Starting phenix.real_space_refine on Thu Sep 26 17:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/09_2024/6v05_20969.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/09_2024/6v05_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/09_2024/6v05_20969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/09_2024/6v05_20969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/09_2024/6v05_20969.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/09_2024/6v05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.00, 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: 3.22 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: 1.58 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: 4.85 Time building geometry restraints manager: 3.76 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: 4.760 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.510 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- 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 14004 Z= 0.206 Angle : 0.655 9.286 18918 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 246 time to evaluate : 1.677 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: 0.2917 time to fit residues: 102.4028 Evaluate side-chains 161 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 14004 Z= 0.336 Angle : 0.655 6.834 18918 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8584 (mtm) cc_final: 0.8313 (mtp) REVERT: A 546 TRP cc_start: 0.8220 (m100) cc_final: 0.7731 (m100) REVERT: A 650 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 768 MET cc_start: 0.8063 (mtt) cc_final: 0.7756 (ttm) REVERT: A 776 TRP cc_start: 0.8035 (t60) cc_final: 0.7734 (t60) REVERT: B 128 LYS cc_start: 0.8527 (mttt) cc_final: 0.8012 (mptt) REVERT: B 215 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7902 (mmm-85) REVERT: B 278 MET cc_start: 0.8064 (ptm) cc_final: 0.7799 (ptp) REVERT: B 333 TYR cc_start: 0.7909 (t80) cc_final: 0.7287 (t80) REVERT: F 545 MET cc_start: 0.8178 (tmm) cc_final: 0.7555 (tmm) REVERT: F 607 GLU cc_start: 0.7578 (pm20) cc_final: 0.6938 (tm-30) outliers start: 6 outliers final: 3 residues processed: 196 average time/residue: 0.2549 time to fit residues: 73.3761 Evaluate side-chains 150 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 115 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 182 optimal weight: 0.0050 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14004 Z= 0.169 Angle : 0.555 7.130 18918 Z= 0.296 Chirality : 0.044 0.155 1879 Planarity : 0.004 0.062 2579 Dihedral : 4.835 33.904 2037 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.15 % Allowed : 3.81 % Favored : 96.04 % 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: -1.02 (0.19), residues: 1856 helix: 1.38 (0.27), residues: 366 sheet: -0.09 (0.20), residues: 622 loop : -2.10 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 546 HIS 0.004 0.001 HIS F 533 PHE 0.028 0.001 PHE A 197 TYR 0.026 0.001 TYR D 184 ARG 0.009 0.000 ARG A 391 *********************** 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 203 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8301 (mtm) cc_final: 0.7971 (mtm) REVERT: A 546 TRP cc_start: 0.7885 (m100) cc_final: 0.7547 (m100) REVERT: A 738 PHE cc_start: 0.8800 (p90) cc_final: 0.8395 (p90) REVERT: A 768 MET cc_start: 0.8050 (mtt) cc_final: 0.7680 (ttm) REVERT: A 776 TRP cc_start: 0.8036 (t60) cc_final: 0.7683 (t60) REVERT: B 32 MET cc_start: 0.6908 (mmm) cc_final: 0.6659 (mmm) REVERT: B 128 LYS cc_start: 0.8373 (mttt) cc_final: 0.7877 (mptt) REVERT: B 215 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7675 (mmm-85) REVERT: B 278 MET cc_start: 0.8038 (ptm) cc_final: 0.7745 (ptp) REVERT: B 306 MET cc_start: 0.7306 (pmm) cc_final: 0.7025 (pmm) REVERT: B 333 TYR cc_start: 0.7570 (t80) cc_final: 0.7097 (t80) REVERT: F 545 MET cc_start: 0.8148 (tmm) cc_final: 0.7531 (tmm) REVERT: F 607 GLU cc_start: 0.7600 (pm20) cc_final: 0.6987 (tm-30) REVERT: F 639 ASP cc_start: 0.6822 (t0) cc_final: 0.6602 (t0) REVERT: F 653 TYR cc_start: 0.8446 (m-80) cc_final: 0.8134 (m-10) REVERT: F 731 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6498 (t0) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2497 time to fit residues: 74.1520 Evaluate side-chains 149 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.4980 chunk 127 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 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 244 GLN A 666 ASN A 709 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14004 Z= 0.383 Angle : 0.670 6.603 18918 Z= 0.364 Chirality : 0.048 0.212 1879 Planarity : 0.004 0.042 2579 Dihedral : 5.214 29.923 2037 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1856 helix: 1.09 (0.27), residues: 373 sheet: -0.14 (0.19), residues: 648 loop : -2.12 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 745 HIS 0.005 0.001 HIS D 102 PHE 0.029 0.002 PHE A 197 TYR 0.047 0.002 TYR D 107 ARG 0.007 0.001 ARG A 391 *********************** 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 179 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7894 (m-80) cc_final: 0.7667 (m-80) REVERT: A 545 MET cc_start: 0.8403 (mtm) cc_final: 0.7904 (mtm) REVERT: A 546 TRP cc_start: 0.8108 (m100) cc_final: 0.7740 (m100) REVERT: A 650 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 768 MET cc_start: 0.8169 (mtt) cc_final: 0.7885 (ttm) REVERT: A 776 TRP cc_start: 0.7961 (t60) cc_final: 0.7639 (t60) REVERT: B 128 LYS cc_start: 0.8575 (mttt) cc_final: 0.8056 (mmtt) REVERT: B 215 ARG cc_start: 0.8371 (tpp80) cc_final: 0.7866 (mmm-85) REVERT: B 278 MET cc_start: 0.8091 (ptm) cc_final: 0.7889 (ptp) REVERT: B 306 MET cc_start: 0.7498 (pmm) cc_final: 0.7161 (pmm) REVERT: B 333 TYR cc_start: 0.8110 (t80) cc_final: 0.7468 (t80) REVERT: C 49 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7332 (tm-30) REVERT: E 64 MET cc_start: 0.8893 (ptp) cc_final: 0.8511 (ptp) REVERT: F 576 TRP cc_start: 0.8618 (t60) cc_final: 0.8376 (t60) REVERT: F 607 GLU cc_start: 0.7733 (pm20) cc_final: 0.7105 (tm-30) REVERT: F 639 ASP cc_start: 0.6973 (t0) cc_final: 0.6758 (t0) REVERT: F 653 TYR cc_start: 0.8584 (m-80) cc_final: 0.8309 (m-10) outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.2621 time to fit residues: 69.1546 Evaluate side-chains 141 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 40.0000 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 0 optimal weight: 70.0000 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 0.0770 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN F 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14004 Z= 0.183 Angle : 0.557 7.334 18918 Z= 0.297 Chirality : 0.045 0.275 1879 Planarity : 0.003 0.042 2579 Dihedral : 4.668 34.794 2037 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 (0.19), residues: 1856 helix: 1.65 (0.27), residues: 365 sheet: 0.02 (0.19), residues: 649 loop : -1.90 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.003 0.001 HIS A 196 PHE 0.023 0.001 PHE A 197 TYR 0.031 0.001 TYR D 107 ARG 0.004 0.000 ARG A 421 *********************** 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 193 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8373 (mtm) cc_final: 0.8077 (mtm) REVERT: A 546 TRP cc_start: 0.7833 (m100) cc_final: 0.7268 (m100) REVERT: A 650 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 741 MET cc_start: 0.7524 (mtm) cc_final: 0.7180 (mtt) REVERT: A 776 