Starting phenix.real_space_refine on Sun Sep 13 03:23:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6a_22074/09_2026/6x6a_22074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6a_22074/09_2026/6x6a_22074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x6a_22074/09_2026/6x6a_22074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6a_22074/09_2026/6x6a_22074.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x6a_22074/09_2026/6x6a_22074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6a_22074/09_2026/6x6a_22074.map" } resolution = 3.6 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= 0.002 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 100 5.16 5 C 13051 2.51 5 N 3429 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "G" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1107 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1053 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 123} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.05, per 1000 atoms: 0.20 Number of scatterers: 20240 At special positions: 0 Unit cell: (129.525, 161.7, 114.675, 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 100 16.00 O 3660 8.00 N 3429 7.00 C 13051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.48 Conformation dependent library (CDL) restraints added in 815.8 milliseconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 39 sheets defined 18.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 30 through 49 removed outlier: 4.191A pdb=" N TYR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.540A pdb=" N VAL A 120 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.608A pdb=" N ASN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.295A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 786 through 793 removed outlier: 3.825A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.297A pdb=" N THR A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'B' and resid 1132 through 1137 removed outlier: 3.565A pdb=" N GLY B1137 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing helix chain 'G' and resid 1256 through 1270 Processing helix chain 'C' and resid 1258 through 1270 removed outlier: 4.133A pdb=" N ALA C1262 " --> pdb=" O SER C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1300 removed outlier: 4.120A pdb=" N MET C1299 " --> pdb=" O SER C1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.801A pdb=" N TYR D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.544A pdb=" N VAL D 120 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.622A pdb=" N ASN D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 694 No H-bonds generated for 'chain 'D' and resid 692 through 694' Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 730 through 743 Processing helix chain 'D' and resid 758 through 762 Processing helix chain 'D' and resid 763 through 771 removed outlier: 4.095A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 Processing helix chain 'D' and resid 786 through 793 removed outlier: 4.033A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 827 removed outlier: 4.393A pdb=" N THR D 816 " --> pdb=" O HIS D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 863 Processing helix chain 'E' and resid 1132 through 1137 Processing helix chain 'E' and resid 1141 through 1145 Processing helix chain 'I' and resid 1256 through 1270 Processing helix chain 'F' and resid 1228 through 1236 removed outlier: 3.788A pdb=" N SER F1233 " --> pdb=" O ILE F1229 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL F1234 " --> pdb=" O PRO F1230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F1236 " --> pdb=" O THR F1232 " (cutoff:3.500A) Processing helix chain 'F' and resid 1258 through 1270 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 5.954A pdb=" N ASP A 55 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 75 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.652A pdb=" N LEU A 100 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL G1217 " --> pdb=" O ALA B1185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE B1187 " --> pdb=" O LEU G1215 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU G1215 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.135A pdb=" N ALA A 155 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.491A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE A 200 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.679A pdb=" N SER A 263 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 258 removed outlier: 9.093A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.470A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 354 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 376 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 414 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 378 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.527A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB2, first strand: chain 'A' and resid 547 through 552 removed outlier: 6.458A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 578 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.457A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP A 729 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1089 through 1092 removed outlier: 3.671A pdb=" N VAL B1091 " --> pdb=" O LEU B1097 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B1097 " --> pdb=" O VAL B1091 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1123 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1116 through 1118 removed outlier: 3.837A pdb=" N VAL B1164 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B1199 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1230 through 1231 removed outlier: 3.550A pdb=" N LEU G1284 " --> pdb=" O VAL G1231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 1238 through 1239 removed outlier: 3.531A pdb=" N