Starting phenix.real_space_refine on Thu Jul 31 17:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v05_20969/07_2025/6v05_20969.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v05_20969/07_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_20969/07_2025/6v05_20969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v05_20969/07_2025/6v05_20969.map" model { file = "/net/cci-nas-00/data/ceres_data/6v05_20969/07_2025/6v05_20969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v05_20969/07_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-5711/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: 9.01, per 1000 atoms: 0.66 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: 3.11 Conformation dependent library (CDL) restraints added in 1.9 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: 1.64 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: 4.46 Time building geometry restraints manager: 3.73 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: 2.890 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- 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 : 1.415 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: 0.2849 time to fit residues: 99.9782 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 : 1.400 ------------------------------------------------------------------------------- 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 = 25123.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122294 restraints weight = 54271.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122996 restraints weight = 41531.397| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- 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 : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8543 (mtm) cc_final: 0.8305 (mtp) REVERT: A 546 TRP cc_start: 0.8217 (m100) cc_final: 0.7762 (m100) REVERT: A 768 MET cc_start: 0.8020 (mtt) cc_final: 0.7790 (ttm) REVERT: A 776 TRP cc_start: 0.8049 (t60) cc_final: 0.7755 (t60) REVERT: B 128 LYS cc_start: 0.8432 (mttt) cc_final: 0.8018 (mptt) REVERT: B 215 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7966 (mmm-85) REVERT: B 333 TYR cc_start: 0.8069 (t80) cc_final: 0.7442 (t80) REVERT: F 545 MET cc_start: 0.7848 (tmm) cc_final: 0.7329 (tmm) REVERT: F 607 GLU cc_start: 0.7379 (pm20) cc_final: 0.7009 (tm-30) outliers start: 6 outliers final: 3 residues processed: 196 average time/residue: 0.2498 time to fit residues: 71.6936 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 : 1.378 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 chunk 144 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121379 restraints weight = 24985.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120936 restraints weight = 49321.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122219 restraints weight = 40075.597| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14005 Z= 0.196 Angle : 0.613 6.110 18920 Z= 0.332 Chirality : 0.046 0.153 1879 Planarity : 0.004 0.059 2579 Dihedral : 5.191 33.911 2037 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.93 % 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: -1.26 (0.19), residues: 1856 helix: 1.01 (0.27), residues: 372 sheet: -0.21 (0.19), residues: 627 loop : -2.22 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 228 HIS 0.004 0.001 HIS D 102 PHE 0.028 0.002 PHE A 197 TYR 0.024 0.002 TYR D 184 ARG 0.007 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 630) hydrogen bonds : angle 5.31168 ( 1788) SS BOND : bond 0.01333 ( 1) SS BOND : angle 2.28844 ( 2) covalent geometry : bond 0.00442 (14004) covalent geometry : angle 0.61240 (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 186 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7201 (mm-30) REVERT: A 546 TRP cc_start: 0.8071 (m100) cc_final: 0.7612 (m100) REVERT: A 650 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 776 TRP cc_start: 0.8048 (t60) cc_final: 0.7743 (t60) REVERT: B 32 MET cc_start: 0.6883 (mmm) cc_final: 0.6645 (mmm) REVERT: B 128 LYS cc_start: 0.8376 (mttt) cc_final: 0.7955 (mmtt) REVERT: B 215 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7846 (mmm-85) REVERT: B 333 TYR cc_start: 0.8082 (t80) cc_final: 0.7513 (t80) REVERT: F 607 GLU cc_start: 0.7539 (pm20) cc_final: 0.7132 (tm-30) REVERT: F 653 TYR cc_start: 0.8527 (m-80) cc_final: 0.8234 (m-10) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.2574 time to fit residues: 70.3513 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 : 1.373 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 0.3980 chunk 122 optimal weight: 50.0000 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 8 optimal weight: 50.0000 chunk 185 optimal weight: 0.0070 chunk 163 optimal weight: 0.