Starting phenix.real_space_refine on Sat Jul 4 20:42:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.map" model { file = "/net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plz_13507/07_2026/7plz_13507.cif" } resolution = 3.2 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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 9 5.49 5 Mg 3 5.21 5 S 145 5.16 5 C 14825 2.51 5 N 3938 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23278 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MG': 1, '9UE': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.31, per 1000 atoms: 0.23 Number of scatterers: 23278 At special positions: 0 Unit cell: (170.5, 207.9, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 145 16.00 P 9 15.00 Mg 3 11.99 O 4355 8.00 N 3938 7.00 C 14825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 860.2 milliseconds 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5422 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 35 sheets defined 55.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.950A pdb=" N ILE A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.680A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.322A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.262A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.136A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.936A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.730A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.591A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.532A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.557A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.553A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.091A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 127 removed outlier: 4.100A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.661A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.618A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.007A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.237A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.943A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.951A pdb=" N ILE D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.624A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 192 through 207 Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.244A pdb=" N VAL D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 268 removed outlier: 4.243A pdb=" N TYR D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.112A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 4.023A pdb=" N GLN D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 Processing helix chain 'D' and resid 318 through 337 removed outlier: 3.766A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 367 through 375 Processing helix chain 'D' and resid 392 through 424 Processing helix chain 'D' and resid 448 through 480 Processing helix chain 'D' and resid 483 through 487 removed outlier: 3.609A pdb=" N LEU D 486 " --> pdb=" O PRO D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'D' and resid 504 through 515 removed outlier: 3.557A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 563 through 569 removed outlier: 3.555A pdb=" N LYS D 569 " --> pdb=" O LEU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.521A pdb=" N ILE D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 593 removed outlier: 4.131A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 635 through 653 Processing helix chain 'D' and resid 674 through 685 Processing helix chain 'D' and resid 686 through 697 removed outlier: 3.927A pdb=" N GLY D 697 " --> pdb=" O ILE D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 723 through 736 Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 754 through 792 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 127 removed outlier: 4.091A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.691A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 332 through 336 removed outlier: 4.587A pdb=" N LYS F 336 " --> pdb=" O PRO F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.005A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.269A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 67 through 79 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.006A pdb=" N PHE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 141 through 150 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 127 removed outlier: 4.098A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 