Starting phenix.real_space_refine on Thu May 15 22:39:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v05_20969/05_2025/6v05_20969.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v05_20969/05_2025/6v05_20969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v05_20969/05_2025/6v05_20969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v05_20969/05_2025/6v05_20969.map" model { file = "/net/cci-nas-00/data/ceres_data/6v05_20969/05_2025/6v05_20969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v05_20969/05_2025/6v05_20969.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.049 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 38 5.16 5 C 8518 2.51 5 N 2407 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13705 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5429 Classifications: {'peptide': 758} Incomplete info: {'backbone_only': 138} Link IDs: {'PTRANS': 28, 'TRANS': 729} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 571 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 257 Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2522 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 329} Chain breaks: 4 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 919 Classifications: {'peptide': 181} Incomplete info: {'backbone_only': 112} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 169} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 236 Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "F" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 2 Time building chain proxies: 8.49, per 1000 atoms: 0.62 Number of scatterers: 13705 At special positions: 0 Unit cell: (145.35, 125.8, 139.4, 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 38 16.00 O 2742 8.00 N 2407 7.00 C 8518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 804 " - pdb=" SG CYS F 467 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2938 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 18 sheets defined 21.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.634A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.620A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.589A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 298 through 314 removed outlier: 4.189A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 369 removed outlier: 4.185A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.796A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.723A pdb=" N SER A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.999A pdb=" N LEU B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.942A pdb=" N GLU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.634A pdb=" N GLN C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 209 removed outlier: 3.871A pdb=" N MET C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.793A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 removed outlier: 3.785A pdb=" N GLN D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.129A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 4.025A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.798A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.619A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.606A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.742A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 553 removed outlier: 3.945A pdb=" N LEU F 549 " --> pdb=" O MET F 545 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET F 552 " --> pdb=" O TYR F 548 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.517A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.348A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 4.889A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.364A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.750A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 12.197A pdb=" N ALA A 343 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N GLY A 275 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 329 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 336 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 325 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 355 removed outlier: 5.967A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 399 