VAL G1273 " --> pdb=" O HIS G1239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 1247 through 1251 removed outlier: 3.512A pdb=" N TYR G1324 " --> pdb=" O GLU G1301 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU G1301 " --> pdb=" O TYR G1324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1306 through 1308 removed outlier: 4.176A pdb=" N VAL G1336 " --> pdb=" O TRP G1346 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP G1346 " --> pdb=" O VAL G1336 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP G1338 " --> pdb=" O LEU G1344 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU G1344 " --> pdb=" O ASP G1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1238 through 1241 removed outlier: 6.069A pdb=" N VAL C1246 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1306 through 1309 removed outlier: 3.851A pdb=" N LEU C1309 " --> pdb=" O CYS C1288 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS C1288 " --> pdb=" O LEU C1309 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C1332 " --> pdb=" O VAL C1350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 60 removed outlier: 4.291A pdb=" N PHE D 56 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR D 73 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE D 58 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG D 71 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN D 60 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER D 69 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.686A pdb=" N LEU D 100 " --> pdb=" O LEU E1194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.463A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 237 through 239 Processing sheet with id=AC8, first strand: chain 'D' and resid 256 through 258 removed outlier: 9.030A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AD1, first strand: chain 'D' and resid 351 through 357 removed outlier: 6.686A pdb=" N MET D 367 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA D 355 " --> pdb=" O TRP D 365 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP D 365 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU D 376 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 414 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 378 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 427 through 429 Processing sheet with id=AD3, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AD4, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.586A pdb=" N VAL D 572 " --> pdb=" O MET D 595 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS D 576 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE D 591 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER D 578 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.309A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1116 through 1118 removed outlier: 3.646A pdb=" N CYS E1116 " --> pdb=" O HIS E1165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1199 through 1200 removed outlier: 3.934A pdb=" N ARG E1199 " --> pdb=" O VAL E1206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1230 through 1231 removed outlier: 3.773A pdb=" N LEU I1284 " --> pdb=" O VAL I1231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1237 through 1238 Processing sheet with id=AE1, first strand: chain 'I' and resid 1290 through 1294 removed outlier: 7.476A pdb=" N VAL I1336 " --> pdb=" O VAL I1345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1273 through 1274 removed outlier: 3.997A pdb=" N THR F1247 " --> pdb=" O ARG F1240 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL F1246 " --> pdb=" O VAL F1325 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1290 through 1293 removed outlier: 6.616A pdb=" N ASP F1338 " --> pdb=" O LEU F1344 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU F1344 " --> pdb=" O ASP F1338 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1779 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: 4.53 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3347 1.32 - 1.44: 5827 1.44 - 1.57: 11501 1.57 - 1.69: 7 1.69 - 1.81: 156 Bond restraints: 20838 Sorted by residual: bond pdb=" C TYR A 731 " pdb=" O TYR A 731 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.48e+01 bond pdb=" C GLY A 728 " pdb=" O GLY A 728 " ideal model delta sigma weight residual 1.233 1.196 0.037 9.80e-03 1.04e+04 1.40e+01 bond pdb=" C ARG A 371 " pdb=" O ARG A 371 " ideal model delta sigma weight residual 1.244 1.211 0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" N ASN E1140 " pdb=" CA ASN E1140 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.60e+00 bond pdb=" C SER A 730 " pdb=" O SER A 730 " ideal model delta sigma weight residual 1.235 1.197 0.039 1.26e-02 6.30e+03 9.48e+00 ... (remaining 20833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 26818 2.68 - 5.35: 1254 5.35 - 8.03: 180 8.03 - 10.71: 41 10.71 - 13.38: 5 Bond angle restraints: 28298 Sorted by residual: angle pdb=" N ASN E1140 " pdb=" CA ASN E1140 " pdb=" C ASN E1140 " ideal model delta sigma weight residual 112.75 124.46 -11.71 1.36e+00 5.41e-01 7.42e+01 angle pdb=" N LYS I1220 " pdb=" CA LYS I1220 " pdb=" C LYS I1220 " ideal model delta sigma weight residual 111.28 120.22 -8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N TRP D 729 " pdb=" CA TRP D 729 " pdb=" C TRP D 729 " ideal model delta sigma weight residual 111.96 123.41 -11.45 1.41e+00 5.03e-01 6.59e+01 angle pdb=" CA TRP D 729 " pdb=" C TRP D 729 " pdb=" N SER D 730 " ideal model delta sigma weight residual 117.34 126.21 -8.87 1.22e+00 6.72e-01 5.28e+01 angle pdb=" N ILE I1302 " pdb=" CA ILE I1302 " pdb=" C ILE I1302 " ideal model delta sigma weight residual 107.75 117.75 -10.00 1.42e+00 4.96e-01 4.96e+01 ... (remaining 28293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11053 17.76 - 35.52: 1061 35.52 - 53.28: 169 53.28 - 71.03: 47 71.03 - 88.79: 