Starting phenix.real_space_refine on Thu Sep 26 08:59:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3q_27870/09_2024/8e3q_27870.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3q_27870/09_2024/8e3q_27870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3q_27870/09_2024/8e3q_27870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3q_27870/09_2024/8e3q_27870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3q_27870/09_2024/8e3q_27870.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3q_27870/09_2024/8e3q_27870.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.124 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 80 5.16 5 C 8157 2.51 5 N 2214 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12739 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9348 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 66, 'TRANS': 1111} Chain breaks: 13 Chain: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 448 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2942 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 15, 'TRANS': 349} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9658 SG CYS C 41 29.296 90.239 96.332 1.00 72.45 S ATOM 9722 SG CYS C 49 26.663 91.779 98.639 1.00 80.81 S ATOM 9757 SG CYS C 55 27.485 88.030 98.906 1.00 77.72 S Time building chain proxies: 7.51, per 1000 atoms: 0.59 Number of scatterers: 12739 At special positions: 0 Unit cell: (87.98, 107.07, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 80 16.00 O 2287 8.00 N 2214 7.00 C 8157 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " Number of angles added : 3 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 30 sheets defined 9.3% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.584A pdb=" N ARG A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.588A pdb=" N THR A 304 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1370 Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 4.152A pdb=" N ARG A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1422 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.719A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.819A pdb=" N ILE C 5 " --> pdb=" O MET C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.530A pdb=" N LEU C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.546A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.749A pdb=" N ASP B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 101 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315 removed outlier: 4.157A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A1339 " --> pdb=" O THR A1310 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1347 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 7 " --> pdb=" O LEU A1347 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A1349 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR A 5 " --> pdb=" O LEU A1349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24 removed outlier: 4.674A pdb=" N PHE A 22 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLU A 27 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ARG A 28 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 43 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 84 removed outlier: 3.566A pdb=" N SER A 80 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.493A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 260 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.673A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 331 removed outlier: 3.865A pdb=" N ILE A 330 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LYS A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 376 removed outlier: 6.316A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 477 through 481 removed outlier: 4.103A pdb=" N ASN A 477 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 528 removed outlier: 6.742A pdb=" N ILE A 998 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR A 526 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 996 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.895A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 574 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.602A pdb=" N TYR A 617 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 626 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 637 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 628 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 651 Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 removed outlier: 3.649A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 803 " --> pdb=" O GLN A 798 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.505A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.550A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER A 941 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 955 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1021 through 1027 removed outlier: 5.441A pdb=" N ALA A1022 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A1039 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1046 through 1049 Processing sheet with id=AC1, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 5.468A pdb=" N VAL A1100 " --> pdb=" O CYS A1126 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A1126 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 3.680A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1196 " --> pdb=" O GLU A1199 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1212 through 1218 removed outlier: 3.918A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLN A1237 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU A1243 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.795A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.795A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET A1282 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG A1298 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 109 through 114 removed outlier: 5.347A pdb=" N PHE B 110 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N THR B 403 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 112 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.501A pdb=" N THR B 144 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 138 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE B 143 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE B 156 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 145 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.552A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.870A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 247 through 252 Processing sheet with id=AD2, first strand: chain 'B' and resid 291 through 296 removed outlier: 6.315A pdb=" N ALA B 306 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 294 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 304 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 296 " --> pdb=" O TRP B 302 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP B 302 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.741A pdb=" N ALA B 336 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 368 " --> pdb=" O PHE B 358 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1116 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: 5.47 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4144 1.34 - 1.46: 2905 1.46 - 1.58: 5869 1.58 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 13047 Sorted by residual: bond pdb=" N GLN B 189 " pdb=" CA GLN B 189 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.93e+00 bond pdb=" N TRP B 188 " pdb=" CA TRP B 188 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" N TYR B 187 " pdb=" CA TYR B 187 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.21e-02 6.83e+03 6.76e+00 bond pdb=" N SER B 190 " pdb=" CA SER B 190 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.91e+00 bond pdb=" CB PRO A 494 " pdb=" CG PRO A 494 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 ... (remaining 13042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 17267 1.57 - 3.14: 359 3.14 - 4.71: 58 4.71 - 6.28: 11 6.28 - 7.84: 1 Bond angle restraints: 17696 Sorted by residual: angle pdb=" C TYR A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.69e+01 angle pdb=" N VAL A 647 " pdb=" CA VAL A 647 " pdb=" C VAL A 647 " ideal model delta sigma weight residual 113.53 110.26 3.27 9.80e-01 1.04e+00 1.12e+01 angle pdb=" N ASN B 289 " pdb=" CA ASN B 289 " pdb=" C ASN B 289 " ideal model delta sigma weight residual 107.20 112.76 -5.56 1.70e+00 3.46e-01 1.07e+01 angle pdb=" CA GLN B 189 " pdb=" C GLN B 189 " pdb=" O GLN B 189 " ideal model delta sigma weight residual 121.72 118.15 3.57 1.18e+00 7.18e-01 9.16e+00 angle pdb=" N GLU A1417 " pdb=" CA GLU A1417 " pdb=" CB GLU A1417 " ideal model delta sigma weight residual 110.12 114.49 -4.37 1.47e+00 4.63e-01 8.83e+00 ... (remaining 17691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7139 17.72 - 35.43: 514 35.43 - 53.15: 87 53.15 - 70.87: 22 70.87 - 88.58: 9 Dihedral angle restraints: 7771 sinusoidal: 3134 harmonic: 4637 Sorted by residual: dihedral pdb=" CA ASP A 936 " pdb=" C ASP A 936 " pdb=" N ILE A 937 " pdb=" CA ILE A 937 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN A 85 " pdb=" C GLN A 85 " pdb=" N LEU A 86 " pdb=" CA LEU A 86 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA HIS B 171 " pdb=" C HIS B 171 " pdb=" N ASN B 172 " pdb=" CA ASN B 172 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1208 0.031 - 0.063: 484 0.063 - 0.094: 139 0.094 - 0.125: 133 0.125 - 0.157: 9 Chirality restraints: 1973 Sorted by residual: chirality pdb=" CA TRP B 252 " pdb=" N TRP B 252 " pdb=" C TRP B 252 " pdb=" CB TRP B 252 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE A 998 " pdb=" N ILE A 998 " pdb=" C ILE A 998 " pdb=" CB ILE A 998 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1970 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 252 " 0.023 2.00e-02 2.50e+03 2.52e-02 1.58e+01 pdb=" CG TRP B 252 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 252 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 252 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 252 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 252 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 252 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 252 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 252 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 493 " -0.043 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 494 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 332 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C TYR A 332 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 332 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 333 " 0.014 2.00e-02 2.50e+03 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1435 2.75 - 3.29: 11692 3.29 - 3.83: 21795 3.83 - 4.36: 27795 4.36 - 4.90: 47371 Nonbonded interactions: 110088 Sorted by model distance: nonbonded pdb=" OG1 THR A1173 " pdb=" O ILE A1212 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS A 199 " pdb=" OE2 GLU B 364 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS A1219 " pdb=" O ILE C 11 " model vdw 2.231 3.120 nonbonded pdb=" OG SER B 170 " pdb=" O ASN B 172 " model vdw 2.232 3.040 nonbonded pdb=" O ASN B 289 " pdb=" OG SER B 307 " model vdw 2.234 3.040 ... (remaining 110083 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.610 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13047 Z= 0.183 Angle : 0.569 7.844 17696 Z= 0.317 Chirality : 0.044 0.157 1973 Planarity : 0.004 0.063 2259 Dihedral : 13.137 88.585 4773 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.71 % Favored : 94.97 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1571 helix: 0.45 (0.58), residues: 93 sheet: 0.23 (0.20), residues: 645 loop : -0.97 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 252 HIS 0.005 0.001 HIS A 866 PHE 0.018 0.001 PHE A1160 TYR 0.023 0.001 TYR A 938 ARG 0.003 0.000 ARG A 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: B 246 ASP cc_start: 0.7575 (m-30) cc_final: 0.7325 (m-30) outliers start: 2 outliers final: 1 residues processed: 197 average time/residue: 1.4962 time to fit residues: 316.4195 Evaluate side-chains 125 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 648 GLN ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 GLN A1209 GLN A1264 ASN A1352 GLN B 76 GLN B 310 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13047 Z= 0.224 Angle : 0.587 6.869 17696 Z= 0.308 Chirality : 0.046 0.210 