TRP cc_start: 0.7887 (t60) cc_final: 0.7495 (t60) REVERT: A 791 PHE cc_start: 0.8355 (p90) cc_final: 0.8100 (p90) REVERT: B 128 LYS cc_start: 0.8474 (mttt) cc_final: 0.7963 (mmtt) REVERT: B 215 ARG cc_start: 0.8337 (tpp80) cc_final: 0.7921 (mmm-85) REVERT: B 306 MET cc_start: 0.7421 (pmm) cc_final: 0.7039 (pmm) REVERT: B 333 TYR cc_start: 0.7802 (t80) cc_final: 0.7386 (t80) REVERT: F 545 MET cc_start: 0.8192 (tmm) cc_final: 0.7571 (tmm) REVERT: F 576 TRP cc_start: 0.8537 (t60) cc_final: 0.8304 (t60) REVERT: F 607 GLU cc_start: 0.7814 (pm20) cc_final: 0.7050 (tm-30) REVERT: F 634 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7543 (mtm110) REVERT: F 653 TYR cc_start: 0.8589 (m-80) cc_final: 0.8368 (m-10) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2589 time to fit residues: 73.0376 Evaluate side-chains 140 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 60.0000 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14004 Z= 0.461 Angle : 0.720 7.505 18918 Z= 0.388 Chirality : 0.050 0.213 1879 Planarity : 0.005 0.044 2579 Dihedral : 5.319 31.959 2037 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -1.00 (0.19), residues: 1856 helix: 1.28 (0.27), residues: 364 sheet: -0.13 (0.20), residues: 633 loop : -1.98 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 745 HIS 0.007 0.001 HIS B 64 PHE 0.029 0.002 PHE A 197 TYR 0.026 0.002 TYR D 159 ARG 0.007 0.001 ARG A 391 *********************** 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 172 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7843 (m-80) cc_final: 0.7591 (m-80) REVERT: A 545 MET cc_start: 0.8463 (mtm) cc_final: 0.8052 (mtm) REVERT: A 546 TRP cc_start: 0.8144 (m100) cc_final: 0.7790 (m100) REVERT: A 650 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 741 MET cc_start: 0.7665 (mtm) cc_final: 0.7370 (mtt) REVERT: A 776 TRP cc_start: 0.7969 (t60) cc_final: 0.7591 (t60) REVERT: B 128 LYS cc_start: 0.8564 (mttt) cc_final: 0.8082 (mptt) REVERT: B 178 ASP cc_start: 0.7697 (m-30) cc_final: 0.7413 (m-30) REVERT: B 215 ARG cc_start: 0.8523 (tpp80) cc_final: 0.8121 (mmm-85) REVERT: B 290 ILE cc_start: 0.8156 (tp) cc_final: 0.7918 (pt) REVERT: B 306 MET cc_start: 0.7559 (pmm) cc_final: 0.7202 (pmm) REVERT: B 333 TYR cc_start: 0.8275 (t80) cc_final: 0.7564 (t80) REVERT: D 54 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7795 (tt0) REVERT: D 74 ASP cc_start: 0.7392 (m-30) cc_final: 0.7075 (m-30) REVERT: E 64 MET cc_start: 0.8840 (ptp) cc_final: 0.8545 (ptp) REVERT: F 545 MET cc_start: 0.8362 (tmm) cc_final: 0.7668 (tmm) REVERT: F 607 GLU cc_start: 0.7858 (pm20) cc_final: 0.7214 (tm-30) REVERT: F 634 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7662 (mtm110) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2543 time to fit residues: 65.0024 Evaluate side-chains 140 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14004 Z= 0.194 Angle : 0.585 7.034 18918 Z= 0.310 Chirality : 0.045 0.171 1879 Planarity : 0.004 0.049 2579 Dihedral : 4.712 30.326 2037 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 1.63 (0.28), residues: 365 sheet: -0.06 (0.20), residues: 631 loop : -1.81 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.003 0.001 HIS A 196 PHE 0.024 0.001 PHE A 197 TYR 0.034 0.001 TYR D 79 ARG 0.004 0.000 ARG F 767 *********************** 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 184 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7858 (m-80) cc_final: 0.7618 (m-80) REVERT: A 545 MET cc_start: 0.8478 (mtm) cc_final: 0.8081 (mtm) REVERT: A 546 TRP cc_start: 0.7837 (m100) cc_final: 0.7317 (m100) REVERT: A 650 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 776 TRP cc_start: 0.7846 (t60) cc_final: 