127 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.673A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 260 Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 350 through 355 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 3.981A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.640A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 4.945A pdb=" N SER A 342 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 349 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 344 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.641A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.767A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.197A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 38 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 50 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 100 through 103 removed outlier: 7.655A pdb=" N VAL D 659 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE D 160 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N CYS D 661 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER D 162 " --> pdb=" O CYS D 661 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN D 157 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU D 436 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE D 159 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE D 438 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL D 161 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AB9, first strand: chain 'D' and resid 341 through 344 removed outlier: 5.026A pdb=" N SER D 342 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA D 349 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 344 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 377 through 381 Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AC3, first strand: chain 'D' and resid 700 through 703 Processing sheet with id=AC4, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.828A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD1, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AD2, first strand: chain 'E' and resid 103 through 105 Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.856A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'G' and resid 238 through 241 1216 hydrogen bonds defined for protein. 3387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5511 1.33 - 1.46: 7497 1.46 - 1.60: 10517 1.60 - 1.73: 9 1.73 - 1.86: 242 Bond restraints: 23776 Sorted by residual: bond pdb=" O3 PO4 G 403 " pdb=" P PO4 G 403 " ideal model delta sigma weight residual 1.569 1.503 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" O3 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" O4 PO4 G 403 " pdb=" P PO4 G 403 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" O4 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.26e+00 ... (remaining 23771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 31839 3.17 - 6.34: 264 6.34 - 9.51: 21 9.51 - 12.68: 9 12.68 - 15.85: 1 Bond angle restraints: 32134 Sorted by residual: angle pdb=" C20 9UE C 405 " pdb=" C8 9UE C 405 " pdb=" C7 9UE C 405 " ideal model delta sigma weight residual 118.25 102.40 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C20 9UE C 404 " pdb=" C8 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 118.25 105.83 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C20 9UE G 401 " pdb=" C8 9UE G 401 " pdb=" C7 9UE G 401 " ideal model delta sigma weight residual 118.25 106.24 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 117.91 10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C1' ADP F 401 " pdb=" C2' ADP F 401 " pdb=" C3' ADP F 401 " ideal model delta sigma weight residual 111.00 100.60 10.40 3.00e+00 1.11e-01 1.20e+01 ... (remaining 32129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14039 35.94 - 71.88: 235 71.88 - 107.82: 63 107.82 - 143.76: 13 143.76 - 179.69: 39 Dihedral angle restraints: 14389 sinusoidal: 5969 harmonic: 8420 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.73 148.27 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.88 148.12 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O1B ADP G 402 " pdb=" O3A ADP G 402 " pdb=" PB ADP G 402 " pdb=" PA ADP G 402 " ideal model delta sinusoidal sigma weight residual 300.00 152.16 147.84 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 14386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3170 0.085 - 0.171: 320 0.171 - 0.256: 8 0.256 - 0.341: 2 0.341 - 0.427: 