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.535A pdb=" N ASP A 740 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A 445 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL F 784 " --> pdb=" O TRP F 776 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TRP F 776 " --> pdb=" O VAL F 784 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER F 786 " --> pdb=" O LEU F 774 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU F 774 " --> pdb=" O SER F 786 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA F 788 " --> pdb=" O ILE F 772 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE F 772 " --> pdb=" O ALA F 788 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA F 770 " --> pdb=" O PRO F 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR F 735 " --> pdb=" O THR F 720 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 716 " --> pdb=" O TRP F 739 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 628 " --> pdb=" O ILE F 719 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 610 " --> pdb=" O LYS F 598 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY F 590 " --> pdb=" O TYR F 618 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 567 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS F 467 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.586A pdb=" N VAL B 71 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 74 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 81 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 95 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.537A pdb=" N SER B 118 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.646A pdb=" N VAL B 216 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 230 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 218 " --> pdb=" O TRP B 228 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.911A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 259 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 291 removed outlier: 3.815A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 330 through 333 Processing sheet with id=AB5, first strand: chain 'B' and resid 372 through 374 Processing sheet with id=AB6, first strand: chain 'C' and resid 95 through 100 removed outlier: 5.334A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 133 removed outlier: 4.362A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.575A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 654 through 655 removed outlier: 7.445A pdb=" N ALA F 654 " --> pdb=" O THR F 667 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1788 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: 4.28 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4349 1.33 - 1.45: 2234 1.45 - 1.57: 7347 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 14004 Sorted by residual: bond pdb=" N ILE A 254 " pdb=" CA ILE A 254 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.31e+00 bond pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 1.455 1.493 -0.039 1.27e-02 6.20e+03 9.20e+00 bond pdb=" N GLN A 179 " pdb=" CA GLN A 179 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.23e-02 6.61e+03 8.88e+00 bond pdb=" CA TRP C 117 " pdb=" C TRP C 117 " ideal model delta sigma weight residual 1.521 1.556 -0.034 1.17e-02 7.31e+03 8.55e+00 ... (remaining 13999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 18401 1.86 - 3.71: 452 3.71 - 5.57: 58 5.57 - 7.43: 4 7.43 - 9.29: 3 Bond angle restraints: 18918 Sorted by residual: angle pdb=" CA ILE A 177 " pdb=" C ILE A 177 " pdb=" O ILE A 177 " ideal model delta sigma weight residual 122.63 118.33 4.30 8.70e-01 1.32e+00 2.44e+01 angle pdb=" N SER C 198 " pdb=" CA SER C 198 " pdb=" C SER C 198 " ideal model delta sigma weight residual 111.14 106.01 5.13 1.08e+00 8.57e-01 2.26e+01 angle pdb=" CA GLN A 178 " pdb=" C GLN A 178 " pdb=" O GLN A 178 " ideal model delta sigma weight residual 120.82 116.08 4.74 1.05e+00 9.07e-01 2.04e+01 angle pdb=" C LEU C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.84 114.46 5.38 1.25e+00 6.40e-01 1.85e+01 angle pdb=" C ILE C 67 " pdb=" N PRO C 68 " pdb=" CA PRO C 68 " ideal model delta sigma weight residual 119.84 124.94 -5.10 1.25e+00 6.40e-01 1.66e+01 ... (remaining 