0.7493 (t60) REVERT: B 128 LYS cc_start: 0.8460 (mttt) cc_final: 0.8008 (tptt) REVERT: B 215 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8078 (mmm-85) REVERT: B 306 MET cc_start: 0.7380 (pmm) cc_final: 0.7157 (pmm) REVERT: B 333 TYR cc_start: 0.7946 (t80) cc_final: 0.7305 (t80) REVERT: F 501 LEU cc_start: 0.8797 (mm) cc_final: 0.8540 (tp) REVERT: F 545 MET cc_start: 0.8194 (tmm) cc_final: 0.7645 (tmm) REVERT: F 607 GLU cc_start: 0.7937 (pm20) cc_final: 0.7197 (tm-30) REVERT: F 653 TYR cc_start: 0.8606 (m-80) cc_final: 0.8379 (m-10) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2433 time to fit residues: 67.2944 Evaluate side-chains 141 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 40.0000 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** 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 495 GLN F 523 ASN F 731 ASN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14004 Z= 0.176 Angle : 0.568 7.182 18918 Z= 0.300 Chirality : 0.044 0.152 1879 Planarity : 0.004 0.044 2579 Dihedral : 4.517 32.732 2037 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 1.82 (0.28), residues: 364 sheet: -0.08 (0.20), residues: 637 loop : -1.70 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.005 0.001 HIS A 196 PHE 0.022 0.001 PHE A 197 TYR 0.029 0.001 TYR D 79 ARG 0.005 0.000 ARG F 634 *********************** 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 184 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 MET cc_start: 0.8427 (mtm) cc_final: 0.8209 (mtm) REVERT: A 546 TRP cc_start: 0.7692 (m100) cc_final: 0.7158 (m100) REVERT: A 650 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 651 ASN cc_start: 0.9061 (m110) cc_final: 0.8753 (m-40) REVERT: A 741 MET cc_start: 0.7383 (mtm) cc_final: 0.7078 (mtt) REVERT: A 769 SER cc_start: 0.9227 (t) cc_final: 0.8724 (m) REVERT: A 776 TRP cc_start: 0.7868 (t60) cc_final: 0.7471 (t60) REVERT: B 127 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 128 LYS cc_start: 0.8408 (mttt) cc_final: 0.7956 (tptt) REVERT: B 215 ARG cc_start: 0.8427 (tpp80) cc_final: 0.7995 (mmm-85) REVERT: C 39 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7961 (tp30) REVERT: F 501 LEU cc_start: 0.8772 (mm) cc_final: 0.8549 (tp) REVERT: F 545 MET cc_start: 0.8124 (tmm) cc_final: 0.7664 (tmm) REVERT: F 607 GLU cc_start: 0.8021 (pm20) cc_final: 0.7700 (tm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2484 time to fit residues: 67.4441 Evaluate side-chains 143 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 99 ASN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14004 Z= 0.218 Angle : 0.594 7.349 18918 Z= 0.314 Chirality : 0.045 0.165 1879 Planarity : 0.004 0.048 2579 Dihedral : 4.569 33.411 2037 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % 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: -0.59 (0.20), residues: 1856 helix: 1.72 (0.28), residues: 365 sheet: -0.07 (0.20), residues: 643 loop : -1.62 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 228 HIS 0.003 0.001 HIS B 64 PHE 0.027 0.001 PHE A 197 TYR 0.027 0.001 TYR D 79 ARG 0.008 0.001 ARG F 634 *********************** 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 180 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7829 (m-80) cc_final: 0.7464 (m-80) REVERT: A 546 TRP cc_start: 0.7687 (m100) cc_final: 0.7152 (m100) REVERT: A 650 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 651 ASN cc_start: 0.9041 (m110) cc_final: 0.8706 (m-40) REVERT: A 741 MET cc_start: 0.7472 (mtm) cc_final: 0.7179 (mtt) REVERT: A 769 SER cc_start: 0.9250 (t) cc_final: 0.8711 (m) REVERT: A 776 TRP cc_start: 0.7884 (t60) cc_final: 0.7506 (t60) REVERT: B 127 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8239 (mt-10) REVERT: B 128 LYS cc_start: 0.8435 (mttt) cc_final: 0.7982 (tptt) REVERT: B 215 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8082 (mmm-85) REVERT: B 368 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: C 39 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8055 (tp30) REVERT: F 501 LEU cc_start: 0.8800 (mm) cc_final: 0.8575 (tp) REVERT: F 545 MET cc_start: 0.8191 (tmm) cc_final: 0.7683 (tmm) REVERT: F 607 GLU cc_start: 0.8153 (pm20) cc_final: 0.7705 (tm-30) REVERT: F 800 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6308 (mm-30) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2362 time to fit residues: 63.5842 Evaluate side-chains 145 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 185 optimal weight: 0.4980 chunk 170 optimal weight: 9.9990 chunk 147 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14004 Z= 0.291 Angle : 0.641 7.639 18918 Z= 0.341 Chirality : 0.047 0.221 1879 Planarity : 0.004 0.044 2579 Dihedral : 4.825 33.066 2037 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.63 (0.20), residues: 1856 helix: 1.58 (0.28), residues: 364 sheet: -0.03 (0.20), residues: 640 loop : -1.65 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 745 HIS 0.004 0.001 HIS B 64 PHE 0.027 0.001 PHE A 197 TYR 0.024 0.002 TYR A 230 ARG 0.009 0.001 ARG F 634 ********************** 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 176 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7879 (m-80) cc_final: 0.7552 (m-80) REVERT: A 546 TRP cc_start: 0.7720 (m100) cc_final: 0.7072 (m100) REVERT: A 646 MET cc_start: 0.8195 (tpt) cc_final: 0.7769 (tpt) REVERT: A 650 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 651 ASN cc_start: 0.9063 (m110) cc_final: 0.8771 (m-40) REVERT: A 741 MET cc_start: 0.7522 (mtm) cc_final: 0.7202 (mtt) REVERT: A 776 TRP cc_start: 0.7880 (t60) cc_final: 0.7508 (t60) REVERT: B 127 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 128 LYS cc_start: 0.8469 (mttt) cc_final: 0.8005 (tptt) REVERT: B 215 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8153 (mmm-85) REVERT: C 39 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8218 (tp30) REVERT: D 55 LEU cc_start: 0.8305 (mm) cc_final: 0.8092 (mm) REVERT: D 74 ASP cc_start: 0.7375 (m-30) cc_final: 0.7014 (m-30) REVERT: F 501 LEU cc_start: 0.8863 (mm) cc_final: 0.8650 (tp) REVERT: F 545 MET cc_start: 0.8260 (tmm) cc_final: 0.7717 (tmm) REVERT: F 607 GLU cc_start: 0.8243 (pm20) cc_final: 0.7763 (tm-30) REVERT: F 800 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6280 (mm-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2261 time to fit residues: 60.6097 Evaluate side-chains 144 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN F 731 ASN F 789 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.144863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125484 restraints weight = 25012.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125347 restraints weight = 53118.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126090 restraints weight = 45291.248| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14004 Z= 0.170 Angle : 0.581 7.491 18918 Z= 0.304 Chirality : 0.044 0.189 1879 Planarity : 0.004 0.056 2579 Dihedral : 4.445 31.644 2037 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.49 (0.20), residues: 1856 helix: 1.72 (0.28), residues: 366 sheet: 0.01 (0.20), residues: 644 loop : -1.54 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 546 HIS 0.003 0.001 HIS B 64 PHE 0.027 0.001 PHE A 197 TYR 0.023 0.001 TYR D 184 ARG 0.013 0.001 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.85 seconds wall clock time: 47 minutes 33.82 seconds (2853.82 seconds total)