7 Chirality restraints: 3507 Sorted by residual: chirality pdb=" C10 9UE G 401 " pdb=" C18 9UE G 401 " pdb=" C9 9UE G 401 " pdb=" N2 9UE G 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C10 9UE C 405 " pdb=" C18 9UE C 405 " pdb=" C9 9UE C 405 " pdb=" N2 9UE C 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 3504 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 147 " 0.114 9.50e-02 1.11e+02 6.57e-02 2.29e+01 pdb=" NE ARG F 147 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG F 147 " 0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG F 147 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG F 147 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 147 " -0.116 9.50e-02 1.11e+02 6.62e-02 2.29e+01 pdb=" NE ARG G 147 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG G 147 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG G 147 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG G 147 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.115 9.50e-02 1.11e+02 6.61e-02 2.28e+01 pdb=" NE ARG C 147 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.022 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 171 2.62 - 3.19: 20993 3.19 - 3.76: 34567 3.76 - 4.33: 49506 4.33 - 4.90: 82033 Nonbonded interactions: 187270 Sorted by model distance: nonbonded pdb=" OG1 THR C 202 " pdb=" OE2 GLU F 270 " model vdw 2.054 3.040 nonbonded pdb=" OE2 GLU C 270 " pdb=" OG1 THR G 202 " model vdw 2.076 3.040 nonbonded pdb=" NH2 ARG A 791 " pdb=" O GLU B 11 " model vdw 2.160 3.120 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASN F 111 " pdb=" NH1 ARG F 177 " model vdw 2.194 3.120 ... (remaining 187265 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 5 through 375) selection = (chain 'F' and resid 5 through 375) selection = (chain 'G' and resid 5 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.070 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.005 0.066 23777 Z= 0.209 Angle : 0.823 15.851 32134 Z= 0.456 Chirality : 0.053 0.427 3507 Planarity : 0.007 0.087 4110 Dihedral : 18.931 179.694 8967 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.13 (0.13), residues: 2840 helix: -1.03 (0.11), residues: 1386 sheet: -0.16 (0.24), residues: 403 loop : -0.27 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.080 0.009 ARG F 147 TYR 0.029 0.006 TYR E 141 PHE 0.021 0.002 PHE D 441 TRP 0.031 0.003 TRP G 79 HIS 0.010 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (23776) covalent geometry : angle 0.82333 / 0.46 (32134) hydrogen bonds : bond 0.15015 / 10.08 ( 1210) hydrogen bonds : angle 6.81330 / 4.78 ( 3387) Misc. bond : bond 0.00296 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 490 TYR cc_start: 0.6979 (m-80) cc_final: 0.6658 (m-80) REVERT: A 708 PHE cc_start: 0.7602 (t80) cc_final: 0.7387 (t80) REVERT: A 790 MET cc_start: 0.1893 (mmm) cc_final: 0.1682 (mmt) REVERT: B 116 LEU cc_start: 0.8970 (mt) cc_final: 0.8765 (mm) REVERT: D 305 MET cc_start: 0.7978 (tpt) cc_final: 0.7728 (tpt) REVERT: F 192 ILE cc_start: 0.8887 (tt) cc_final: 0.8685 (tp) REVERT: E 104 VAL cc_start: 0.4208 (t) cc_final: 0.3978 (t) REVERT: E 139 ILE cc_start: 0.4833 (mt) cc_final: 0.4453 (mp) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1974 time to fit residues: 136.6717 Evaluate side-chains 220 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN A 398 ASN A 406 HIS A 410 ASN A 497 ASN A 632 HIS C 128 ASN C 161 HIS C 353 GLN B 75 GLN D 191 ASN D 264 GLN D 398 ASN D 497 ASN D 638 HIS D 639 GLN D 657 HIS E 75 GLN G 40 HIS G 161 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075073 restraints weight = 48079.873| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.44 r_work: 0.2920 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23777 Z= 0.193 Angle : 0.672 8.744 32134 Z= 0.342 Chirality : 0.047 0.435 3507 Planarity : 0.004 0.048 4110 Dihedral : 19.663 178.664 3315 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.17 % Allowed : 6.54 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.98 (0.15), residues: 2840 helix: 1.01 (0.13), residues: 1405 sheet: 0.42 (0.25), residues: 396 loop : 0.47 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.021 0.002 TYR E 141 PHE 0.025 0.002 PHE B 16 TRP 0.020 0.002 TRP A 484 HIS 0.010 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (23776) covalent geometry : angle 0.67231 / 0.34 (32134) hydrogen bonds : bond 0.04552 / 2.97 ( 1210) hydrogen bonds : angle 4.78931 / 3.35 ( 3387) Misc. bond : bond 0.00244 