Starting phenix.real_space_refine on Wed Mar 4 12:41:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v05_20969/03_2026/6v05_20969.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v05_20969/03_2026/6v05_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_20969/03_2026/6v05_20969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v05_20969/03_2026/6v05_20969.map" model { file = "/net/cci-nas-00/data/ceres_data/6v05_20969/03_2026/6v05_20969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v05_20969/03_2026/6v05_20969.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PHE:plan': 7, 'ASP:plan': 13, 'HIS:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 10, 'ASN:plan1': 6, 'TYR:plan': 3} 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: {'GLU:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG%COO:plan': 1} 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: {'ARG:plan': 7, 'GLN:plan1': 13, 'PHE:plan': 1, 'ASP:plan': 7, 'GLU:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'TYR:plan': 5} 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: 3.21, per 1000 atoms: 0.23 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: 1.24 Conformation dependent library (CDL) restraints added in 512.2 milliseconds 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: 0.55 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: 2.54 Time building geometry restraints manager: 1.64 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: 4.200 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (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 ARG 0.040 0.001 ARG F 634 TYR 0.019 0.001 TYR D 79 PHE 0.011 0.001 PHE F 738 TRP 0.025 0.001 TRP B 228 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00290 (14004) covalent geometry : angle 0.65502 (18918) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.75290 ( 2) hydrogen bonds : bond 0.23875 ( 630) hydrogen bonds : angle 8.68134 ( 1788) *********************** 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 : 0.509 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: 0.7722 (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: 0.7941 (mptt) REVERT: B 215 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7720 (mmm-85) REVERT: B 337 LEU cc_start: 0.8093 (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: 0.8207 (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: 0.5961 (m-30) outliers start: 10 outliers final: 2 residues processed: 251 average time/residue: 0.1280 time to fit residues: 45.0078 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123538 restraints weight = 25344.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124900 restraints weight = 52750.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124873 restraints weight = 32369.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125099 restraints weight = 22549.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125484 restraints weight = 19535.266| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14005 Z= 0.223 Angle : 0.654 6.859 18920 Z= 0.357 Chirality : 0.047 0.210 1879 Planarity : 0.004 0.054 2579 Dihedral : 5.439 30.740 2037 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.37 % Allowed : 8.43 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.18), residues: 1856 helix: 0.57 (0.26), residues: 364 sheet: -0.48 (0.19), residues: 651 loop : -2.36 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 488 TYR 0.023 0.002 TYR A 578 PHE 0.031 0.002 PHE A 197 TRP 0.019 0.002 TRP B 228 HIS 0.006 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00500 (14004) covalent geometry : angle 0.65382 (18918) SS BOND : bond 0.00367 ( 1) SS BOND : angle 0.53469 ( 2) hydrogen bonds : bond 0.04853 ( 630) hydrogen bonds : angle 5.77077 ( 1788) *********************** 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 195 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8531 (tpp) cc_final: 0.8285 (tpt) REVERT: A 545 MET cc_start: 0.8536 (mtm) cc_final: 0.8311 (mtp) REVERT: A 546 TRP cc_start: 0.8183 (m100) cc_final: 0.7750 (m100) REVERT: A 768 MET cc_start: 0.8014 (mtt) cc_final: 0.7779 (ttm) REVERT: A 776 TRP cc_start: 0.8005 (t60) cc_final: 0.7711 (t60) REVERT: B 128 LYS cc_start: 0.8426 (mttt) cc_final: 0.8010 (mptt) REVERT: B 215 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7913 (mmm-85) REVERT: B 333 TYR cc_start: 0.8045 (t80) cc_final: 0.7424 (t80) REVERT: F 459 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6750 (p0) REVERT: F 545 MET cc_start: 0.7812 (tmm) cc_final: 0.7311 (tmm) REVERT: F 607 GLU cc_start: 0.7364 (pm20) cc_final: 0.7016 (tm-30) outliers start: 5 outliers final: 2 residues processed: 194 average time/residue: 0.1165 time to fit residues: 33.1012 Evaluate side-chains 149 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 147 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 14 optimal weight: 50.0000 chunk 24 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 A 709 ASN D 69 GLN D 82 ASN F 534 ASN ** F 731 ASN ** 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 = 0.3805 r_free = 0.3805 target = 0.141417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121649 restraints weight = 25385.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122990 restraints weight = 55653.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123349 restraints weight = 33175.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123329 restraints weight = 24165.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123705 restraints weight = 21634.029| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14005 Z= 0.231 Angle : 0.645 6.343 18920 Z= 0.350 Chirality : 0.047 0.151 1879 Planarity : 0.004 0.054 2579 Dihedral : 5.332 33.527 2037 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.07 % Allowed : 5.75 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1856 helix: 0.94 (0.26), residues: 372 sheet: -0.27 (0.19), residues: 654 loop : -2.23 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 391 TYR 0.023 0.002 TYR D 184 PHE 0.030 0.002 PHE A 197 TRP 0.017 0.002 TRP B 228 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00522 (14004) covalent geometry : angle 0.64468 (18918) SS BOND : bond 0.00367 ( 1) SS BOND : angle 2.24894 ( 2) hydrogen bonds : bond 0.04844 ( 630) hydrogen bonds : angle 5.39693 ( 1788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8398 (tpp) cc_final: 0.8126 (tpt) REVERT: A 545 MET cc_start: 0.8363 (mtm) cc_final: 0.7945 (mtm) REVERT: A 546 TRP cc_start: 0.8131 (m100) cc_final: 0.7684 (m100) REVERT: A 650 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 776 TRP cc_start: 0.8054 (t60) cc_final: 0.7703 (t60) REVERT: B 32 MET cc_start: 0.6824 (mmm) cc_final: 0.6584 (mmm) REVERT: B 128 LYS cc_start: 0.8386 (mttt) cc_final: 0.7942 (mmtt) REVERT: B 215 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7890 (mmm-85) REVERT: B 333 TYR cc_start: 0.8205 (t80) cc_final: 0.7593 (t80) REVERT: F 607 GLU cc_start: 0.7486 (pm20) cc_final: 0.7135 (tm-30) REVERT: F 653 TYR cc_start: 0.8557 (m-80) cc_final: 0.8267 (m-10) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1078 time to fit residues: 28.9510 Evaluate side-chains 144 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 109 optimal weight: 0.0870 chunk 168 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- 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 ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122128 restraints weight = 25539.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123168 restraints weight = 51794.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121898 restraints weight = 26045.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121906 restraints weight = 21235.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122138 restraints weight = 19021.563| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14005 Z= 0.218 Angle : 0.635 6.198 18920 Z= 0.344 Chirality : 0.048 0.297 1879 Planarity : 0.004 0.044 2579 Dihedral : 5.153 30.222 2037 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.07 % Allowed : 5.