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.145229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124716 restraints weight = 24850.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124676 restraints weight = 51013.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125380 restraints weight = 43897.134| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14005 Z= 0.119 Angle : 0.557 6.266 18920 Z= 0.297 Chirality : 0.045 0.259 1879 Planarity : 0.003 0.048 2579 Dihedral : 4.662 30.361 2037 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -0.82 (0.19), residues: 1856 helix: 1.58 (0.27), residues: 367 sheet: -0.01 (0.20), residues: 631 loop : -1.97 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.003 0.001 HIS D 102 PHE 0.027 0.001 PHE A 197 TYR 0.037 0.001 TYR D 107 ARG 0.005 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 630) hydrogen bonds : angle 4.86860 ( 1788) SS BOND : bond 0.00587 ( 1) SS BOND : angle 0.82146 ( 2) covalent geometry : bond 0.00262 (14004) covalent geometry : angle 0.55717 (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 187 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7457 (m-80) cc_final: 0.7241 (m-80) REVERT: A 368 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7204 (mm-30) REVERT: A 531 TYR cc_start: 0.8853 (t80) cc_final: 0.8626 (t80) REVERT: A 546 TRP cc_start: 0.7872 (m100) cc_final: 0.7496 (m100) REVERT: A 650 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 738 PHE cc_start: 0.8777 (p90) cc_final: 0.8475 (p90) REVERT: A 776 TRP cc_start: 0.7936 (t60) cc_final: 0.7534 (t60) REVERT: B 32 MET cc_start: 0.6977 (mmm) cc_final: 0.6706 (mmm) REVERT: B 128 LYS cc_start: 0.8278 (mttt) cc_final: 0.7935 (mmtt) REVERT: B 215 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7805 (mmm-85) REVERT: B 333 TYR cc_start: 0.7967 (t80) cc_final: 0.7475 (t80) REVERT: F 545 MET cc_start: 0.7825 (tmm) cc_final: 0.7369 (tmm) REVERT: F 607 GLU cc_start: 0.7567 (pm20) cc_final: 0.7105 (tm-30) REVERT: F 653 TYR cc_start: 0.8535 (m-80) cc_final: 0.8312 (m-10) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.2517 time to fit residues: 70.0063 Evaluate side-chains 145 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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: 0.0030 chunk 119 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 153 optimal weight: 0.1980 chunk 14 optimal weight: 60.0000 chunk 48 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.6396 ------------------------------------------------------------------------------- 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 D 82 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122633 restraints weight = 25301.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122427 restraints weight = 52613.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123180 restraints weight = 44025.115| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14005 Z= 0.172 Angle : 0.591 9.228 18920 Z= 0.316 Chirality : 0.046 0.222 1879 Planarity : 0.004 0.040 2579 Dihedral : 4.773 34.465 2037 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -0.80 (0.19), residues: 1856 helix: 1.49 (0.27), residues: 365 sheet: -0.05 (0.19), residues: 650 loop : -1.89 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 745 HIS 0.004 0.001 HIS B 64 PHE 0.023 0.001 PHE A 197 TYR 0.021 0.002 TYR D 107 ARG 0.005 0.000 ARG F 488 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 630) hydrogen bonds : angle 4.94328 ( 1788) SS BOND : bond 0.01202 ( 1) SS BOND : angle 2.45713 ( 2) covalent geometry : bond 0.00391 (14004) covalent geometry : angle 0.59031 (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 185 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 368 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7111 (mm-30) REVERT: A 546 TRP cc_start: 0.7929 (m100) cc_final: 0.7725 (m100) REVERT: A 650 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 776 TRP cc_start: 0.7950 (t60) cc_final: 0.7593 (t60) REVERT: B 128 LYS cc_start: 0.8418 (mttt) cc_final: 0.7988 (mmtt) REVERT: B 215 ARG cc_start: 0.8346 (tpp80) cc_final: 0.8001 (mmm-85) REVERT: B 333 TYR cc_start: 0.8125 (t80) cc_final: 0.7564 (t80) REVERT: D 74 ASP cc_start: 0.7041 (m-30) cc_final: 0.6827 (m-30) REVERT: E 64 MET cc_start: 0.8889 (ptp) cc_final: 0.8643 (ptp) REVERT: F 545 MET cc_start: 0.7912 (tmm) cc_final: 0.7471 (tmm) REVERT: F 607 GLU cc_start: 0.7565 (pm20) cc_final: 0.7097 (tm-30) REVERT: F 653 TYR cc_start: 0.8619 (m-80) cc_final: 0.8401 (m-10) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2462 time to fit residues: 68.3388 Evaluate side-chains 145 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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: 2.9990 chunk 161 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 153 optimal weight: 0.0060 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 144 optimal weight: 0.2980 chunk 126 optimal weight: 50.0000 chunk 129 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 D 82 ASN D 99 ASN F 523 ASN F 731 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127342 restraints weight = 25227.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128206 restraints weight = 48114.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128413 restraints weight = 34565.664| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3680 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= 0.116 Angle : 0.552 7.276 18920 Z= 0.292 Chirality : 0.044 0.247 1879 Planarity : 0.003 0.040 2579 Dihedral : 4.476 31.529 2037 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.64 (0.19), residues: 1856 helix: 1.71 (0.27), residues: 364 sheet: 0.01 (0.20), residues: 649 loop : -1.79 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.004 0.001 HIS A 196 PHE 0.024 0.001 PHE A 197 TYR 0.033 0.001 TYR D 107 ARG 0.003 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 630) hydrogen bonds : angle 4.69906 ( 1788) SS BOND : bond 0.00349 ( 1) SS BOND : angle 1.26555 ( 2) covalent geometry : bond 0.00261 (14004) covalent geometry : angle 0.55173 (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 187 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7386 (m-80) cc_final: 0.7146 (m-80) REVERT: A 650 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 741 MET cc_start: 0.7516 (mtm) cc_final: 0.7217 (mtt) REVERT: A 769 SER cc_start: 0.9168 (t) cc_final: 0.8578 (m) REVERT: A 776 TRP cc_start: 0.7837 (t60) cc_final: 0.7471 (t60) REVERT: B 128 LYS cc_start: 0.8271 (mttt) cc_final: 0.7848 (mmtt) REVERT: B 178 ASP cc_start: 0.7533 (m-30) cc_final: 0.7309 (m-30) REVERT: B 215 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7936 (mmm-85) REVERT: B 333 TYR cc_start: 0.7962 (t80) cc_final: 0.7477 (t80) REVERT: C 80 LEU cc_start: 0.8025 (tt) cc_final: 0.7092 (mt) REVERT: E 64 MET cc_start: 0.8772 (ptp) cc_final: 0.8468 (ptp) REVERT: F 545 MET cc_start: 0.7707 (tmm) cc_final: 0.7385 (tmm) REVERT: F 607 GLU cc_start: 0.7522 (pm20) cc_final: 0.7086 (tm-30) REVERT: F 653 TYR cc_start: 0.8606 (m-80) cc_final: 0.8373 (m-10) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2596 time to fit residues: 71.3918 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 : 1.482 ------------------------------------------------------------------------------- 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: 5.9990 chunk 179 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 99 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119619 restraints weight = 25448.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121363 restraints weight = 55164.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121474 restraints weight = 29727.551| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14005 Z= 0.263 Angle : 0.681 11.576 18920 Z= 0.365 Chirality : 0.049 0.302 1879 Planarity : 0.004 0.037 2579 Dihedral : 5.076 30.289 2037 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -0.83 (0.19), residues: 1856 helix: 1.40 (0.27), residues: 365 sheet: -0.13 (0.20), residues: 651 loop : -1.81 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 745 HIS 0.005 0.001 HIS B 64 PHE 0.026 0.002 PHE A 197 TYR 0.028 0.002 TYR D 205 ARG 0.006 0.001 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 630) hydrogen bonds : angle 5.13900 ( 1788) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.62496 ( 2) covalent geometry : bond 0.00604 (14004) covalent geometry : angle 0.68108 (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 181 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7712 (m-80) cc_final: 0.7482 (m-80) REVERT: A 650 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 776 TRP cc_start: 0.7871 (t60) cc_final: 0.7505 (t60) REVERT: B 128 LYS cc_start: 0.8480 (mttt) cc_final: 0.7982 (mmtt) REVERT: B 178 ASP cc_start: 0.7673 (m-30) cc_final: 0.7405 (m-30) REVERT: B 215 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8131 (mmm-85) REVERT: B 306 MET cc_start: 0.7546 (pmm) cc_final: 0.7326 (pmm) REVERT: B 333 TYR