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8432 (mmm) cc_final: 0.8113 (mmm) REVERT: A 305 MET cc_start: 0.8595 (tpp) cc_final: 0.8384 (tpp) REVERT: A 648 MET cc_start: 0.9074 (mmp) cc_final: 0.8755 (mmm) REVERT: A 790 MET cc_start: 0.2048 (mmm) cc_final: 0.1798 (mmt) REVERT: C 82 MET cc_start: 0.9292 (tpt) cc_final: 0.8896 (tpt) REVERT: B 73 MET cc_start: 0.6024 (ptm) cc_final: 0.5466 (ppp) REVERT: B 93 PHE cc_start: 0.7775 (m-80) cc_final: 0.7286 (m-80) REVERT: D 135 MET cc_start: 0.7934 (mmt) cc_final: 0.7672 (mmm) REVERT: D 305 MET cc_start: 0.8343 (tpt) cc_final: 0.7544 (tpt) REVERT: D 323 MET cc_start: 0.8452 (mmm) cc_final: 0.8247 (mmm) REVERT: D 367 ASP cc_start: 0.7636 (t0) cc_final: 0.7340 (t0) REVERT: F 157 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: G 157 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: G 354 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8188 (pt0) outliers start: 29 outliers final: 14 residues processed: 274 average time/residue: 0.1646 time to fit residues: 71.8640 Evaluate side-chains 212 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 354 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 101 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 280 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN C 353 GLN D 216 ASN D 410 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.075791 restraints weight = 47850.088| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.40 r_work: 0.2934 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23777 Z= 0.145 Angle : 0.595 10.331 32134 Z= 0.296 Chirality : 0.044 0.323 3507 Planarity : 0.004 0.040 4110 Dihedral : 17.956 170.267 3315 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.33 % Allowed : 8.07 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.60 (0.16), residues: 2840 helix: 1.57 (0.14), residues: 1391 sheet: 0.68 (0.25), residues: 400 loop : 0.72 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 110 TYR 0.018 0.001 TYR A 758 PHE 0.021 0.001 PHE D 553 TRP 0.015 0.002 TRP C 340 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (23776) covalent geometry : angle 0.59540 / 0.30 (32134) hydrogen bonds : bond 0.03854 / 2.52 ( 1210) hydrogen bonds : angle 4.41198 / 3.10 ( 3387) Misc. bond : bond 0.00159 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8432 (mmm) cc_final: 0.8125 (mmm) REVERT: A 790 MET cc_start: 0.1722 (mmm) cc_final: 0.1482 (mmt) REVERT: C 157 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: C 325 MET cc_start: 0.8835 (tpp) cc_final: 0.8499 (mmm) REVERT: B 93 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7269 (m-10) REVERT: D 135 MET cc_start: 0.7964 (mmt) cc_final: 0.7752 (mmm) REVERT: D 299 ILE cc_start: 0.7705 (mm) cc_final: 0.7229 (tt) REVERT: D 305 MET cc_start: 0.8332 (tpt) cc_final: 0.7593 (tpt) REVERT: D 323 MET cc_start: 0.8456 (mmm) cc_final: 0.8233 (mmm) outliers start: 33 outliers final: 18 residues processed: 242 average time/residue: 0.1411 time to fit residues: 54.8972 Evaluate side-chains 207 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 261 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 ASN F 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077545 restraints weight = 47915.270| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.63 r_work: 0.2903 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23777 Z= 0.173 Angle : 0.596 9.080 32134 Z= 0.296 Chirality : 0.045 0.359 3507 Planarity : 0.004 0.037 4110 Dihedral : 17.668 175.312 3315 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.61 % Allowed : 8.76 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.63 (0.16), residues: 2840 helix: 1.64 (0.14), residues: 1391 sheet: 0.62 (0.25), residues: 400 loop : 0.71 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 110 TYR 0.022 0.001 TYR A 758 PHE 0.019 0.001 PHE B 96 TRP 0.028 0.002 TRP D 484 HIS 0.009 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (23776) covalent geometry : angle 0.59624 / 0.30 (32134) hydrogen bonds : bond 0.03905 / 2.54 ( 1210) hydrogen bonds : angle 4.33398 / 3.03 ( 3387) Misc. bond : bond 0.00219 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8525 (mmm) cc_final: 0.8256 (mmm) REVERT: C 157 ASP cc_start: 0.7959 (m-30) cc_final: 0.7670 (m-30) REVERT: C 276 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8650 (tp30) REVERT: C 325 MET cc_start: 0.8847 (tpp) cc_final: 0.8450 (mmm) REVERT: B 93 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: D 135 MET cc_start: 