458) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.62107 ( 16) hydrogen bonds : bond 0.05041 ( 701) hydrogen bonds : angle 5.49536 ( 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 178 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7665 (tpp) cc_final: 0.7135 (tpt) REVERT: A 335 THR cc_start: 0.8684 (p) cc_final: 0.8455 (m) REVERT: A 406 ARG cc_start: 0.5974 (mtm180) cc_final: 0.5516 (mtp180) REVERT: A 469 ARG cc_start: 0.6629 (mtt90) cc_final: 0.1860 (ptp90) REVERT: A 618 MET cc_start: 0.2252 (ttt) cc_final: 0.1507 (mtp) REVERT: A 975 LEU cc_start: 0.5474 (tp) cc_final: 0.5097 (tp) REVERT: E 73 ILE cc_start: 0.4971 (tp) cc_final: 0.4572 (tt) REVERT: B 5 MET cc_start: 0.3103 (tpp) cc_final: 0.2658 (pmm) REVERT: B 93 TYR cc_start: 0.5785 (t80) cc_final: 0.5449 (t80) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.1122 time to fit residues: 29.9815 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 : 0.538 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN A1152 ASN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.172186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.147931 restraints weight = 60491.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.150503 restraints weight = 106163.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.150592 restraints weight = 46820.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.150936 restraints weight = 36231.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.151302 restraints weight = 29928.303| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- 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: 19 | |-----------------------------------------------------------------------------| |-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: 19 | |-----------------------------------------------------------------------------| r_final: 0.4467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15829 Z= 0.129 Angle : 0.626 10.754 21474 Z= 0.323 Chirality : 0.043 0.256 2451 Planarity : 0.004 0.049 2716 Dihedral : 5.440 57.279 2300 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.12 % Allowed : 3.28 % Favored : 96.61 % 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: -1.91 (0.18), residues: 2005 helix: -0.07 (0.19), residues: 696 sheet: -1.43 (0.25), residues: 402 loop : -2.13 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 444 TYR 0.017 0.001 TYR A 132 PHE 0.021 0.001 PHE A 850 TRP 0.016 0.001 TRP A 164 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00279 (15821) covalent geometry : angle 0.62590 (21458) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.59695 ( 16) hydrogen bonds : bond 0.04801 ( 701) hydrogen bonds : angle 5.26497 ( 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 187 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.7083 (ppt170) cc_final: 0.6773 (ttt180) REVERT: A 194 MET cc_start: 0.7716 (tpp) cc_final: 0.7140 (tpt) REVERT: A 335 THR cc_start: 0.8664 (p) cc_final: 0.8447 (m) REVERT: A 406 ARG cc_start: 0.5826 (mtm180) cc_final: 0.5414 (mtp180) REVERT: A 469 ARG cc_start: 0.6289 (mtt90) cc_final: 0.2724 (ptp-110) REVERT: A 800 MET cc_start: 0.7389 (tpt) cc_final: 0.7019 (tpt) REVERT: A 975 LEU cc_start: 0.5183 (tp) cc_final: 0.4940 (tp) REVERT: E 73 ILE cc_start: 0.4811 (tp) cc_final: 0.4370 (tt) REVERT: B 5 MET cc_start: 0.3062 (tpp) cc_final: 0.2542 (pmm) REVERT: B 93 TYR cc_start: 0.5700 (t80) cc_final: 0.5335 (t80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.1142 time to fit residues: 32.2547 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 : 0.486 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 ASN ** 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 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 = 0.4760 r_free = 0.4760 target = 0.172379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.144541 restraints weight = 76931.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.147170 restraints weight = 92718.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.147787 restraints weight = 44449.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.148278 restraints weight = 30856.