12 Dihedral angle restraints: 12342 sinusoidal: 5024 harmonic: 7318 Sorted by residual: dihedral pdb=" CA TYR D 770 " pdb=" C TYR D 770 " pdb=" N MET D 771 " pdb=" CA MET D 771 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU C1300 " pdb=" C LEU C1300 " pdb=" N GLU C1301 " pdb=" CA GLU C1301 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA SER I1233 " pdb=" C SER I1233 " pdb=" N VAL I1234 " pdb=" CA VAL I1234 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2410 0.093 - 0.185: 506 0.185 - 0.278: 77 0.278 - 0.370: 16 0.370 - 0.463: 4 Chirality restraints: 3013 Sorted by residual: chirality pdb=" CB ILE C1302 " pdb=" CA ILE C1302 " pdb=" CG1 ILE C1302 " pdb=" CG2 ILE C1302 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA ASN E1140 " pdb=" N ASN E1140 " pdb=" C ASN E1140 " pdb=" CB ASN E1140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE D 426 " pdb=" CA ILE D 426 " pdb=" CG1 ILE D 426 " pdb=" CG2 ILE D 426 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 3010 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I1292 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.64e+01 pdb=" C VAL I1292 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL I1292 " 0.026 2.00e-02 2.50e+03 pdb=" N SER I1293 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 393 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLU A 393 " -0.065 2.00e-02 2.50e+03 pdb=" O GLU A 393 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 394 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 393 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLU D 393 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU D 393 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU D 394 " -0.021 2.00e-02 2.50e+03 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2520 2.74 - 3.28: 19071 3.28 - 3.82: 35094 3.82 - 4.36: 41632 4.36 - 4.90: 71084 Nonbonded interactions: 169401 Sorted by model distance: nonbonded pdb=" OH TYR A 644 " pdb=" O SER C1213 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR D 73 " pdb=" OD2 ASP D 164 " model vdw 2.210 3.040 nonbonded pdb=" CG TYR G1238 " pdb=" OE2 GLU G1267 " model vdw 2.213 3.260 nonbonded pdb=" O LYS A 348 " pdb=" OD1 ASP A 370 " model vdw 2.225 3.040 nonbonded pdb=" OG SER D 230 " pdb=" OD1 ASN D 231 " model vdw 2.254 3.040 ... (remaining 169396 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 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and ((resid 1079 through 1080 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1081 through 1212)) selection = chain 'E' } ncs_group { reference = (chain 'C' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1276 or (resid 1277 and (name N or name CA or name C \ or name O or name CB )) or resid 1278 through 1350)) selection = (chain 'F' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1225 or (resid 1226 and (name N or name CA or name C \ or name O or name CB )) or resid 1227 or (resid 1228 through 1229 and (name N o \ r name CA or name C or name O or name CB )) or resid 1230 through 1350)) selection = (chain 'G' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1276 or (resid 1277 and (name N or name CA or name C or name O or na \ me CB )) or resid 1278 through 1350)) selection = (chain 'I' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1350)) } 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=0.45 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: 4.490 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: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.490 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.010 0.112 20838 Z= 0.444 Angle : 1.291 13.382 28298 Z= 0.727 Chirality : 0.078 0.463 3013 Planarity : 0.009 0.085 3657 Dihedral : 14.434 88.793 7646 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 1.27 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.80 (0.15), residues: 2508 helix: -1.59 (0.23), residues: 378 sheet: -2.25 (0.17), residues: 724 loop : -1.66 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G1333 TYR 0.056 0.004 TYR A 781 PHE 0.056 0.004 PHE D 711 TRP 0.039 0.004 TRP A 375 HIS 0.024 0.003 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01009 / 0.44 (20838) covalent geometry : angle 1.29059 / 0.73 (28298) hydrogen bonds : bond 0.14437 / 9.85 ( 668) hydrogen bonds : angle 8.57491 / 6.04 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8060 (t0) cc_final: 0.7526 (t70) REVERT: A 738 MET cc_start: 0.8501 (mmm) cc_final: 0.8223 (mmm) REVERT: B 1099 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.6868 (mtp180) REVERT: B 1119 MET cc_start: 0.6018 (ptp) cc_final: 0.5776 (pmm) REVERT: B 1178 ASP cc_start: 0.7384 (t0) cc_final: 0.7111 (t70) REVERT: B 1203 HIS cc_start: 0.6519 (m-70) cc_final: 0.6314 (m170) REVERT: G 1263 ILE cc_start: 0.7810 (pt) cc_final: 0.7471 (pt) REVERT: G 1330 SER cc_start: 0.7451 (t) cc_final: 0.7018 (m) REVERT: C 1260 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7124 (ttt-90) REVERT: C 1286 MET cc_start: 0.3543 (ptt) cc_final: 0.3216 (ptm) REVERT: D 251 ASP cc_start: 0.8025 (m-30) cc_final: 0.7723 (t0) REVERT: D 684 GLN cc_start: 0.7870 (mp10) cc_final: 0.7034 (mp10) REVERT: E 1096 ASN cc_start: 0.7374 (t0) cc_final: 0.7122 (t0) REVERT: E 1119 MET cc_start: 0.5535 (tpp) cc_final: 0.5066 (mpp) REVERT: I 1227 ARG cc_start: 0.6008 (tpp-160) cc_final: 0.5740 (tpp-160) REVERT: I 1338 ASP cc_start: 0.6554 (t0) cc_final: 0.6299 (t0) REVERT: F 1289 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7157 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 276 average time/residue: 0.1720 time to fit residues: 71.4063 Evaluate side-chains 207 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.5271 > 50:) chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 516 GLN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 ASN B1204 HIS ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN D 516 GLN E1140 ASN E1165 HIS I1335 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.116118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081900 restraints weight = 48326.