0.7873 (mmt) cc_final: 0.7436 (mmm) REVERT: D 211 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8022 (p) REVERT: D 299 ILE cc_start: 0.7744 (mm) cc_final: 0.7247 (tt) REVERT: D 305 MET cc_start: 0.8422 (tpt) cc_final: 0.7729 (tpt) REVERT: D 323 MET cc_start: 0.8496 (mmm) cc_final: 0.8296 (mmm) REVERT: F 47 MET cc_start: 0.8507 (tpp) cc_final: 0.8031 (tpp) REVERT: E 73 MET cc_start: 0.0841 (ptt) cc_final: 0.0277 (tmm) REVERT: E 123 GLU cc_start: 0.9145 (tp30) cc_final: 0.8932 (tm-30) outliers start: 40 outliers final: 18 residues processed: 228 average time/residue: 0.1350 time to fit residues: 50.3558 Evaluate side-chains 194 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075010 restraints weight = 47552.963| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.39 r_work: 0.2916 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23777 Z= 0.146 Angle : 0.574 10.656 32134 Z= 0.282 Chirality : 0.044 0.343 3507 Planarity : 0.004 0.037 4110 Dihedral : 16.916 175.175 3315 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.45 % Allowed : 10.17 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.68 (0.16), residues: 2840 helix: 1.73 (0.14), residues: 1387 sheet: 0.62 (0.25), residues: 400 loop : 0.65 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 110 TYR 0.020 0.001 TYR A 758 PHE 0.036 0.001 PHE D 553 TRP 0.030 0.002 TRP D 484 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (23776) covalent geometry : angle 0.57396 / 0.28 (32134) hydrogen bonds : bond 0.03652 / 2.38 ( 1210) hydrogen bonds : angle 4.24513 / 2.97 ( 3387) Misc. bond : bond 0.00615 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8478 (mmm) cc_final: 0.8219 (mmm) REVERT: C 157 ASP cc_start: 0.7927 (m-30) cc_final: 0.7625 (m-30) REVERT: C 276 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (tp30) REVERT: C 325 MET cc_start: 0.8834 (tpp) cc_final: 0.8454 (mmm) REVERT: B 93 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: D 211 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7958 (p) REVERT: D 299 ILE cc_start: 0.7729 (mm) cc_final: 0.7230 (tt) REVERT: D 323 MET cc_start: 0.8487 (mmm) cc_final: 0.8283 (mmm) REVERT: F 192 ILE cc_start: 0.9205 (tp) cc_final: 0.8988 (pt) outliers start: 36 outliers final: 22 residues processed: 219 average time/residue: 0.1368 time to fit residues: 48.8436 Evaluate side-chains 198 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 162 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 125 ASN F 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.115234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073287 restraints weight = 47812.298| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.39 r_work: 0.2884 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23777 Z= 0.204 Angle : 0.608 11.262 32134 Z= 0.300 Chirality : 0.046 0.438 3507 Planarity : 0.004 0.038 4110 Dihedral : 16.851 175.938 3315 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.37 % Allowed : 10.70 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.52 (0.16), residues: 2840 helix: 1.66 (0.14), residues: 1386 sheet: 0.37 (0.26), residues: 389 loop : 0.56 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.018 0.001 TYR A 758 PHE 0.028 0.001 PHE D 553 TRP 0.018 0.002 TRP D 484 HIS 0.008 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (23776) covalent geometry : angle 0.60815 / 0.30 (32134) hydrogen bonds : bond 0.04028 / 2.62 ( 1210) hydrogen bonds : angle 4.32840 / 3.03 ( 3387) Misc. bond : bond 0.00633 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8510 (mmm) cc_final: 0.8262 (mmm) REVERT: C 157 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: C 276 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8609 (tp30) REVERT: C 325 MET cc_start: 0.8837 (tpp) cc_final: 0.8443 (mmm) REVERT: B 93 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7233 (m-10) REVERT: B 120 MET cc_start: 0.3707 (ptm) cc_final: 0.3480 (ptp) REVERT: D 211 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8085 (p) REVERT: D 299 ILE cc_start: 0.7704 (mm) cc_final: 0.7222 (tt) REVERT: F 192 ILE cc_start: 0.9234 (tp) cc_final: 0.9030 (pt) REVERT: F 283 MET cc_start: 0.8991 (mmp) cc_final: 0.8773 (mmm) REVERT: E 120 MET cc_start: 0.3203 (tmm) cc_final: 0.2610 (mmm) outliers start: 34 outliers final: 23 residues processed: 197 average time/residue: 0.1451 time to fit residues: 47.4730 Evaluate side-chains 187 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 118 