1973 Planarity : 0.004 0.055 2259 Dihedral : 5.215 87.856 1734 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.58 % Favored : 95.04 % Rotamer: Outliers : 1.79 % Allowed : 9.11 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1571 helix: -0.01 (0.53), residues: 105 sheet: 0.22 (0.20), residues: 648 loop : -0.96 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 273 HIS 0.008 0.001 HIS A 866 PHE 0.018 0.001 PHE A1160 TYR 0.010 0.001 TYR B 66 ARG 0.004 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 1072 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: B 246 ASP cc_start: 0.7584 (m-30) cc_final: 0.7213 (m-30) REVERT: B 372 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6680 (mpp) outliers start: 25 outliers final: 4 residues processed: 157 average time/residue: 1.4921 time to fit residues: 252.9644 Evaluate side-chains 138 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 372 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 120 optimal weight: 0.0170 chunk 98 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 HIS ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A1209 GLN A1264 ASN B 76 GLN B 310 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13047 Z= 0.159 Angle : 0.541 8.353 17696 Z= 0.280 Chirality : 0.045 0.176 1973 Planarity : 0.004 0.069 2259 Dihedral : 4.613 20.575 1732 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.95 % Favored : 95.74 % Rotamer: Outliers : 1.72 % Allowed : 11.33 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1571 helix: 0.13 (0.54), residues: 105 sheet: 0.26 (0.20), residues: 644 loop : -0.92 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 273 HIS 0.007 0.001 HIS A 866 PHE 0.012 0.001 PHE A1160 TYR 0.008 0.001 TYR B 66 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.458 Fit side-chains REVERT: A 1072 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: A 1199 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5806 (tt0) REVERT: A 1413 MET cc_start: 0.6926 (mmt) cc_final: 0.6684 (mmt) REVERT: B 246 ASP cc_start: 0.7518 (m-30) cc_final: 0.7100 (m-30) REVERT: B 372 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6664 (mpp) outliers start: 24 outliers final: 6 residues processed: 158 average time/residue: 1.5793 time to fit residues: 268.9978 Evaluate side-chains 138 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 372 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 HIS ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A1209 GLN A1264 ASN B 60 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13047 Z= 0.314 Angle : 0.614 9.202 17696 Z= 0.317 Chirality : 0.047 0.196 1973 Planarity : 0.005 0.079 2259 Dihedral : 5.000 22.635 1732 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.46 % Favored : 95.23 % Rotamer: Outliers : 2.87 % Allowed : 12.55 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1571 helix: 0.04 (0.53), residues: 105 sheet: 0.15 (0.20), residues: 644 loop : -0.93 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 273 HIS 0.006 0.001 HIS A 866 PHE 0.019 0.002 PHE A1160 TYR 0.010 0.002 TYR A 189 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.364 Fit side-chains REVERT: A 1072 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: A 1199 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5834 (tt0) REVERT: A 1209 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7328 (mm-40) REVERT: A 1413 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6850 (mmt) REVERT: B 372 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6732 (mpp) outliers start: 40 outliers final: 8 residues processed: 162 average time/residue: 1.4639 time to fit residues: 256.2222 Evaluate side-chains 140 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1413 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 664 HIS ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A1209 GLN ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13047 Z= 0.321 Angle : 0.613 8.814 17696 Z= 0.317 Chirality : 0.047 0.185 1973 Planarity : 0.005 0.078 2259 Dihedral : 5.128 22.932 1732 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.77 % Favored : 94.97 % Rotamer: Outliers : 3.01 % Allowed : 13.34 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1571 helix: -0.06 (0.52), residues: 105 sheet: 0.07 (0.20), residues: 637 loop : -1.00 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 273 HIS 0.008 0.001 HIS A 664 PHE 0.015 0.002 PHE A1160 TYR 0.010 0.002 TYR A 189 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.530 Fit side-chains REVERT: A 858 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 870 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: A 902 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6485 (mtt-85) REVERT: A 1199 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5830 (tt0) REVERT: B 372 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6741 (mpp) outliers start: 42 outliers final: 11 residues processed: 160 average time/residue: 1.4325 time to fit residues: 248.0390 Evaluate side-chains 144 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 HIS ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 HIS A1209 GLN ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 ASN ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 215 ASN B 310 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13047 Z= 0.152 Angle : 0.542 8.799 17696 Z= 0.279 Chirality : 0.044 0.174 1973 Planarity : 0.004 0.072 2259 Dihedral : 4.730 20.468 1732 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.33 % Favored : 95.42 % Rotamer: Outliers : 2.22 % Allowed : 14.92 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1571 helix: 0.11 (0.53), residues: 105 sheet: 0.13 (0.20), residues: 636 loop : -0.90 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 273 HIS 0.022 0.001 HIS A 664 PHE 0.016 0.001 PHE A 185 TYR 0.010 0.001 TYR A1120 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.504 Fit side-chains REVERT: A 1199 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5798 (tt0) REVERT: A 1209 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: B 372 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6647 (mpp) outliers start: 31 outliers final: 9 residues processed: 155 average time/residue: 1.4704 time to