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080131 restraints weight = 27405.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081376 restraints weight = 21589.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081567 restraints weight = 17230.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.081649 restraints weight = 16430.663| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20838 Z= 0.200 Angle : 0.696 9.930 28298 Z= 0.364 Chirality : 0.048 0.198 3013 Planarity : 0.006 0.068 3657 Dihedral : 6.387 38.848 2751 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.91 % Allowed : 8.84 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2508 helix: -0.17 (0.26), residues: 370 sheet: -1.85 (0.17), residues: 768 loop : -1.31 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 769 TYR 0.017 0.002 TYR C1290 PHE 0.017 0.002 PHE I1228 TRP 0.040 0.002 TRP A 375 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (20838) covalent geometry : angle 0.69565 / 0.36 (28298) hydrogen bonds : bond 0.04597 / 3.06 ( 668) hydrogen bonds : angle 6.88672 / 4.87 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8210 (t0) cc_final: 0.7668 (t70) REVERT: A 738 MET cc_start: 0.8974 (mmm) cc_final: 0.8729 (mmm) REVERT: B 1187 PHE cc_start: 0.7936 (m-80) cc_final: 0.7646 (m-10) REVERT: B 1194 LEU cc_start: 0.8253 (mt) cc_final: 0.7791 (mt) REVERT: G 1251 TYR cc_start: 0.7275 (m-80) cc_final: 0.6567 (m-80) REVERT: G 1320 PHE cc_start: 0.5087 (p90) cc_final: 0.4711 (p90) REVERT: G 1330 SER cc_start: 0.7484 (t) cc_final: 0.7108 (m) REVERT: C 1260 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7321 (ttt-90) REVERT: C 1264 ASP cc_start: 0.6494 (m-30) cc_final: 0.6268 (m-30) REVERT: C 1286 MET cc_start: 0.3601 (ptt) cc_final: 0.3134 (ptm) REVERT: C 1323 PHE cc_start: 0.5081 (t80) cc_final: 0.4775 (t80) REVERT: D 251 ASP cc_start: 0.8066 (m-30) cc_final: 0.7699 (t0) REVERT: D 684 GLN cc_start: 0.7779 (mp10) cc_final: 0.7211 (mp10) REVERT: D 738 MET cc_start: 0.9306 (mmm) cc_final: 0.9102 (mmm) REVERT: E 1096 ASN cc_start: 0.7486 (t0) cc_final: 0.6985 (t0) REVERT: E 1184 MET cc_start: 0.7693 (tmm) cc_final: 0.7442 (tmm) REVERT: I 1321 SER cc_start: 0.7079 (m) cc_final: 0.6610 (t) REVERT: I 1322 GLU cc_start: 0.7554 (pp20) cc_final: 0.7270 (pp20) REVERT: I 1338 ASP cc_start: 0.6367 (t0) cc_final: 0.6130 (t0) REVERT: F 1260 ARG cc_start: 0.7079 (mtp-110) cc_final: 0.6025 (ptm160) REVERT: F 1289 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7120 (mtm-85) outliers start: 20 outliers final: 13 residues processed: 238 average time/residue: 0.1735 time to fit residues: 61.9578 Evaluate side-chains 221 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1239 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 201 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 237 optimal weight: 0.0570 chunk 189 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 810 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 HIS B1204 HIS ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** I1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.116886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082373 restraints weight = 48250.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081240 restraints weight = 27209.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082424 restraints weight = 20609.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082621 restraints weight = 16883.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082682 restraints weight = 16053.775| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20838 Z= 0.143 Angle : 0.633 10.312 28298 Z= 0.328 Chirality : 0.045 0.195 3013 Planarity : 0.005 0.060 3657 Dihedral : 5.887 35.763 2746 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.18 % Allowed : 12.51 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.16), residues: 2508 helix: 0.27 (0.27), residues: 372 sheet: -1.51 (0.18), residues: 741 loop : -1.17 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1260 TYR 0.014 0.001 TYR A 835 PHE 0.024 0.001 PHE G1272 TRP 0.038 0.001 TRP A 375 HIS 0.007 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (20838) covalent geometry : angle 0.63300 / 0.33 (28298) hydrogen bonds : bond 0.04006 / 2.64 ( 668) hydrogen bonds : angle 6.35097 / 4.52 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8193 (t0) cc_final: 0.7633 (t70) REVERT: A 771 MET cc_start: 0.7691 (mtt) cc_final: 0.7423 (mtt) REVERT: B 1129 PHE cc_start: 0.7478 (m-80) cc_final: 0.7183 (m-80) REVERT: B 1187 PHE cc_start: 0.7858 (m-80) cc_final: 0.7622 (m-10) REVERT: G 1251 TYR cc_start: 0.7108 (m-80) cc_final: 0.6608 (m-80) REVERT: C 1260 ARG cc_start: 0.7651 (mtp180) cc_final: 0.7340 (ttt-90) REVERT: C 1264 ASP cc_start: 0.6405 (m-30) cc_final: 0.6172 (m-30) REVERT: C 1268 MET cc_start: 0.4185 (mmp) cc_final: 0.3947 (mmt) REVERT: C 1286 MET cc_start: 0.3771 (ptt) cc_final: 0.3324 (ptm) REVERT: D 251 ASP cc_start: 0.8083 (m-30) cc_final: 0.7716 (t0) REVERT: D 738 MET cc_start: 0.9294 (mmm) cc_final: 0.9067 (mmm) REVERT: E 1096 ASN cc_start: 0.7349 (t0) cc_final: 0.6867 (t0) REVERT: I 1321 SER cc_start: 0.6950 (m) cc_final: 0.6453 (t) REVERT: I 1322 GLU cc_start: 0.7613 (pp20) cc_final: 0.7373 (pp20) REVERT: I 1335 GLN cc_start: 0.4997 (tm-30) cc_final: 0.4723 (mp10) REVERT: I 1338 ASP cc_start: 0.6492 (t0) cc_final: 0.6257 (t0) REVERT: F 1231 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6680 (p) REVERT: F 1236 LEU cc_start: 0.7814 (mt) cc_final: 0.7479 (tp) REVERT: F 1260 ARG cc_start: 0.7040 (mtp-110) cc_final: 0.6063 (ptm160) REVERT: F 1289 ARG cc_start: 0.7250 (mtt180) cc_final: 0.7019 (mtm-85) outliers start: 26 outliers final: 11 residues processed: 243 average time/residue: 0.1747 time to fit residues: 63.7392 Evaluate side-chains 218 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1239 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 122 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 134 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 798 ASN ** I1335 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 = 0.4007 r_free = 0.4007 target = 0.117196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083063 restraints weight = 48400.