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073547 restraints weight = 47638.796| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.38 r_work: 0.2886 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23777 Z= 0.193 Angle : 0.601 11.392 32134 Z= 0.296 Chirality : 0.045 0.442 3507 Planarity : 0.004 0.052 4110 Dihedral : 16.652 175.656 3315 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.61 % Allowed : 11.02 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.52 (0.16), residues: 2840 helix: 1.67 (0.14), residues: 1392 sheet: 0.44 (0.25), residues: 407 loop : 0.52 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.018 0.001 TYR A 758 PHE 0.024 0.001 PHE D 553 TRP 0.016 0.002 TRP A 484 HIS 0.007 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (23776) covalent geometry : angle 0.60117 / 0.30 (32134) hydrogen bonds : bond 0.03934 / 2.56 ( 1210) hydrogen bonds : angle 4.29805 / 3.00 ( 3387) Misc. bond : bond 0.00623 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8519 (mmm) cc_final: 0.8317 (mmm) REVERT: A 671 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7681 (t80) REVERT: C 157 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: C 276 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8618 (tp30) REVERT: C 325 MET cc_start: 0.8836 (tpp) cc_final: 0.8471 (mmm) REVERT: B 93 PHE cc_start: 0.7871 (m-80) cc_final: 0.7171 (m-80) REVERT: B 120 MET cc_start: 0.3890 (ptm) cc_final: 0.3678 (ptp) REVERT: D 211 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8121 (p) REVERT: D 299 ILE cc_start: 0.7700 (mm) cc_final: 0.7245 (tt) REVERT: F 283 MET cc_start: 0.8978 (mmp) cc_final: 0.8748 (mmm) REVERT: E 120 MET cc_start: 0.3196 (OUTLIER) cc_final: 0.2117 (tmm) outliers start: 40 outliers final: 26 residues processed: 198 average time/residue: 0.1462 time to fit residues: 48.0430 Evaluate side-chains 188 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 30 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.116345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074747 restraints weight = 47478.255| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.37 r_work: 0.2910 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23777 Z= 0.144 Angle : 0.581 10.712 32134 Z= 0.284 Chirality : 0.044 0.395 3507 Planarity : 0.003 0.045 4110 Dihedral : 16.542 174.855 3315 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.37 % Allowed : 11.06 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.59 (0.16), residues: 2840 helix: 1.73 (0.14), residues: 1396 sheet: 0.44 (0.26), residues: 407 loop : 0.54 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.018 0.001 TYR A 758 PHE 0.021 0.001 PHE D 553 TRP 0.016 0.002 TRP D 484 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (23776) covalent geometry : angle 0.58066 / 0.28 (32134) hydrogen bonds : bond 0.03591 / 2.36 ( 1210) hydrogen bonds : angle 4.21737 / 2.95 ( 3387) Misc. bond : bond 0.00468 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.7523 (t80) REVERT: C 157 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: C 276 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8605 (tp30) REVERT: C 325 MET cc_start: 0.8799 (tpp) cc_final: 0.8439 (mmm) REVERT: B 93 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: B 120 MET cc_start: 0.3745 (ptm) cc_final: 0.3465 (ptp) REVERT: D 211 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8115 (p) REVERT: D 299 ILE cc_start: 0.7704 (mm) cc_final: 0.7241 (tt) REVERT: D 323 MET cc_start: 0.8545 (mmm) cc_final: 0.8295 (mmm) REVERT: E 73 MET cc_start: 0.2066 (ptt) cc_final: 0.1132 (tmm) REVERT: E 120 MET cc_start: 0.3226 (OUTLIER) cc_final: 0.2172 (tmm) outliers start: 34 outliers final: 23 residues processed: 202 average time/residue: 0.1589 time to fit residues: 52.7074 Evaluate side-chains 190 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 276 optimal weight: 0.0470 chunk 69 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 40 HIS C 353 GLN ** F 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076168 restraints weight = 47882.484| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.39 r_work: 0.2940 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23777 Z= 0.112 Angle : 0.563 10.755 32134 Z= 0.274 Chirality : 0.043 0.372 3507 Planarity : 0.003 0.047 4110 Dihedral : 16.348 173.810 3315 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.05 % Allowed : 11.55 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.73 (0.16), residues: 2840 helix: 1.83 (0.14), residues: 