cc_start: 0.8270 (t80) cc_final: 0.7577 (t80) REVERT: D 74 ASP cc_start: 0.7254 (m-30) cc_final: 0.7031 (m-30) REVERT: F 545 MET cc_start: 0.8028 (tmm) cc_final: 0.7513 (tmm) REVERT: F 607 GLU cc_start: 0.7599 (pm20) cc_final: 0.7232 (tm-30) REVERT: F 653 TYR cc_start: 0.8581 (m-80) cc_final: 0.8375 (m-10) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2391 time to fit residues: 65.6545 Evaluate side-chains 140 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 110 optimal weight: 0.4980 chunk 122 optimal weight: 40.0000 chunk 170 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 13 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 666 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120741 restraints weight = 25116.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122585 restraints weight = 51433.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122137 restraints weight = 25382.532| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 14005 Z= 0.287 Angle : 0.720 11.846 18920 Z= 0.387 Chirality : 0.050 0.333 1879 Planarity : 0.005 0.047 2579 Dihedral : 5.371 34.121 2037 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -1.04 (0.19), residues: 1856 helix: 1.19 (0.27), residues: 364 sheet: -0.28 (0.20), residues: 627 loop : -1.86 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 745 HIS 0.006 0.001 HIS B 64 PHE 0.026 0.002 PHE A 197 TYR 0.029 0.002 TYR D 107 ARG 0.007 0.001 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 630) hydrogen bonds : angle 5.32153 ( 1788) SS BOND : bond 0.00383 ( 1) SS BOND : angle 2.55165 ( 2) covalent geometry : bond 0.00656 (14004) covalent geometry : angle 0.71943 (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 177 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.537 Fit side-chains REVERT: A 401 ASP cc_start: 0.8277 (t0) cc_final: 0.7946 (t0) REVERT: A 545 MET cc_start: 0.8425 (mtm) cc_final: 0.8187 (mtt) REVERT: A 650 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 741 MET cc_start: 0.7774 (mtm) cc_final: 0.7403 (mtt) REVERT: A 776 TRP cc_start: 0.7886 (t60) cc_final: 0.7532 (t60) REVERT: B 128 LYS cc_start: 0.8364 (mttt) cc_final: 0.7937 (mmtt) REVERT: B 178 ASP cc_start: 0.7708 (m-30) cc_final: 0.7498 (m-30) REVERT: B 215 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8198 (mmm-85) REVERT: B 306 MET cc_start: 0.7686 (pmm) cc_final: 0.7445 (pmm) REVERT: B 333 TYR cc_start: 0.8366 (t80) cc_final: 0.7642 (t80) REVERT: C 67 ILE cc_start: 0.9329 (mm) cc_final: 0.9096 (mm) REVERT: D 74 ASP cc_start: 0.7178 (m-30) cc_final: 0.6934 (m-30) REVERT: F 800 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6434 (mm-30) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2329 time to fit residues: 62.2130 Evaluate side-chains 138 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 45 optimal weight: 0.0470 chunk 77 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 368 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 99 ASN F 731 ASN F 789 GLN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124383 restraints weight = 25139.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125207 restraints weight = 50804.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125821 restraints weight = 38269.496| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14005 Z= 0.123 Angle : 0.593 8.069 18920 Z= 0.314 Chirality : 0.045 0.258 1879 Planarity : 0.004 0.040 2579 Dihedral : 4.693 34.530 2037 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.72 (0.20), residues: 1856 helix: 1.59 (0.28), residues: 362 sheet: -0.11 (0.20), residues: 640 loop : -1.71 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.003 0.001 HIS A 533 PHE 0.027 0.001 PHE A 197 TYR 0.025 0.001 TYR D 184 ARG 0.007 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 630) hydrogen bonds : angle 4.85177 ( 1788) SS BOND : bond 0.00418 ( 1) SS BOND : angle 1.74670 ( 2) covalent geometry : bond 0.00273 (14004) covalent geometry : angle 0.59320 (18918) *********************** REFINEMENT MACRO_CYCLE 9 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: 0 poor density : 184 time to evaluate : 1.457 Fit side-chains REVERT: A 197 PHE cc_start: 0.7463 (m-80) cc_final: 0.7222 (m-80) REVERT: A 650 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 651 ASN cc_start: 0.8998 (m110) cc_final: 0.8793 (m-40) REVERT: A 776 TRP cc_start: 0.7872 (t60) cc_final: 0.7528 (t60) REVERT: B 128 LYS cc_start: 0.8319 (mttt) cc_final: 0.7844 (mmtt) REVERT: B 215 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8104 (mmm-85) REVERT: B 306 MET cc_start: 0.7460 (pmm) cc_final: 0.7234 (pmm) REVERT: C 30 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.6490 (mmm-85) REVERT: F 545 MET cc_start: 0.7777 (tmm) cc_final: 0.7391 (tmm) REVERT: F 607 GLU cc_start: 0.7608 (pm20) cc_final: 0.7177 (tm-30) REVERT: F 739 TRP cc_start: 0.7253 (p-90) cc_final: 0.6910 (p-90) REVERT: F 800 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6205 (mm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2469 time to fit residues: 67.8527 Evaluate side-chains 146 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 368 GLN D 50 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120718 restraints weight = 24941.