fit residues: 246.6231 Evaluate side-chains 140 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 409 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1209 GLN B 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13047 Z= 0.173 Angle : 0.544 10.349 17696 Z= 0.279 Chirality : 0.044 0.180 1973 Planarity : 0.004 0.070 2259 Dihedral : 4.682 20.249 1732 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.97 % Rotamer: Outliers : 1.94 % Allowed : 16.00 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1571 helix: 0.14 (0.53), residues: 105 sheet: 0.14 (0.20), residues: 637 loop : -0.88 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 273 HIS 0.006 0.001 HIS A 866 PHE 0.010 0.001 PHE A1311 TYR 0.010 0.001 TYR A 655 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.435 Fit side-chains REVERT: A 63 ARG cc_start: 0.6681 (mmp80) cc_final: 0.6465 (mmp80) REVERT: A 1199 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5810 (tt0) REVERT: A 1209 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: B 372 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6686 (mpp) outliers start: 27 outliers final: 8 residues processed: 153 average time/residue: 1.4965 time to fit residues: 247.2594 Evaluate side-chains 140 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 120 optimal weight: 0.4980 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1209 GLN B 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13047 Z= 0.368 Angle : 0.649 10.241 17696 Z= 0.332 Chirality : 0.048 0.182 1973 Planarity : 0.005 0.069 2259 Dihedral : 5.193 22.950 1732 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.96 % Favored : 94.72 % Rotamer: Outliers : 2.15 % Allowed : 16.07 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1571 helix: -0.04 (0.52), residues: 105 sheet: 0.04 (0.20), residues: 637 loop : -0.98 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 273 HIS 0.006 0.001 HIS A 866 PHE 0.016 0.002 PHE B 143 TYR 0.011 0.002 TYR A 396 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.323 Fit side-chains REVERT: A 870 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: A 1199 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5820 (tt0) REVERT: A 1209 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7278 (mm-40) REVERT: B 372 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6754 (mpp) outliers start: 30 outliers final: 13 residues processed: 151 average time/residue: 1.4679 time to fit residues: 239.1604 Evaluate side-chains 141 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.0030 chunk 135 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1209 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13047 Z= 0.155 Angle : 0.552 9.852 17696 Z= 0.282 Chirality : 0.045 0.175 1973 Planarity : 0.004 0.072 2259 Dihedral : 4.763 20.701 1732 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.65 % Favored : 95.23 % Rotamer: Outliers : 1.22 % Allowed : 17.22 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1571 helix: 0.11 (0.53), residues: 105 sheet: 0.09 (0.20), residues: 644 loop : -0.88 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 273 HIS 0.006 0.001 HIS A1385 PHE 0.017 0.001 PHE A 185 TYR 0.010 0.001 TYR A1120 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.452 Fit side-chains REVERT: A 63 ARG cc_start: 0.6672 (mmp80) cc_final: 0.6422 (mmp80) REVERT: A 1199 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: A 1209 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: B 246 ASP cc_start: 0.7728 (m-30) cc_final: 0.7365 (m-30) REVERT: B 372 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6645 (mpp) outliers start: 17 outliers final: 9 residues processed: 145 average time/residue: 1.5037 time to fit residues: 235.9139 Evaluate side-chains 137 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.0040 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 0.0370 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.1072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1209 GLN A1214 GLN A1264 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13047 Z= 0.190 Angle : 0.562 9.630 17696 Z= 0.287 Chirality : 0.045 0.178 1973 Planarity : 0.004 0.070 2259 Dihedral : 4.754 20.148 1732 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.04 % Rotamer: Outliers : 1.08 % Allowed : 17.43 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1571 helix: 0.13 (0.53), residues: 105 sheet: 0.12 (0.20), residues: 625 loop : -0.91 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 273 HIS 0.006 0.001 HIS A 866 PHE 0.017 0.001 PHE B 143 TYR 0.014 0.001 TYR A 617 ARG 0.006 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3142 Ramachandran restraints generated. 1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.372 Fit side-chains REVERT: A 63 ARG cc_start: 0.6679 (mmp80) cc_final: 0.6406 (mmp80) REVERT: A 1199 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5822 (tt0) REVERT: A 1209 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: B 246 ASP cc_start: 0.7748 (m-30) cc_final: 0.7377 (m-30) REVERT: B 372 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6708 (mpp) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 1.4213 time to fit residues: 210.6710 Evaluate side-chains 135 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1199 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 129 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1209 GLN A1214 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118722 restraints weight = 16725.595| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.59 r_work: 0.3374 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13047 Z= 0.150 Angle : 0.545 10.140 17696 Z= 0.277 Chirality : 0.044 0.177 1973 Planarity : 0.004 0.070 2259 Dihedral : 4.621 20.007 1732 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.43 % Allowed : 17.36 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1571 helix: 0.18 (0.54), residues: 105 sheet: 0.16 (0.20), residues: 627 loop : -0.85 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 273 HIS 0.006 0.001 HIS A1385 PHE 0.016 0.001 PHE A 185 TYR 0.009 0.001 TYR A 655 ARG 0.006 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4669.83 seconds wall clock time: 82 minutes 49.24 seconds (4969.24 seconds total)