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1856 helix: 1.13 (0.27), residues: 372 sheet: -0.25 (0.19), residues: 641 loop : -2.14 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 197 TYR 0.037 0.002 TYR D 107 PHE 0.028 0.002 PHE A 197 TRP 0.018 0.002 TRP F 745 HIS 0.005 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00491 (14004) covalent geometry : angle 0.63527 (18918) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.99844 ( 2) hydrogen bonds : bond 0.04613 ( 630) hydrogen bonds : angle 5.20003 ( 1788) *********************** 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 184 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8328 (tpp) cc_final: 0.8093 (tpt) REVERT: A 545 MET cc_start: 0.8467 (mtm) cc_final: 0.8023 (mtm) REVERT: A 546 TRP cc_start: 0.8049 (m100) cc_final: 0.7606 (m100) REVERT: A 650 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 741 MET cc_start: 0.7689 (mtm) cc_final: 0.7364 (mtt) REVERT: A 769 SER cc_start: 0.9207 (t) cc_final: 0.8934 (t) REVERT: A 776 TRP cc_start: 0.7950 (t60) cc_final: 0.7633 (t60) REVERT: B 32 MET cc_start: 0.6747 (mmm) cc_final: 0.6513 (mmm) REVERT: B 128 LYS cc_start: 0.8529 (mttt) cc_final: 0.8105 (mmtt) REVERT: B 178 ASP cc_start: 0.7536 (m-30) cc_final: 0.7247 (m-30) REVERT: B 215 ARG cc_start: 0.8351 (tpp80) cc_final: 0.7996 (mmm-85) REVERT: B 333 TYR cc_start: 0.8242 (t80) cc_final: 0.7605 (t80) REVERT: E 64 MET cc_start: 0.8907 (ptp) cc_final: 0.8637 (ptp) REVERT: F 545 MET cc_start: 0.8036 (tmm) cc_final: 0.7505 (tmm) REVERT: F 576 TRP cc_start: 0.8598 (t60) cc_final: 0.8310 (t60) REVERT: F 607 GLU cc_start: 0.7596 (pm20) cc_final: 0.7162 (tm-30) REVERT: F 768 MET cc_start: 0.6554 (ttp) cc_final: 0.4644 (ttp) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.1109 time to fit residues: 30.1628 Evaluate side-chains 147 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 146 optimal weight: 0.0570 chunk 53 optimal weight: 9.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123617 restraints weight = 25404.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124491 restraints weight = 49493.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125050 restraints weight = 39267.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126374 restraints weight = 25640.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126480 restraints weight = 20721.929| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14005 Z= 0.136 Angle : 0.572 6.331 18920 Z= 0.306 Chirality : 0.045 0.213 1879 Planarity : 0.004 0.041 2579 Dihedral : 4.789 35.112 2037 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1856 helix: 1.51 (0.27), residues: 366 sheet: -0.10 (0.20), residues: 621 loop : -1.90 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 83 TYR 0.026 0.001 TYR D 184 PHE 0.028 0.001 PHE A 197 TRP 0.017 0.001 TRP B 93 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00303 (14004) covalent geometry : angle 0.57140 (18918) SS BOND : bond 0.00386 ( 1) SS BOND : angle 2.30995 ( 2) hydrogen bonds : bond 0.03905 ( 630) hydrogen bonds : angle 4.90410 ( 1788) *********************** 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 184 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7509 (m-80) cc_final: 0.7238 (m-80) REVERT: A 369 MET cc_start: 0.8366 (tpp) cc_final: 0.8039 (tpt) REVERT: A 531 TYR cc_start: 0.8834 (t80) cc_final: 0.8580 (t80) REVERT: A 545 MET cc_start: 0.8350 (mtm) cc_final: 0.8067 (mtm) REVERT: A 546 TRP cc_start: 0.7852 (m100) cc_final: 0.7325 (m100) REVERT: A 650 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7563 (tm-30) REVERT: A 776 TRP cc_start: 0.7849 (t60) cc_final: 0.7519 (t60) REVERT: B 128 LYS cc_start: 0.8419 (mttt) cc_final: 0.8026 (mmtt) REVERT: B 178 ASP cc_start: 0.7410 (m-30) cc_final: 0.7136 (m-30) REVERT: B 215 ARG cc_start: 0.8261 (tpp80) cc_final: 0.8044 (mmm-85) REVERT: B 333 TYR cc_start: 0.8071 (t80) cc_final: 0.7523 (t80) REVERT: F 545 MET cc_start: 0.7729 (tmm) cc_final: 0.7405 (tmm) REVERT: F 576 TRP cc_start: 0.8460 (t60) cc_final: 0.8223 (t60) REVERT: F 607 GLU cc_start: 0.7564 (pm20) cc_final: 0.7184 (tm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1060 time to fit residues: 28.9946 Evaluate side-chains 142 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 119 optimal weight: 30.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119564 restraints weight = 25354.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120464 restraints weight = 54663.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120945 restraints weight = 38078.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122221 restraints weight = 25156.