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121948 restraints weight = 51120.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122583 restraints weight = 35364.570| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14005 Z= 0.182 Angle : 0.635 9.810 18920 Z= 0.337 Chirality : 0.046 0.306 1879 Planarity : 0.004 0.050 2579 Dihedral : 4.817 33.287 2037 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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 (0.20), residues: 1856 helix: 1.52 (0.28), residues: 362 sheet: -0.11 (0.20), residues: 634 loop : -1.70 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 745 HIS 0.003 0.001 HIS B 64 PHE 0.028 0.001 PHE A 197 TYR 0.023 0.002 TYR A 230 ARG 0.009 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 630) hydrogen bonds : angle 4.94307 ( 1788) SS BOND : bond 0.00390 ( 1) SS BOND : angle 2.31043 ( 2) covalent geometry : bond 0.00416 (14004) covalent geometry : angle 0.63484 (18918) ********************** REFINEMENT MACRO_CYCLE 10 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 177 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.498 Fit side-chains REVERT: A 197 PHE cc_start: 0.7537 (m-80) cc_final: 0.7257 (m-80) REVERT: A 646 MET cc_start: 0.8105 (tpp) cc_final: 0.7755 (tpp) REVERT: A 650 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 651 ASN cc_start: 0.9083 (m110) cc_final: 0.8839 (m-40) REVERT: A 741 MET cc_start: 0.7471 (mtm) cc_final: 0.7108 (mtt) REVERT: A 776 TRP cc_start: 0.7918 (t60) cc_final: 0.7533 (t60) REVERT: A 777 MET cc_start: 0.8828 (mmm) cc_final: 0.8444 (mtp) REVERT: B 128 LYS cc_start: 0.8323 (mttt) cc_final: 0.7835 (mmtt) REVERT: B 215 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8049 (mmm-85) REVERT: B 306 MET cc_start: 0.7550 (pmm) cc_final: 0.7307 (pmm) REVERT: C 30 ARG cc_start: 0.6731 (mmm-85) cc_final: 0.6493 (mmm-85) REVERT: C 39 GLU cc_start: 0.8082 (tp30) cc_final: 0.7628 (tp30) REVERT: C 67 ILE cc_start: 0.9259 (mm) cc_final: 0.9003 (mm) REVERT: D 74 ASP cc_start: 0.7107 (m-30) cc_final: 0.6849 (m-30) REVERT: D 218 MET cc_start: 0.8242 (mtt) cc_final: 0.8004 (ttm) REVERT: F 545 MET cc_start: 0.7907 (tmm) cc_final: 0.7425 (tmm) REVERT: F 768 MET cc_start: 0.6103 (ttt) cc_final: 0.4914 (ttt) REVERT: F 800 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6417 (mm-30) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2468 time to fit residues: 65.8457 Evaluate side-chains 140 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 22 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 125 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 28 optimal weight: 0.0050 chunk 30 optimal weight: 7.9990 chunk 174 optimal weight: 0.4980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN D 50 GLN D 54 GLN F 731 ASN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128915 restraints weight = 25633.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124387 restraints weight = 27062.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122570 restraints weight = 30062.415| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14005 Z= 0.121 Angle : 0.582 8.102 18920 Z= 0.306 Chirality : 0.045 0.284 1879 Planarity : 0.004 0.061 2579 Dihedral : 4.501 31.838 2037 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -0.62 (0.20), residues: 1856 helix: 1.65 (0.28), residues: 363 sheet: -0.06 (0.20), residues: 640 loop : -1.62 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 228 HIS 0.004 0.001 HIS A 196 PHE 0.026 0.001 PHE A 197 TYR 0.025 0.001 TYR D 184 ARG 0.011 0.001 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 630) hydrogen bonds : angle 4.72900 ( 1788) SS BOND : bond 0.00449 ( 1) SS BOND : angle 1.58537 ( 2) covalent geometry : bond 0.00276 (14004) covalent geometry : angle 0.58145 (18918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.61 seconds wall clock time: 68 minutes 43.19 seconds (4123.19 seconds total)