1390 sheet: 0.48 (0.26), residues: 407 loop : 0.65 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 110 TYR 0.017 0.001 TYR A 758 PHE 0.019 0.001 PHE B 96 TRP 0.016 0.002 TRP D 484 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (23776) covalent geometry : angle 0.56331 / 0.27 (32134) hydrogen bonds : bond 0.03280 / 2.15 ( 1210) hydrogen bonds : angle 4.12327 / 2.89 ( 3387) Misc. bond : bond 0.00370 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7499 (t80) REVERT: C 157 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: C 276 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8629 (tp30) REVERT: C 325 MET cc_start: 0.8774 (tpp) cc_final: 0.8419 (mmm) REVERT: B 36 MET cc_start: 0.7142 (tpp) cc_final: 0.6684 (tpp) REVERT: B 93 PHE cc_start: 0.7941 (m-80) cc_final: 0.7264 (m-10) REVERT: D 211 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8100 (p) REVERT: D 299 ILE cc_start: 0.7747 (mm) cc_final: 0.7265 (tt) REVERT: D 790 MET cc_start: 0.2686 (mmm) cc_final: 0.1786 (ppp) REVERT: F 325 MET cc_start: 0.7885 (tpt) cc_final: 0.7507 (tpt) REVERT: E 73 MET cc_start: 0.1819 (ptt) cc_final: 0.0949 (tmm) REVERT: E 120 MET cc_start: 0.2710 (OUTLIER) cc_final: 0.1929 (tmm) outliers start: 26 outliers final: 18 residues processed: 203 average time/residue: 0.1570 time to fit residues: 51.9901 Evaluate side-chains 201 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 130 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074863 restraints weight = 47723.538| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.40 r_work: 0.2912 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23777 Z= 0.151 Angle : 0.601 11.466 32134 Z= 0.293 Chirality : 0.044 0.400 3507 Planarity : 0.004 0.056 4110 Dihedral : 16.452 175.357 3315 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.29 % Allowed : 11.47 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.65 (0.16), residues: 2840 helix: 1.78 (0.14), residues: 1394 sheet: 0.47 (0.26), residues: 407 loop : 0.58 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 768 TYR 0.013 0.001 TYR A 758 PHE 0.024 0.001 PHE D 553 TRP 0.016 0.002 TRP D 484 HIS 0.009 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (23776) covalent geometry : angle 0.60056 / 0.29 (32134) hydrogen bonds : bond 0.03608 / 2.38 ( 1210) hydrogen bonds : angle 4.18654 / 2.93 ( 3387) Misc. bond : bond 0.00477 / 0.25 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7516 (t80) REVERT: C 157 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: C 325 MET cc_start: 0.8781 (tpp) cc_final: 0.8400 (mmm) REVERT: B 93 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7263 (m-10) REVERT: D 211 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8117 (p) REVERT: D 299 ILE cc_start: 0.7777 (mm) cc_final: 0.7299 (tt) REVERT: D 790 MET cc_start: 0.2675 (mmm) cc_final: 0.1797 (ppp) REVERT: F 325 MET cc_start: 0.8009 (tpt) cc_final: 0.7668 (tpt) REVERT: E 73 MET cc_start: 0.1858 (ptt) cc_final: 0.0984 (tmm) REVERT: E 120 MET cc_start: 0.2953 (OUTLIER) cc_final: 0.2124 (tmm) REVERT: G 119 MET cc_start: 0.8756 (ttm) cc_final: 0.8523 (ttm) outliers start: 32 outliers final: 25 residues processed: 197 average time/residue: 0.1595 time to fit residues: 51.3013 Evaluate side-chains 197 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain G residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 132 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073735 restraints weight = 47399.178| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.38 r_work: 0.2890 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23777 Z= 0.186 Angle : 0.620 12.733 32134 Z= 0.302 Chirality : 0.045 0.436 3507 Planarity : 0.004 0.045 4110 Dihedral : 16.699 176.343 3315 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.37 % Allowed : 11.59 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.54 (0.16), residues: 2840 helix: 1.70 (0.14), residues: 1394 sheet: 0.36 (0.26), residues: 389 loop : 0.52 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 110 TYR 0.013 0.001 TYR A 758 PHE 0.024 0.001 PHE D 553 TRP 0.018 0.002 TRP D 484 HIS 0.010 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (23776) covalent geometry : angle 0.61972 / 0.30 (32134) hydrogen bonds : bond 0.03875 / 2.54 ( 1210) hydrogen bonds : angle 4.26356 / 2.98 ( 3387) Misc. bond : bond 0.00571 / 0.30 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8418.66 seconds wall clock time: 144 minutes 11.31 seconds (8651.31 seconds total)