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122282 restraints weight = 20976.943| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14005 Z= 0.246 Angle : 0.670 7.359 18920 Z= 0.362 Chirality : 0.049 0.281 1879 Planarity : 0.004 0.039 2579 Dihedral : 5.189 32.152 2037 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1856 helix: 1.30 (0.27), residues: 363 sheet: -0.20 (0.20), residues: 642 loop : -1.99 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 366 TYR 0.031 0.002 TYR D 107 PHE 0.025 0.002 PHE A 197 TRP 0.020 0.002 TRP A 745 HIS 0.005 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00560 (14004) covalent geometry : angle 0.67019 (18918) SS BOND : bond 0.00360 ( 1) SS BOND : angle 1.86610 ( 2) hydrogen bonds : bond 0.04849 ( 630) hydrogen bonds : angle 5.18694 ( 1788) *********************** 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 174 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8456 (tpp) cc_final: 0.8248 (tpt) REVERT: A 545 MET cc_start: 0.8480 (mtm) cc_final: 0.8164 (mtm) REVERT: A 546 TRP cc_start: 0.7997 (m100) cc_final: 0.7524 (m100) REVERT: A 650 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 741 MET cc_start: 0.7648 (mtm) cc_final: 0.7286 (mtt) REVERT: A 776 TRP cc_start: 0.7854 (t60) cc_final: 0.7531 (t60) REVERT: B 128 LYS cc_start: 0.8459 (mttt) cc_final: 0.8069 (mptt) REVERT: B 178 ASP cc_start: 0.7462 (m-30) cc_final: 0.7258 (m-30) REVERT: B 215 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8160 (mmm-85) REVERT: B 333 TYR cc_start: 0.8333 (t80) cc_final: 0.7611 (t80) REVERT: F 545 MET cc_start: 0.7950 (tmm) cc_final: 0.7477 (tmm) REVERT: F 576 TRP cc_start: 0.8596 (t60) cc_final: 0.8362 (t60) REVERT: F 634 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7633 (mtm110) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1060 time to fit residues: 27.7157 Evaluate side-chains 139 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 142 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 99 ASN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123349 restraints weight = 25352.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125012 restraints weight = 52843.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125287 restraints weight = 31005.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125299 restraints weight = 22520.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125694 restraints weight = 20254.310| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4011 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= 0.138 Angle : 0.589 8.108 18920 Z= 0.313 Chirality : 0.045 0.272 1879 Planarity : 0.004 0.049 2579 Dihedral : 4.784 30.556 2037 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 1856 helix: 1.49 (0.28), residues: 364 sheet: -0.15 (0.20), residues: 637 loop : -1.82 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.040 0.002 TYR D 79 PHE 0.027 0.001 PHE A 197 TRP 0.018 0.001 TRP B 93 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00309 (14004) covalent geometry : angle 0.58897 (18918) SS BOND : bond 0.00351 ( 1) SS BOND : angle 0.97365 ( 2) hydrogen bonds : bond 0.04003 ( 630) hydrogen bonds : angle 4.91446 ( 1788) *********************** 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 185 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7668 (m-80) cc_final: 0.7358 (m-80) REVERT: A 369 MET cc_start: 0.8437 (tpp) cc_final: 0.8110 (tpt) REVERT: A 545 MET cc_start: 0.8424 (mtm) cc_final: 0.8156 (mtm) REVERT: A 546 TRP cc_start: 0.7805 (m100) cc_final: 0.7276 (m100) REVERT: A 650 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 738 PHE cc_start: 0.8774 (p90) cc_final: 0.8505 (p90) REVERT: A 776 TRP cc_start: 0.7833 (t60) cc_final: 0.7509 (t60) REVERT: B 128 LYS cc_start: 0.8379 (mttt) cc_final: 0.8011 (tptt) REVERT: B 215 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8164 (mmm-85) REVERT: B 333 TYR cc_start: 0.8136 (t80) cc_final: 0.7488 (t80) REVERT: F 545 MET cc_start: 0.7823 (tmm) cc_final: 0.7511 (tmm) REVERT: F 576 TRP cc_start: 0.8537 (t60) cc_final: 0.8304 (t60) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1062 time to fit residues: 29.7450 Evaluate side-chains 144 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 302 ASN B 368 GLN F 523 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 = 0.3815 r_free = 0.3815 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121340 restraints weight = 25129.