18913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7034 17.93 - 35.86: 682 35.86 - 53.78: 89 53.78 - 71.71: 15 71.71 - 89.64: 11 Dihedral angle restraints: 7831 sinusoidal: 2928 harmonic: 4903 Sorted by residual: dihedral pdb=" CA GLN F 466 " pdb=" C GLN F 466 " pdb=" N CYS F 467 " pdb=" CA CYS F 467 " ideal model delta harmonic sigma weight residual 180.00 143.70 36.30 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CA ALA D 83 " pdb=" C ALA D 83 " pdb=" N ASP D 84 " pdb=" CA ASP D 84 " ideal model delta harmonic sigma weight residual 180.00 144.31 35.69 0 5.00e+00 4.00e-02 5.10e+01 dihedral pdb=" CA MET B 221 " pdb=" C MET B 221 " pdb=" N GLU B 222 " pdb=" CA GLU B 222 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 7828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1514 0.062 - 0.124: 315 0.124 - 0.186: 40 0.186 - 0.249: 6 0.249 - 0.311: 4 Chirality restraints: 1879 Sorted by residual: chirality pdb=" CA ILE A 177 " pdb=" N ILE A 177 " pdb=" C ILE A 177 " pdb=" CB ILE A 177 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1876 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 173 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG D 173 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG D 173 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU D 174 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 306 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C ASP A 306 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 306 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 302 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C THR A 302 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 302 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 303 " -0.016 2.00e-02 2.50e+03 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 139 2.62 - 3.19: 11725 3.19 - 3.76: 19423 3.76 - 4.33: 25478 4.33 - 4.90: 42608 Nonbonded interactions: 99373 Sorted by model distance: nonbonded pdb=" OD1 ASP D 45 " pdb=" N GLY D 46 " model vdw 2.054 3.120 nonbonded pdb=" O GLN D 41 " pdb=" OD1 ASP D 45 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR F 531 " pdb=" OD1 ASP F 568 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR F 548 " pdb=" ND2 ASN F 606 " model vdw 2.214 3.120 ... (remaining 99368 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 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.980 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.043 14005 Z= 0.194 Angle : 0.655 9.286 18920 Z= 0.421 Chirality : 0.053 0.311 1879 Planarity : 0.004 0.054 2579 Dihedral : 13.874 89.638 4890 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 0.75 % Allowed : 4.93 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.86 (0.17), residues: 1856 helix: -1.75 (0.22), residues: 352 sheet: -0.76 (0.20), residues: 602 loop : -2.82 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 228 HIS 0.002 0.001 HIS D 102 PHE 0.011 0.001 PHE F 738 TYR 0.019 0.001 TYR D 79 ARG 0.040 0.001 ARG F 634 Details of bonding type rmsd hydrogen bonds : bond 0.23875 ( 630) hydrogen bonds : angle 8.68134 ( 1788) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.75290 ( 2) covalent geometry : bond 0.00290 (14004) covalent geometry : angle 0.65502 (18918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 TRP cc_start: 0.8277 (m100) cc_final: 0.8009 (m100) REVERT: A 748 ASN cc_start: 0.7723 (m110) cc_final: 0.7368 (t0) REVERT: B 35 LEU cc_start: 0.8705 (mm) cc_final: 0.8501 (mm) REVERT: B 128 LYS cc_start: 0.8475 (mttt) cc_final: 0.7940 (mptt) REVERT: B 215 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7720 (mmm-85) REVERT: B 337 LEU cc_start: 0.8092 (tp) cc_final: 0.7746 (mp) REVERT: C 47 LEU cc_start: 0.9123 (mt) cc_final: 0.8682 (pt) REVERT: E 64 MET cc_start: 0.8612 (ptp) cc_final: 0.8206 (ptp) REVERT: F 576 TRP cc_start: 0.8197 (t60) cc_final: 0.7982 (t60) REVERT: F 607 GLU cc_start: 0.7594 (pm20) cc_final: 0.6970 (tm-30) REVERT: F 639 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.5962 (m-30) outliers start: 10 outliers final: 2 residues processed: 251 average time/residue: 0.2885 time to fit residues: 100.8312 Evaluate side-chains 161 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 371 GLN A 411 GLN A 523 ASN A 666 ASN B 229 GLN B 301 GLN B 302 ASN B 334 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN E 33 ASN F 459 ASN F 563 ASN F 731 ASN F 748 ASN F 765 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122056 restraints weight = 25123.