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081578 restraints weight = 27308.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083148 restraints weight = 20521.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083293 restraints weight = 16433.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083386 restraints weight = 15816.438| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20838 Z= 0.129 Angle : 0.607 10.187 28298 Z= 0.313 Chirality : 0.045 0.195 3013 Planarity : 0.005 0.057 3657 Dihedral : 5.436 26.806 2742 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.09 % Allowed : 13.96 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2508 helix: 0.54 (0.28), residues: 373 sheet: -1.31 (0.18), residues: 735 loop : -1.11 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1260 TYR 0.024 0.001 TYR F1251 PHE 0.013 0.001 PHE F1248 TRP 0.041 0.001 TRP A 375 HIS 0.008 0.001 HIS F1249 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (20838) covalent geometry : angle 0.60699 / 0.31 (28298) hydrogen bonds : bond 0.03663 / 2.41 ( 668) hydrogen bonds : angle 6.03649 / 4.32 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8193 (t0) cc_final: 0.7665 (t70) REVERT: G 1227 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7971 (mmp-170) REVERT: G 1251 TYR cc_start: 0.7169 (m-80) cc_final: 0.6652 (m-80) REVERT: C 1260 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7260 (ttt-90) REVERT: C 1268 MET cc_start: 0.4207 (mmp) cc_final: 0.3964 (mmt) REVERT: D 251 ASP cc_start: 0.8052 (m-30) cc_final: 0.7651 (t0) REVERT: E 1096 ASN cc_start: 0.7315 (t0) cc_final: 0.6844 (t0) REVERT: I 1321 SER cc_start: 0.6880 (m) cc_final: 0.6353 (t) REVERT: I 1323 PHE cc_start: 0.6136 (t80) cc_final: 0.5810 (t80) REVERT: I 1338 ASP cc_start: 0.6633 (t0) cc_final: 0.6381 (t0) REVERT: F 1231 VAL cc_start: 0.6987 (OUTLIER) cc_final: 0.6699 (p) REVERT: F 1260 ARG cc_start: 0.6990 (mtp-110) cc_final: 0.6082 (ptm160) REVERT: F 1289 ARG cc_start: 0.7247 (mtt180) cc_final: 0.7009 (mtm-85) outliers start: 46 outliers final: 18 residues processed: 256 average time/residue: 0.1670 time to fit residues: 65.0028 Evaluate side-chains 211 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 207 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 189 optimal weight: 0.2980 chunk 209 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 HIS ** I1335 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 = 0.3998 r_free = 0.3998 target = 0.116696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082518 restraints weight = 48265.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081209 restraints weight = 28473.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082207 restraints weight = 23092.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082390 restraints weight = 19138.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082528 restraints weight = 16909.674| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20838 Z= 0.147 Angle : 0.613 9.673 28298 Z= 0.314 Chirality : 0.045 0.342 3013 Planarity : 0.005 0.069 3657 Dihedral : 5.293 26.221 2740 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.04 % Allowed : 14.73 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.17), residues: 2508 helix: 0.57 (0.28), residues: 374 sheet: -1.24 (0.18), residues: 733 loop : -1.08 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1260 TYR 0.014 0.001 TYR A 363 PHE 0.036 0.001 PHE E1182 TRP 0.044 0.001 TRP A 375 HIS 0.008 0.001 HIS D 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (20838) covalent geometry : angle 0.61257 / 0.31 (28298) hydrogen bonds : bond 0.03622 / 2.38 ( 668) hydrogen bonds : angle 5.92479 / 4.22 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8175 (t0) cc_final: 0.7650 (t70) REVERT: B 1184 MET cc_start: 0.7346 (ppp) cc_final: 0.6833 (tmm) REVERT: G 1220 LYS cc_start: 0.5735 (tptp) cc_final: 0.5065 (tppt) REVERT: G 1261 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8123 (mmtm) REVERT: G 1323 PHE cc_start: 0.7006 (t80) cc_final: 0.6744 (t80) REVERT: C 1260 ARG cc_start: 0.7588 (mtp180) cc_final: 0.7207 (ttt-90) REVERT: C 1268 MET cc_start: 0.4355 (mmp) cc_final: 0.4108 (mmt) REVERT: D 251 ASP cc_start: 0.8037 (m-30) cc_final: 0.7619 (t0) REVERT: D 771 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6793 (mpt) REVERT: E 1096 ASN cc_start: 0.7256 (t0) cc_final: 0.6803 (t0) REVERT: I 1261 LYS cc_start: 0.7674 (tppt) cc_final: 0.7472 (tptt) REVERT: I 1321 SER cc_start: 0.6927 (m) cc_final: 0.6386 (t) REVERT: I 1338 ASP cc_start: 0.6517 (t0) cc_final: 0.6242 (t0) REVERT: I 1346 TRP cc_start: 0.6176 (t60) cc_final: 0.5287 (t60) REVERT: F 1236 LEU cc_start: 0.7745 (mt) cc_final: 0.7413 (tp) REVERT: F 1260 ARG cc_start: 0.6955 (mtp-110) cc_final: 0.6047 (ptm160) outliers start: 45 outliers final: 29 residues processed: 241 average time/residue: 0.1500 time to fit residues: 55.7483 Evaluate side-chains 225 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1332 ILE Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 243 optimal weight: 0.0020 chunk 217 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 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 = 0.4009 r_free = 0.4009 target = 0.117297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083401 restraints weight = 47682.