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121560 restraints weight = 52003.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122238 restraints weight = 43839.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124192 restraints weight = 28340.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124243 restraints weight = 20407.821| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14005 Z= 0.145 Angle : 0.588 7.792 18920 Z= 0.313 Chirality : 0.045 0.294 1879 Planarity : 0.004 0.044 2579 Dihedral : 4.681 34.608 2037 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.07 % Allowed : 1.42 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1856 helix: 1.61 (0.28), residues: 364 sheet: -0.08 (0.20), residues: 651 loop : -1.71 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.028 0.002 TYR D 79 PHE 0.026 0.001 PHE A 197 TRP 0.017 0.001 TRP B 93 HIS 0.003 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00327 (14004) covalent geometry : angle 0.58800 (18918) SS BOND : bond 0.00533 ( 1) SS BOND : angle 1.75977 ( 2) hydrogen bonds : bond 0.04015 ( 630) hydrogen bonds : angle 4.81853 ( 1788) *********************** 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 182 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7659 (m-80) cc_final: 0.7421 (m-80) REVERT: A 545 MET cc_start: 0.8431 (mtm) cc_final: 0.8054 (mtm) REVERT: A 546 TRP cc_start: 0.7730 (m100) cc_final: 0.7162 (m100) REVERT: A 646 MET cc_start: 0.8000 (tpt) cc_final: 0.7733 (tpt) REVERT: A 650 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 738 PHE cc_start: 0.8786 (p90) cc_final: 0.8493 (p90) REVERT: A 776 TRP cc_start: 0.7853 (t60) cc_final: 0.7483 (t60) REVERT: B 128 LYS cc_start: 0.8362 (mttt) cc_final: 0.7984 (tptt) REVERT: B 215 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8164 (mmm-85) REVERT: B 263 TYR cc_start: 0.5403 (p90) cc_final: 0.5153 (p90) REVERT: B 333 TYR cc_start: 0.8152 (t80) cc_final: 0.7463 (t80) REVERT: C 67 ILE cc_start: 0.9204 (mm) cc_final: 0.8944 (mm) REVERT: D 82 ASN cc_start: 0.7938 (t0) cc_final: 0.7727 (t0) REVERT: F 545 MET cc_start: 0.7888 (tmm) cc_final: 0.7526 (tmm) REVERT: F 576 TRP cc_start: 0.8521 (t60) cc_final: 0.8288 (t60) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1059 time to fit residues: 29.0274 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 : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 83 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 154 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 122 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 302 ASN B 368 GLN D 54 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 789 GLN ** F 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126519 restraints weight = 25545.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127817 restraints weight = 47596.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128493 restraints weight = 33468.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128480 restraints weight = 25931.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128825 restraints weight = 21972.922| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14005 Z= 0.107 Angle : 0.571 7.793 18920 Z= 0.301 Chirality : 0.045 0.261 1879 Planarity : 0.004 0.049 2579 Dihedral : 4.429 32.362 2037 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1856 helix: 1.70 (0.28), residues: 365 sheet: -0.00 (0.20), residues: 644 loop : -1.62 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.032 0.001 TYR D 107 PHE 0.026 0.001 PHE A 197 TRP 0.017 0.001 TRP B 93 HIS 0.002 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00238 (14004) covalent geometry : angle 0.57040 (18918) SS BOND : bond 0.00561 ( 1) SS BOND : angle 1.73999 ( 2) hydrogen bonds : bond 0.03548 ( 630) hydrogen bonds : angle 4.66898 ( 1788) *********************** 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 186 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 546 TRP cc_start: 0.7568 (m100) cc_final: 0.7059 (m100) REVERT: A 650 