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122294 restraints weight = 54271.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122996 restraints weight = 41531.558| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14005 Z= 0.228 Angle : 0.655 6.834 18920 Z= 0.358 Chirality : 0.048 0.200 1879 Planarity : 0.005 0.052 2579 Dihedral : 5.496 31.021 2037 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.45 % Allowed : 8.43 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.66 (0.18), residues: 1856 helix: 0.51 (0.26), residues: 365 sheet: -0.50 (0.19), residues: 651 loop : -2.37 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 745 HIS 0.006 0.001 HIS D 102 PHE 0.031 0.002 PHE A 197 TYR 0.024 0.002 TYR A 578 ARG 0.005 0.001 ARG F 488 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 630) hydrogen bonds : angle 5.79966 ( 1788) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.57661 ( 2) covalent geometry : bond 0.00510 (14004) covalent geometry : angle 0.65517 (18918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8533 (mtm) cc_final: 0.8296 (mtp) REVERT: A 546 TRP cc_start: 0.8216 (m100) cc_final: 0.7767 (m100) REVERT: A 768 MET cc_start: 0.8010 (mtt) cc_final: 0.7796 (ttm) REVERT: A 776 TRP cc_start: 0.8047 (t60) cc_final: 0.7754 (t60) REVERT: B 128 LYS cc_start: 0.8422 (mttt) cc_final: 0.8022 (mptt) REVERT: B 215 ARG cc_start: 0.8309 (tpp80) cc_final: 0.7971 (mmm-85) REVERT: B 333 TYR cc_start: 0.8071 (t80) cc_final: 0.7446 (t80) REVERT: F 545 MET cc_start: 0.7822 (tmm) cc_final: 0.7310 (tmm) REVERT: F 607 GLU cc_start: 0.7367 (pm20) cc_final: 0.7014 (tm-30) outliers start: 6 outliers final: 3 residues processed: 196 average time/residue: 0.2524 time to fit residues: 72.0006 Evaluate side-chains 150 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 123 optimal weight: 50.0000 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 411 GLN A 666 ASN A 709 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 82 ASN F 534 ASN F 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120196 restraints weight = 25130.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121618 restraints weight = 51963.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122048 restraints weight = 34714.377| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14005 Z= 0.259 Angle : 0.669 6.483 18920 Z= 0.363 Chirality : 0.048 0.154 1879 Planarity : 0.005 0.056 2579 Dihedral : 5.463 33.911 2037 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.15 % Allowed : 6.42 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.38 (0.19), residues: 1856 helix: 0.86 (0.26), residues: 372 sheet: -0.32 (0.19), residues: 632 loop : -2.25 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 745 HIS 0.005 0.001 HIS D 102 PHE 0.029 0.002 PHE A 197 TYR 0.025 0.002 TYR A 578 ARG 0.013 0.001 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 630) hydrogen bonds : angle 5.48180 ( 1788) SS BOND : bond 0.00307 ( 1) SS BOND : angle 2.24527 ( 2) covalent geometry : bond 0.00585 (14004) covalent geometry : angle 0.66839 (18918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8355 (mtm) cc_final: 0.7925 (mtm) REVERT: A 546 TRP cc_start: 0.8212 (m100) cc_final: 0.7743 (m100) REVERT: A 650 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 776 TRP cc_start: 0.8053 (t60) cc_final: 0.7727 (t60) REVERT: B 32 MET cc_start: 0.6781 (mmm) cc_final: 0.6523 (mmm) REVERT: B 128 LYS cc_start: 0.8403 (mttt) cc_final: 0.8008 (mmtt) REVERT: B 215 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7938 (mmm-85) REVERT: B 333 TYR cc_start: 0.8244 (t80) cc_final: 0.7664 (t80) REVERT: F 607 GLU cc_start: 0.7486 (pm20) cc_final: 0.7160 (tm-30) REVERT: F 653 TYR cc_start: 0.8573 (m-80) cc_final: 0.8300 (m-10) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.2517 time to fit residues: 68.2262 Evaluate side-chains 143 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 50.0000 chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 8 optimal weight: 50.0000 chunk 185 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 666 ASN F 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126901 restraints weight = 25131.