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.148595 restraints weight = 27625.146| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4448 r_free = 0.4448 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4448 r_free = 0.4448 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.4124 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= 0.127 Angle : 0.619 10.950 21474 Z= 0.320 Chirality : 0.043 0.183 2451 Planarity : 0.004 0.049 2716 Dihedral : 5.227 54.490 2300 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.12 % Allowed : 2.08 % Favored : 97.80 % 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: -1.71 (0.18), residues: 2005 helix: 0.04 (0.20), residues: 696 sheet: -1.16 (0.26), residues: 388 loop : -2.04 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.021 0.002 TYR A 852 PHE 0.020 0.001 PHE A 850 TRP 0.014 0.001 TRP A 164 HIS 0.004 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00271 (15821) covalent geometry : angle 0.61854 (21458) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.60057 ( 16) hydrogen bonds : bond 0.04682 ( 701) hydrogen bonds : angle 5.19503 ( 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 180 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.4743 (t80) cc_final: 0.4410 (t80) REVERT: A 194 MET cc_start: 0.7752 (tpp) cc_final: 0.7169 (tpt) REVERT: A 335 THR cc_start: 0.8620 (p) cc_final: 0.8400 (m) REVERT: A 406 ARG cc_start: 0.5942 (mtm180) cc_final: 0.5437 (mtp180) REVERT: A 469 ARG cc_start: 0.6197 (mtt90) cc_final: 0.2599 (ptp-110) REVERT: A 618 MET cc_start: 0.2315 (ttt) cc_final: 0.1651 (mpp) REVERT: A 975 LEU cc_start: 0.5291 (tp) cc_final: 0.4930 (tp) REVERT: E 73 ILE cc_start: 0.4764 (tp) cc_final: 0.4526 (tt) REVERT: B 5 MET cc_start: 0.3057 (tpp) cc_final: 0.2472 (pmm) REVERT: B 93 TYR cc_start: 0.5544 (t80) cc_final: 0.5137 (t80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1087 time to fit residues: 29.9956 Evaluate side-chains 131 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 6.9990 chunk 138 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 159 optimal weight: 40.0000 chunk 12 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 397 ASN A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN A 841 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.168765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.140193 restraints weight = 79141.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.143602 restraints weight = 105103.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.144357 restraints weight = 40052.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.145038 restraints weight = 28935.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.145572 restraints weight = 24556.524| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4393 r_free = 0.4393 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4393 r_free = 0.4393 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15829 Z= 0.193 Angle : 0.715 11.981 21474 Z= 0.370 Chirality : 0.046 0.195 2451 Planarity : 0.005 0.068 2716 Dihedral : 5.606 56.252 2300 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.68 % 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: -2.03 (0.18), residues: 2005 helix: -0.44 (0.19), residues: 682 sheet: -1.26 (0.26), residues: 383 loop : -2.04 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 444 TYR 0.027 0.002 TYR A 132 PHE 0.038 0.002 PHE A 305 TRP 0.016 0.002 TRP A 164 HIS 0.005 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00437 (15821) covalent geometry : angle 0.71459 (21458) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.68930 ( 16) hydrogen bonds : bond 0.05556 ( 701) hydrogen bonds : angle 5.62464 ( 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 159 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7761 (tpp) cc_final: 0.7125 (tpt) REVERT: A 406 ARG cc_start: 0.6019 (mtm180) cc_final: 0.5655 (mtp180) REVERT: A 446 TYR cc_start: 0.7091 (m-80) cc_final: 0.6792 (m-80) REVERT: A 469 ARG cc_start: 0.6409 (mtt90) cc_final: 0.2629 (ptp-110) REVERT: A 618 MET cc_start: 0.2427 (ttt) cc_final: 0.1617 (mpp) REVERT: A 887 LYS cc_start: 0.7552 (tmmt) cc_final: 0.6559 (mttt) REVERT: A 975 LEU cc_start: 0.5614 (tp) cc_final: 0.5222 (tp) REVERT: E 73 ILE cc_start: 0.5027 (tp) cc_final: 0.4743 (tt) REVERT: B 5 MET cc_start: 0.3342 (tpp) cc_final: 0.2904 (pmm) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1110 time to fit residues: 27.2493 Evaluate side-chains 123 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 0.9980 chunk 187 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 193 optimal weight: 0.0030 chunk 166 optimal weight: 6.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS A 929 ASN ** A1063 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.173983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.148359 restraints weight = 80550.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.150381 restraints weight = 103472.