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082643 restraints weight = 27000.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083650 restraints weight = 21272.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084214 restraints weight = 16996.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084313 restraints weight = 15678.771| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20838 Z= 0.119 Angle : 0.596 8.642 28298 Z= 0.304 Chirality : 0.045 0.191 3013 Planarity : 0.005 0.057 3657 Dihedral : 5.131 26.128 2740 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.72 % Allowed : 14.51 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.17), residues: 2508 helix: 0.67 (0.28), residues: 382 sheet: -1.08 (0.19), residues: 729 loop : -1.10 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1099 TYR 0.016 0.001 TYR F1251 PHE 0.024 0.001 PHE E1182 TRP 0.035 0.001 TRP A 375 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (20838) covalent geometry : angle 0.59637 / 0.30 (28298) hydrogen bonds : bond 0.03474 / 2.30 ( 668) hydrogen bonds : angle 5.79650 / 4.14 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8198 (t0) cc_final: 0.7671 (t70) REVERT: G 1228 PHE cc_start: 0.5682 (m-80) cc_final: 0.5305 (m-80) REVERT: G 1323 PHE cc_start: 0.6863 (t80) cc_final: 0.6521 (t80) REVERT: C 1260 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7232 (ttt-90) REVERT: C 1268 MET cc_start: 0.4296 (mmp) cc_final: 0.4055 (mmt) REVERT: D 251 ASP cc_start: 0.8020 (m-30) cc_final: 0.7577 (t0) REVERT: D 710 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: E 1096 ASN cc_start: 0.7169 (t0) cc_final: 0.6708 (t0) REVERT: I 1321 SER cc_start: 0.6898 (m) cc_final: 0.6411 (t) REVERT: I 1338 ASP cc_start: 0.6546 (t0) cc_final: 0.6272 (t0) REVERT: I 1346 TRP cc_start: 0.6040 (t60) cc_final: 0.5356 (t60) REVERT: F 1221 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7365 (mtp) REVERT: F 1231 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6728 (p) REVERT: F 1236 LEU cc_start: 0.7676 (mt) cc_final: 0.7367 (tp) REVERT: F 1260 ARG cc_start: 0.6918 (mtp-110) cc_final: 0.5934 (ptm160) outliers start: 60 outliers final: 37 residues processed: 255 average time/residue: 0.1658 time to fit residues: 65.1867 Evaluate side-chains 234 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 433 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1347 GLU Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1221 MET Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 229 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 204 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** E1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 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 = 0.3997 r_free = 0.3997 target = 0.116591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082211 restraints weight = 48307.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080587 restraints weight = 29927.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081530 restraints weight = 22804.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081902 restraints weight = 17897.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082081 restraints weight = 16694.609| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20838 Z= 0.157 Angle : 0.617 8.752 28298 Z= 0.312 Chirality : 0.045 0.186 3013 Planarity : 0.005 0.052 3657 Dihedral : 5.097 24.764 2740 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.72 % Allowed : 14.60 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.17), residues: 2508 helix: 0.67 (0.28), residues: 382 sheet: -1.10 (0.19), residues: 739 loop : -1.07 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1227 TYR 0.025 0.001 TYR F1251 PHE 0.026 0.001 PHE I1248 TRP 0.055 0.002 TRP A 375 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (20838) covalent geometry : angle 0.61673 / 0.31 (28298) hydrogen bonds : bond 0.03547 / 2.33 ( 668) hydrogen bonds : angle 5.73169 / 4.07 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8198 (t0) cc_final: 0.7635 (t70) REVERT: B 1183 GLN cc_start: 0.5897 (pm20) cc_final: 0.5650 (pm20) REVERT: G 1228 PHE cc_start: 0.5780 (m-80) cc_final: 0.5362 (m-80) REVERT: G 1261 LYS cc_start: 0.8268 (mmtm) cc_final: 0.8059 (mmtm) REVERT: G 1323 PHE cc_start: 0.6821 (t80) cc_final: 0.6482 (t80) REVERT: C 1260 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7317 (ttt-90) REVERT: D 251 ASP cc_start: 0.8072 (m-30) cc_final: 0.7618 (t0) REVERT: D 345 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9169 (tp) REVERT: D 632 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8279 (tp40) REVERT: D 710 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: E 1096 ASN cc_start: 0.7083 (t0) cc_final: 0.6768 (t0) REVERT: I 1321 SER cc_start: 0.6920 (m) cc_final: 0.6407 (t) REVERT: I 1338 ASP cc_start: 0.6505 (t0) cc_final: 0.6234 (t0) REVERT: I 1346 TRP cc_start: 0.6126 (t60) cc_final: 0.5410 (t60) REVERT: F 1231 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6748 (p) REVERT: F 1236 LEU cc_start: 0.7696 (mt) cc_final: 0.7394 (tp) REVERT: F 1260 ARG cc_start: 0.6988 (mtp-110) cc_final: 0.6276 (ptm160) outliers start: 60 outliers final: 37 residues processed: 251 average time/residue: 0.1564 time to fit residues: 60.9342 Evaluate side-chains 237 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1136 LEU Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1347 GLU Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 225 optimal weight: 0.1980 chunk 182 optimal weight: 0.8980 chunk 228 optimal weight: 9.9990 chunk 180 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 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 = 0.3994 r_free = 0.3994 target = 0.116381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082376 restraints weight = 48296.