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126158 restraints weight = 43913.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126820 restraints weight = 39657.917| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14005 Z= 0.125 Angle : 0.565 6.101 18920 Z= 0.302 Chirality : 0.045 0.265 1879 Planarity : 0.003 0.047 2579 Dihedral : 4.761 30.452 2037 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.19), residues: 1856 helix: 1.50 (0.27), residues: 366 sheet: -0.16 (0.19), residues: 639 loop : -1.99 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.003 0.001 HIS D 102 PHE 0.027 0.001 PHE A 197 TYR 0.031 0.001 TYR D 107 ARG 0.005 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 630) hydrogen bonds : angle 4.94351 ( 1788) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.81292 ( 2) covalent geometry : bond 0.00276 (14004) covalent geometry : angle 0.56478 (18918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 TYR cc_start: 0.8803 (t80) cc_final: 0.8571 (t80) REVERT: A 546 TRP cc_start: 0.7898 (m100) cc_final: 0.7361 (m100) REVERT: A 650 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 768 MET cc_start: 0.8149 (ttm) cc_final: 0.7867 (ttm) REVERT: A 769 SER cc_start: 0.9161 (t) cc_final: 0.8667 (m) REVERT: A 776 TRP cc_start: 0.7935 (t60) cc_final: 0.7611 (t60) REVERT: B 32 MET cc_start: 0.6741 (mmm) cc_final: 0.6516 (mmm) REVERT: B 128 LYS cc_start: 0.8268 (mttt) cc_final: 0.7901 (mmtt) REVERT: B 178 ASP cc_start: 0.7492 (m-30) cc_final: 0.7224 (m-30) REVERT: B 215 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7899 (mmm-85) REVERT: B 333 TYR cc_start: 0.8049 (t80) cc_final: 0.7454 (t80) REVERT: F 545 MET cc_start: 0.7682 (tmm) cc_final: 0.7282 (tmm) REVERT: F 576 TRP cc_start: 0.8384 (t60) cc_final: 0.8149 (t60) REVERT: F 607 GLU cc_start: 0.7513 (pm20) cc_final: 0.7132 (tm-30) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.2554 time to fit residues: 71.6309 Evaluate side-chains 141 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 14 optimal weight: 60.0000 chunk 48 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 129 optimal weight: 0.0570 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 666 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120056 restraints weight = 25317.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120200 restraints weight = 56001.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121000 restraints weight = 46512.447| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14005 Z= 0.217 Angle : 0.634 6.617 18920 Z= 0.343 Chirality : 0.047 0.203 1879 Planarity : 0.004 0.045 2579 Dihedral : 5.075 34.695 2037 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.97 (0.19), residues: 1856 helix: 1.31 (0.27), residues: 366 sheet: -0.17 (0.19), residues: 637 loop : -1.93 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 745 HIS 0.005 0.001 HIS B 64 PHE 0.029 0.002 PHE A 197 TYR 0.024 0.002 TYR D 184 ARG 0.005 0.001 ARG F 488 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 630) hydrogen bonds : angle 5.10460 ( 1788) SS BOND : bond 0.00202 ( 1) SS BOND : angle 2.30721 ( 2) covalent geometry : bond 0.00493 (14004) covalent geometry : angle 0.63391 (18918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7784 (m-80) cc_final: 0.7560 (m-80) REVERT: A 369 MET cc_start: 0.8234 (tpp) cc_final: 0.8018 (tpp) REVERT: A 545 MET cc_start: 0.8078 (mtp) cc_final: 0.7772 (mtp) REVERT: A 546 TRP cc_start: 0.7976 (m100) cc_final: 0.7691 (m100) REVERT: A 650 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 741 MET cc_start: 0.7508 (mtm) cc_final: 0.7203 (mtt) REVERT: A 776 TRP cc_start: 0.7923 (t60) cc_final: 0.7611 (t60) REVERT: B 35 LEU cc_start: 0.8350 (mm) cc_final: 0.8118 (pp) REVERT: B 128 LYS cc_start: 0.8391 (mttt) cc_final: 0.8013 (mptt) REVERT: B 178 ASP cc_start: 0.7584 (m-30) cc_final: 0.7281 (m-30) REVERT: B 215 ARG cc_start: 0.8437 (tpp80) cc_final: 0.8157 (mmm-85) REVERT: B 333 TYR cc_start: 0.8276 (t80) cc_final: 0.7641 (t80) REVERT: B 359 GLN cc_start: 0.7094 (pt0) cc_final: 0.6786 (pt0) REVERT: D 74 ASP cc_start: 0.7132 (m-30) cc_final: 0.6749 (m-30) REVERT: F 545 MET cc_start: 0.8003 (tmm) cc_final: 0.7543 (tmm) REVERT: F 576 TRP cc_start: 0.8507 (t60) cc_final: 0.8282 (t60) REVERT: F 607 GLU cc_start: 0.7609 (pm20) cc_final: 0.7133 (tm-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2600 time to fit residues: 66.6531 Evaluate side-chains 143 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 126 optimal weight: 50.0000 chunk 129 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125478 restraints weight = 25432.