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 651 ASN cc_start: 0.8962 (m110) cc_final: 0.8709 (m-40) REVERT: A 738 PHE cc_start: 0.8698 (p90) cc_final: 0.8387 (p90) REVERT: A 769 SER cc_start: 0.9127 (t) cc_final: 0.8511 (m) REVERT: A 776 TRP cc_start: 0.7772 (t60) cc_final: 0.7438 (t60) REVERT: B 128 LYS cc_start: 0.8215 (mttt) cc_final: 0.7800 (mmtm) REVERT: B 333 TYR cc_start: 0.8020 (t80) cc_final: 0.7382 (t80) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1027 time to fit residues: 29.1029 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 : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 666 ASN A 709 ASN B 302 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127228 restraints weight = 25066.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128422 restraints weight = 47397.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128902 restraints weight = 35690.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130160 restraints weight = 24109.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130226 restraints weight = 20371.914| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14005 Z= 0.103 Angle : 0.571 7.509 18920 Z= 0.299 Chirality : 0.044 0.265 1879 Planarity : 0.004 0.050 2579 Dihedral : 4.323 30.761 2037 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1856 helix: 1.83 (0.28), residues: 363 sheet: 0.05 (0.20), residues: 639 loop : -1.54 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.032 0.001 TYR D 107 PHE 0.027 0.001 PHE A 197 TRP 0.025 0.001 TRP B 228 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00228 (14004) covalent geometry : angle 0.57078 (18918) SS BOND : bond 0.00606 ( 1) SS BOND : angle 1.39112 ( 2) hydrogen bonds : bond 0.03395 ( 630) hydrogen bonds : angle 4.57941 ( 1788) ********************** 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 187 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7268 (m-80) cc_final: 0.7012 (m-80) REVERT: A 546 TRP cc_start: 0.7556 (m100) cc_final: 0.7056 (m100) REVERT: A 650 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 651 ASN cc_start: 0.8913 (m110) cc_final: 0.8656 (m-40) REVERT: A 738 PHE cc_start: 0.8681 (p90) cc_final: 0.8472 (p90) REVERT: A 741 MET cc_start: 0.7347 (mtm) cc_final: 0.6986 (mtt) REVERT: A 769 SER cc_start: 0.9103 (t) cc_final: 0.8497 (m) REVERT: A 776 TRP cc_start: 0.7780 (t60) cc_final: 0.7438 (t60) REVERT: B 128 LYS cc_start: 0.8178 (mttt) cc_final: 0.7673 (mmtm) REVERT: B 333 TYR cc_start: 0.7898 (t80) cc_final: 0.7258 (t80) REVERT: F 800 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6284 (mm-30) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1013 time to fit residues: 29.1184 Evaluate side-chains 148 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 83 optimal weight: 0.6980 chunk 125 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 174 optimal weight: 0.0050 chunk 106 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 302 ASN C 87 GLN ** D 47 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127838 restraints weight = 25128.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129749 restraints weight = 45997.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129585 restraints weight = 27815.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129413 restraints weight = 24730.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129756 restraints weight = 20176.473| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14005 Z= 0.108 Angle : 0.566 9.534 18920 Z= 0.296 Chirality : 0.044 0.268 1879 Planarity : 0.004 0.057 2579 Dihedral : 4.238 29.723 2037 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1856 helix: 1.90 (0.28), residues: 363 sheet: 0.09 (0.20), residues: 638 loop : -1.45 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 97 TYR 0.025 0.001 TYR D 184 PHE 0.029 0.001 PHE A 197 TRP 0.024 0.001 TRP B 228 HIS 0.002 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00243 (14004) covalent geometry : angle 0.56594 (18918) SS BOND : bond 0.00596 ( 1) SS BOND : angle 1.41705 ( 2) hydrogen bonds : bond 0.03391 ( 630) hydrogen bonds : angle 4.50420 ( 1788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.20 seconds wall clock time: 32 minutes 33.48 seconds (1953.48 seconds total)