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080306 restraints weight = 27858.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081884 restraints weight = 21352.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082084 restraints weight = 16903.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082169 restraints weight = 16635.510| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20838 Z= 0.153 Angle : 0.617 9.150 28298 Z= 0.311 Chirality : 0.045 0.222 3013 Planarity : 0.005 0.072 3657 Dihedral : 5.040 24.432 2740 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.31 % Allowed : 15.64 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.17), residues: 2508 helix: 0.68 (0.28), residues: 383 sheet: -1.03 (0.19), residues: 722 loop : -1.07 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1099 TYR 0.018 0.001 TYR A 363 PHE 0.025 0.001 PHE I1248 TRP 0.046 0.001 TRP A 375 HIS 0.005 0.001 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (20838) covalent geometry : angle 0.61682 / 0.31 (28298) hydrogen bonds : bond 0.03479 / 2.29 ( 668) hydrogen bonds : angle 5.66830 / 4.03 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8162 (t0) cc_final: 0.7612 (t70) REVERT: G 1228 PHE cc_start: 0.5830 (m-80) cc_final: 0.5432 (m-80) REVERT: G 1261 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8040 (mmtm) REVERT: G 1323 PHE cc_start: 0.6870 (t80) cc_final: 0.6522 (t80) REVERT: C 1260 ARG cc_start: 0.7652 (mtp180) cc_final: 0.7404 (ttt-90) REVERT: C 1347 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6657 (mp0) REVERT: D 251 ASP cc_start: 0.8108 (m-30) cc_final: 0.7633 (t0) REVERT: D 632 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8268 (tp40) REVERT: D 710 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: E 1096 ASN cc_start: 0.6998 (t0) cc_final: 0.6664 (t0) REVERT: I 1221 MET cc_start: 0.8616 (ppp) cc_final: 0.8214 (tmm) REVERT: I 1321 SER cc_start: 0.6693 (m) cc_final: 0.6145 (t) REVERT: I 1338 ASP cc_start: 0.6445 (t0) cc_final: 0.6160 (t0) REVERT: I 1346 TRP cc_start: 0.6274 (t60) cc_final: 0.5488 (t60) REVERT: F 1221 MET cc_start: 0.6978 (mtp) cc_final: 0.6710 (mmm) REVERT: F 1231 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6689 (p) REVERT: F 1236 LEU cc_start: 0.7678 (mt) cc_final: 0.7439 (tp) REVERT: F 1260 ARG cc_start: 0.7070 (mtp-110) cc_final: 0.6333 (ptm160) outliers start: 51 outliers final: 42 residues processed: 238 average time/residue: 0.1527 time to fit residues: 56.8525 Evaluate side-chains 238 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1136 LEU Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1347 GLU Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 95 optimal weight: 0.0270 chunk 157 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 204 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 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 = 0.4017 r_free = 0.4017 target = 0.117691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083695 restraints weight = 47880.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.081802 restraints weight = 26560.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083434 restraints weight = 21023.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083617 restraints weight = 16411.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083719 restraints weight = 15852.522| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20838 Z= 0.120 Angle : 0.608 10.985 28298 Z= 0.306 Chirality : 0.045 0.201 3013 Planarity : 0.005 0.061 3657 Dihedral : 4.903 23.984 2740 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.31 % Allowed : 16.09 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2508 helix: 0.76 (0.28), residues: 383 sheet: -0.86 (0.20), residues: 694 loop : -1.13 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1099 TYR 0.015 0.001 TYR A 363 PHE 0.028 0.001 PHE I1248 TRP 0.043 0.002 TRP A 375 HIS 0.006 0.001 HIS F1249 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (20838) covalent geometry : angle 0.60766 / 0.31 (28298) hydrogen bonds : bond 0.03347 / 2.21 ( 668) hydrogen bonds : angle 5.57767 / 3.97 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8174 (t0) cc_final: 0.7619 (t70) REVERT: G 1228 PHE cc_start: 0.5789 (m-80) cc_final: 0.5391 (m-80) REVERT: G 1261 LYS cc_start: 0.8307 (mmtm) cc_final: 0.8044 (mmtm) REVERT: G 1323 PHE cc_start: 0.6926 (t80) cc_final: 0.6549 (t80) REVERT: C 1260 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7355 (ttt-90) REVERT: C 1347 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: D 70 HIS cc_start: 0.7587 (m90) cc_final: 0.7235 (m-70) REVERT: D 251 ASP cc_start: 0.8101 (m-30) cc_final: 0.7571 (t0) REVERT: D 345 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9163 (tp) REVERT: D 558 MET cc_start: 0.7878 (ptp) cc_final: 0.7379 (ptp) REVERT: D 595 MET cc_start: 0.8682 (mtp) cc_final: 0.8393 (ttm) REVERT: D 632 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8239 (tp40) REVERT: D 710 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: E 1096 ASN cc_start: 0.6975 (t0) cc_final: 0.6670 (t0) REVERT: E 1117 PHE cc_start: 0.7310 (p90) cc_final: 0.6628 (p90) REVERT: I 1221 MET cc_start: 0.8620 (ppp) cc_final: 0.8177 (tmm) REVERT: I 1321 SER cc_start: 0.6498 (m) cc_final: 0.5927 (t) REVERT: I 1338 ASP cc_start: 0.6517 (t0) cc_final: 0.6216 (t0) REVERT: I 1346 TRP cc_start: 0.6211 (t60) cc_final: 0.5496 (t60) REVERT: F 1231 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6731 (p) REVERT: F 1236 LEU cc_start: 0.7661 (mt) cc_final: 0.7406 (tp) REVERT: F 1260 ARG cc_start: 0.7096 (mtp-110) cc_final: 0.6337 (ptm160) outliers start: 51 outliers final: 38 residues processed: 247 average time/residue: 0.1501 time to fit residues: 56.9855 Evaluate side-chains 240 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1347 GLU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1136 LEU Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1347 GLU Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 200 optimal weight: 0.4980 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 191 optimal weight: 0.0040 chunk 220 optimal weight: 3.