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125463 restraints weight = 52512.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126172 restraints weight = 41231.002| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14005 Z= 0.119 Angle : 0.563 7.349 18920 Z= 0.298 Chirality : 0.045 0.247 1879 Planarity : 0.003 0.042 2579 Dihedral : 4.605 31.664 2037 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.74 (0.19), residues: 1856 helix: 1.67 (0.28), residues: 365 sheet: -0.09 (0.20), residues: 630 loop : -1.81 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.002 0.001 HIS A 196 PHE 0.024 0.001 PHE A 197 TYR 0.031 0.001 TYR D 107 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 630) hydrogen bonds : angle 4.78503 ( 1788) SS BOND : bond 0.00443 ( 1) SS BOND : angle 1.26759 ( 2) covalent geometry : bond 0.00265 (14004) covalent geometry : angle 0.56260 (18918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 545 MET cc_start: 0.7907 (mtp) cc_final: 0.7688 (mtp) REVERT: A 546 TRP cc_start: 0.7752 (m100) cc_final: 0.7233 (m100) REVERT: A 650 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 769 SER cc_start: 0.9154 (t) cc_final: 0.8604 (m) REVERT: A 776 TRP cc_start: 0.7858 (t60) cc_final: 0.7508 (t60) REVERT: B 128 LYS cc_start: 0.8258 (mttt) cc_final: 0.7907 (mptt) REVERT: B 333 TYR cc_start: 0.8081 (t80) cc_final: 0.7500 (t80) REVERT: F 545 MET cc_start: 0.7626 (tmm) cc_final: 0.7346 (tmm) REVERT: F 576 TRP cc_start: 0.8468 (t60) cc_final: 0.8201 (t60) REVERT: F 607 GLU cc_start: 0.7506 (pm20) cc_final: 0.7076 (tm-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2409 time to fit residues: 65.9541 Evaluate side-chains 144 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 123 optimal weight: 50.0000 chunk 69 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122815 restraints weight = 25992.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119269 restraints weight = 28518.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117566 restraints weight = 32617.150| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.083 14005 Z= 0.471 Angle : 0.897 10.377 18920 Z= 0.487 Chirality : 0.057 0.341 1879 Planarity : 0.006 0.066 2579 Dihedral : 6.215 31.188 2037 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.57 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.31 (0.19), residues: 1856 helix: 0.84 (0.27), residues: 364 sheet: -0.39 (0.20), residues: 620 loop : -2.02 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 745 HIS 0.007 0.002 HIS B 64 PHE 0.025 0.003 PHE A 197 TYR 0.038 0.003 TYR D 159 ARG 0.010 0.001 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.06343 ( 630) hydrogen bonds : angle 5.83441 ( 1788) SS BOND : bond 0.00295 ( 1) SS BOND : angle 2.05896 ( 2) covalent geometry : bond 0.01077 (14004) covalent geometry : angle 0.89704 (18918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.429 Fit side-chains REVERT: A 546 TRP cc_start: 0.8238 (m100) cc_final: 0.7887 (m100) REVERT: A 650 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 741 MET cc_start: 0.7816 (mtm) cc_final: 0.7473 (mtt) REVERT: A 776 TRP cc_start: 0.7962 (t60) cc_final: 0.7709 (t60) REVERT: B 128 LYS cc_start: 0.8464 (mttt) cc_final: 0.8139 (mptt) REVERT: B 333 TYR cc_start: 0.8569 (t80) cc_final: 0.7795 (t80) REVERT: F 545 MET cc_start: 0.7675 (tmm) cc_final: 0.7247 (tmm) REVERT: F 800 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6715 (mm-30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2419 time to fit residues: 59.4744 Evaluate side-chains 134 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 50.0000 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 118 optimal weight: 30.0000 chunk 110 optimal weight: 0.5980 chunk 122 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 40.