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.149948 restraints weight = 47306.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.149502 restraints weight = 42927.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.150007 restraints weight = 32129.324| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4448 r_free = 0.4448 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4448 r_free = 0.4448 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15829 Z= 0.120 Angle : 0.611 10.876 21474 Z= 0.316 Chirality : 0.042 0.204 2451 Planarity : 0.004 0.049 2716 Dihedral : 4.999 49.201 2300 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.18 % Allowed : 1.19 % Favored : 98.63 % 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: -1.51 (0.18), residues: 2005 helix: 0.19 (0.20), residues: 680 sheet: -1.12 (0.26), residues: 385 loop : -1.84 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.023 0.001 TYR A 952 PHE 0.024 0.001 PHE A 85 TRP 0.015 0.001 TRP A 164 HIS 0.004 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00251 (15821) covalent geometry : angle 0.61125 (21458) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.75041 ( 16) hydrogen bonds : bond 0.04606 ( 701) hydrogen bonds : angle 5.08386 ( 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 169 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.7769 (tpp) cc_final: 0.7275 (tpt) REVERT: A 406 ARG cc_start: 0.5852 (mtm180) cc_final: 0.5459 (mtp180) REVERT: A 446 TYR cc_start: 0.7244 (m-80) cc_final: 0.6954 (m-80) REVERT: A 517 LYS cc_start: 0.5342 (mtmt) cc_final: 0.4904 (pptt) REVERT: A 618 MET cc_start: 0.2369 (ttt) cc_final: 0.1670 (mpp) REVERT: A 975 LEU cc_start: 0.5163 (tp) cc_final: 0.4824 (tp) REVERT: E 73 ILE cc_start: 0.4890 (tp) cc_final: 0.4607 (tt) REVERT: B 5 MET cc_start: 0.3001 (tpp) cc_final: 0.2475 (pmm) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1132 time to fit residues: 28.8063 Evaluate side-chains 128 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 20.0000 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 113 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A1063 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.172760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.153961 restraints weight = 74918.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.155568 restraints weight = 125786.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.156513 restraints weight = 46372.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.157446 restraints weight = 33210.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.157497 restraints weight = 23819.185| |-----------------------------------------------------------------------------| r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15829 Z= 0.137 Angle : 0.628 11.261 21474 Z= 0.325 Chirality : 0.043 0.179 2451 Planarity : 0.004 0.050 2716 Dihedral : 5.050 49.280 2300 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.24 % Allowed : 0.66 % Favored : 99.11 % 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: -1.44 (0.19), residues: 2005 helix: 0.16 (0.20), residues: 679 sheet: -1.04 (0.26), residues: 389 loop : -1.74 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 540 TYR 0.021 0.002 TYR A 132 PHE 0.026 0.002 PHE A 956 TRP 0.013 0.001 TRP A 164 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00300 (15821) covalent geometry : angle 0.62838 (21458) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.64978 ( 16) hydrogen bonds : bond 0.04774 ( 701) hydrogen bonds : angle 5.12257 ( 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 167 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.6640 (mmt) cc_final: 0.6364 (mmt) REVERT: A 194 MET cc_start: 0.7671 (tpp) cc_final: 0.6991 (tpt) REVERT: A 406 ARG cc_start: 0.5804 (mtm180) cc_final: 0.5468 (mtp180) REVERT: A 446 TYR cc_start: 0.7094 (m-80) cc_final: 0.6740 (m-80) REVERT: A 618 MET cc_start: 0.2522 (ttt) cc_final: 0.1753 (mpp) REVERT: A 947 PHE cc_start: 0.5662 (t80) cc_final: 0.5396 (t80) REVERT: A 975 LEU cc_start: 0.5374 (tp) cc_final: 0.5067 (tp) REVERT: E 73 ILE cc_start: 0.4825 (tp) cc_final: 0.4526 (tt) REVERT: E 110 ARG cc_start: 0.6305 (ttm110) cc_final: 0.5513 (mtt180) REVERT: B 5 MET cc_start: 0.3297 (tpp) cc_final: 0.2626 (pmm) REVERT: C 174 TRP cc_start: 0.2301 (m100) cc_final: 0.1842 (m-90) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1073 time to fit residues: 27.3521 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 : 0.550 ------------------------------------------------------------------------------- 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: 2.9990 chunk 162 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.174596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.161601 restraints weight = 69569.