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN ** G1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1335 GLN ** E1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 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 = 0.4021 r_free = 0.4021 target = 0.117935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083857 restraints weight = 48231.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082155 restraints weight = 26248.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083466 restraints weight = 21264.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083857 restraints weight = 16851.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083885 restraints weight = 16070.268| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20838 Z= 0.117 Angle : 0.612 10.418 28298 Z= 0.306 Chirality : 0.045 0.194 3013 Planarity : 0.005 0.065 3657 Dihedral : 4.851 23.793 2740 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.22 % Allowed : 16.09 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2508 helix: 0.81 (0.28), residues: 383 sheet: -0.87 (0.20), residues: 702 loop : -1.13 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1099 TYR 0.020 0.001 TYR D 79 PHE 0.026 0.001 PHE I1248 TRP 0.041 0.002 TRP A 375 HIS 0.009 0.001 HIS B1165 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (20838) covalent geometry : angle 0.61197 / 0.31 (28298) hydrogen bonds : bond 0.03319 / 2.20 ( 668) hydrogen bonds : angle 5.50931 / 3.92 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8185 (t0) cc_final: 0.7641 (t70) REVERT: G 1228 PHE cc_start: 0.5787 (m-80) cc_final: 0.5390 (m-80) REVERT: G 1261 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8051 (mmtm) REVERT: G 1323 PHE cc_start: 0.6935 (t80) cc_final: 0.6549 (t80) REVERT: C 1260 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7354 (ttt-90) REVERT: C 1268 MET cc_start: 0.4253 (mmm) cc_final: 0.3596 (mmt) REVERT: C 1347 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: D 70 HIS cc_start: 0.7560 (m90) cc_final: 0.7203 (m-70) REVERT: D 251 ASP cc_start: 0.8086 (m-30) cc_final: 0.7543 (t0) REVERT: D 345 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9152 (tp) REVERT: D 558 MET cc_start: 0.7872 (ptp) cc_final: 0.7364 (ptp) REVERT: D 632 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8265 (tp40) REVERT: D 710 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: E 1096 ASN cc_start: 0.6967 (t0) cc_final: 0.6677 (t0) REVERT: E 1117 PHE cc_start: 0.7402 (p90) cc_final: 0.6628 (p90) REVERT: I 1221 MET cc_start: 0.8670 (ppp) cc_final: 0.8259 (tmm) REVERT: I 1321 SER cc_start: 0.6506 (m) cc_final: 0.5898 (t) REVERT: I 1338 ASP cc_start: 0.6570 (t0) cc_final: 0.6283 (t0) REVERT: I 1346 TRP cc_start: 0.6266 (t60) cc_final: 0.5540 (t60) REVERT: F 1231 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6723 (p) REVERT: F 1236 LEU cc_start: 0.7646 (mt) cc_final: 0.7421 (tp) REVERT: F 1260 ARG cc_start: 0.7043 (mtp-110) cc_final: 0.6319 (ptm160) outliers start: 49 outliers final: 38 residues processed: 235 average time/residue: 0.1493 time to fit residues: 54.7789 Evaluate side-chains 241 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1203 HIS Chi-restraints excluded: chain G residue 1292 VAL Chi-restraints excluded: chain G residue 1350 VAL Chi-restraints excluded: chain C residue 1273 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1347 GLU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 710 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1136 LEU Chi-restraints excluded: chain E residue 1200 VAL Chi-restraints excluded: chain I residue 1215 LEU Chi-restraints excluded: chain I residue 1241 VAL Chi-restraints excluded: chain I residue 1293 SER Chi-restraints excluded: chain I residue 1347 GLU Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1231 VAL Chi-restraints excluded: chain F residue 1239 HIS Chi-restraints excluded: chain F residue 1241 VAL Chi-restraints excluded: chain F residue 1325 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 236 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 HIS A 810 ASN G1335 GLN D 374 GLN D 612 HIS ** E1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1335 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 = 0.3921 r_free = 0.3921 target = 0.112342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076670 restraints weight = 48136.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074834 restraints weight = 27894.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075490 restraints weight = 24486.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075913 restraints weight = 19635.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076152 restraints weight = 18080.133| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 20838 Z= 0.291 Angle : 0.699 10.233 28298 Z= 0.355 Chirality : 0.048 0.243 3013 Planarity : 0.005 0.069 3657 Dihedral : 5.228 23.568 2740 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.27 % Allowed : 16.18 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.17), residues: 2508 helix: 0.51 (0.27), residues: 381 sheet: -1.05 (0.19), residues: 734 loop : -1.15 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1099 TYR 0.021 0.002 TYR A 363 PHE 0.024 0.002 PHE E1182 TRP 0.040 0.002 TRP A 375 HIS 0.008 0.001 HIS D 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (20838) covalent geometry : angle 0.69925 / 0.35 (28298) hydrogen bonds : bond 0.03906 / 2.54 ( 668) hydrogen bonds : angle 5.84562 / 4.13 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3549.07 seconds wall clock time: 62 minutes 35.97 seconds (3755.97 seconds total)