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN A 709 ASN B 368 GLN D 69 GLN D 99 ASN F 731 ASN F 789 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123485 restraints weight = 25366.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124837 restraints weight = 51436.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124235 restraints weight = 25417.209| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14005 Z= 0.147 Angle : 0.620 8.147 18920 Z= 0.329 Chirality : 0.046 0.219 1879 Planarity : 0.004 0.041 2579 Dihedral : 5.065 36.377 2037 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.96 (0.19), residues: 1856 helix: 1.39 (0.28), residues: 365 sheet: -0.27 (0.20), residues: 606 loop : -1.81 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 228 HIS 0.003 0.001 HIS B 64 PHE 0.020 0.001 PHE F 572 TYR 0.029 0.002 TYR D 184 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 630) hydrogen bonds : angle 5.04372 ( 1788) SS BOND : bond 0.00216 ( 1) SS BOND : angle 2.45187 ( 2) covalent geometry : bond 0.00328 (14004) covalent geometry : angle 0.61902 (18918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.581 Fit side-chains REVERT: A 545 MET cc_start: 0.8083 (mtp) cc_final: 0.7881 (mtp) REVERT: A 546 TRP cc_start: 0.8008 (m100) cc_final: 0.7374 (m100) REVERT: A 776 TRP cc_start: 0.7847 (t60) cc_final: 0.7546 (t60) REVERT: B 128 LYS cc_start: 0.8287 (mttt) cc_final: 0.7841 (mptt) REVERT: C 30 ARG cc_start: 0.6801 (mmm-85) cc_final: 0.6566 (mmm-85) REVERT: C 67 ILE cc_start: 0.9224 (mm) cc_final: 0.9020 (mm) REVERT: D 109 MET cc_start: 0.7562 (mtt) cc_final: 0.6925 (mtm) REVERT: F 545 MET cc_start: 0.7791 (tmm) cc_final: 0.7543 (tmm) REVERT: F 800 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6350 (mm-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2341 time to fit residues: 62.8711 Evaluate side-chains 147 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1662 > 50: distance: 18 - 43: 12.334 distance: 21 - 40: 6.471 distance: 34 - 40: 7.269 distance: 40 - 41: 4.007 distance: 41 - 42: 20.139 distance: 41 - 44: 7.636 distance: 42 - 43: 15.249 distance: 42 - 48: 20.870 distance: 44 - 45: 5.199 distance: 45 - 46: 9.057 distance: 45 - 47: 6.665 distance: 48 - 49: 20.496 distance: 48 - 139: 12.535 distance: 49 - 50: 30.323 distance: 49 - 52: 30.168 distance: 50 - 51: 13.282 distance: 50 - 59: 27.428 distance: 52 - 53: 26.300 distance: 53 - 54: 13.049 distance: 53 - 55: 7.783 distance: 54 - 56: 20.455 distance: 55 - 57: 5.561 distance: 56 - 58: 11.138 distance: 57 - 58: 9.652 distance: 59 - 60: 31.950 distance: 60 - 61: 25.145 distance: 60 - 63: 10.711 distance: 61 - 62: 24.158 distance: 61 - 68: 9.944 distance: 63 - 64: 6.708 distance: 64 - 65: 4.135 distance: 65 - 66: 8.723 distance: 65 - 67: 8.652 distance: 68 - 69: 15.494 distance: 69 - 70: 15.294 distance: 69 - 72: 37.573 distance: 70 - 71: 33.905 distance: 70 - 73: 34.030 distance: 73 - 74: 9.575 distance: 74 - 75: 22.858 distance: 74 - 77: 26.773 distance: 75 - 76: 22.664 distance: 75 - 81: 9.410 distance: 77 - 78: 6.833 distance: 78 - 79: 55.178 distance: 78 - 80: 44.786 distance: 81 - 82: 15.579 distance: 82 - 83: 10.608 distance: 82 - 85: 19.479 distance: 83 - 84: 18.504 distance: 83 - 89: 19.496 distance: 85 - 86: 16.255 distance: 86 - 87: 19.352 distance: 86 - 88: 27.297 distance: 89 - 90: 14.818 distance: 90 - 91: 13.443 distance: 90 - 93: 11.284 distance: 91 - 92: 12.465 distance: 91 - 94: 11.678 distance: 94 - 95: 9.098 distance: 95 - 96: 11.493 distance: 95 - 98: 12.186 distance: 96 - 102: 10.276 distance: 98 - 99: 19.322 distance: 99 - 100: 12.749 distance: 99 - 101: 9.880 distance: 102 - 103: 8.879 distance: 103 - 104: 26.012 distance: 103 - 106: 9.149 distance: 104 - 105: 16.403 distance: 104 - 110: 27.748 distance: 106 - 107: 9.249 distance: 107 - 108: 16.646 distance: 107 - 109: 12.814 distance: 110 - 111: 12.381 distance: 111 - 112: 17.308 distance: 111 - 114: 6.514 distance: 112 - 113: 9.854 distance: 112 - 116: 14.219 distance: 114 - 115: 11.494