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.160755 restraints weight = 122456.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.159757 restraints weight = 70574.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.159874 restraints weight = 77693.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.160120 restraints weight = 46480.063| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4535 r_free = 0.4535 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4535 r_free = 0.4535 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15829 Z= 0.141 Angle : 0.640 11.527 21474 Z= 0.330 Chirality : 0.043 0.157 2451 Planarity : 0.004 0.048 2716 Dihedral : 5.036 47.982 2300 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.18 % Allowed : 0.66 % 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: -1.43 (0.19), residues: 2005 helix: 0.14 (0.20), residues: 679 sheet: -1.04 (0.26), residues: 389 loop : -1.70 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 444 TYR 0.020 0.002 TYR A 852 PHE 0.023 0.002 PHE A 85 TRP 0.013 0.001 TRP A 164 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00311 (15821) covalent geometry : angle 0.63951 (21458) SS BOND : bond 0.00195 ( 8) SS BOND : angle 0.63442 ( 16) hydrogen bonds : bond 0.04803 ( 701) hydrogen bonds : angle 5.13072 ( 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 162 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8111 (tpp) cc_final: 0.7882 (tpp) REVERT: A 75 MET cc_start: 0.6745 (mmt) cc_final: 0.6509 (mmt) REVERT: A 194 MET cc_start: 0.7665 (tpp) cc_final: 0.7033 (tpt) REVERT: A 301 MET cc_start: 0.7136 (tpt) cc_final: 0.6866 (tpt) REVERT: A 406 ARG cc_start: 0.5845 (mtm180) cc_final: 0.5490 (mtp180) REVERT: A 446 TYR cc_start: 0.7138 (m-80) cc_final: 0.6756 (m-80) REVERT: A 517 LYS cc_start: 0.4604 (mtmt) cc_final: 0.4347 (mttp) REVERT: A 618 MET cc_start: 0.2653 (ttt) cc_final: 0.1872 (mpp) REVERT: A 975 LEU cc_start: 0.5213 (tp) cc_final: 0.4850 (tp) REVERT: E 73 ILE cc_start: 0.4790 (tp) cc_final: 0.4476 (tt) REVERT: E 110 ARG cc_start: 0.6272 (ttm110) cc_final: 0.5505 (mtt180) REVERT: B 5 MET cc_start: 0.3347 (tpp) cc_final: 0.2626 (pmm) REVERT: C 174 TRP cc_start: 0.2278 (m100) cc_final: 0.1864 (m-90) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1086 time to fit residues: 27.2278 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 : 0.562 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 107 optimal weight: 0.0000 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 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 = 0.4809 r_free = 0.4809 target = 0.177034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.164672 restraints weight = 88982.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.165555 restraints weight = 133975.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.165894 restraints weight = 51816.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.166380 restraints weight = 38644.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.166561 restraints weight = 27001.243| |-----------------------------------------------------------------------------| r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4622 r_free = 0.4622 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4622 r_free = 0.4622 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5222 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15829 Z= 0.115 Angle : 0.602 10.703 21474 Z= 0.310 Chirality : 0.042 0.154 2451 Planarity : 0.004 0.049 2716 Dihedral : 4.748 43.666 2300 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % 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: -1.15 (0.19), residues: 2005 helix: 0.46 (0.20), residues: 683 sheet: -0.89 (0.26), residues: 381 loop : -1.62 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.016 0.001 TYR A 512 PHE 0.024 0.001 PHE A 85 TRP 0.011 0.001 TRP A 164 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00239 (15821) covalent geometry : angle 0.60162 (21458) SS BOND : bond 0.00247 ( 8) SS BOND : angle 0.63174 ( 16) hydrogen bonds : bond 0.04400 ( 701) hydrogen bonds : angle 4.89590 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.93 seconds wall clock time: 42 minutes 46.04 seconds (2566.04 seconds total)