Starting phenix.real_space_refine on Thu Mar 5 15:17:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plz_13507/03_2026/7plz_13507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plz_13507/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7plz_13507/03_2026/7plz_13507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plz_13507/03_2026/7plz_13507.map" model { file = "/net/cci-nas-00/data/ceres_data/7plz_13507/03_2026/7plz_13507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plz_13507/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.25, 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: 1.86 Conformation dependent library (CDL) restraints added in 901.0 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: 0.74 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: 4.68 Time building geometry restraints manager: 2.48 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.200 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 covalent geometry : bond 0.00450 (23776) covalent geometry : angle 0.82333 (32134) hydrogen bonds : bond 0.15015 ( 1210) hydrogen bonds : angle 6.81330 ( 3387) Misc. bond : bond 0.00296 ( 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 : 0.883 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: 0.6657 (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: 0.1681 (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: 0.4001 (t) REVERT: E 139 ILE cc_start: 0.4833 (mt) cc_final: 0.4429 (mp) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1860 time to fit residues: 128.3745 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 : 0.799 ------------------------------------------------------------------------------- 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: 0.8980 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: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.117009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075177 restraints weight = 48062.984| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.41 r_work: 0.2922 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23777 Z= 0.192 Angle : 0.672 8.687 32134 Z= 0.342 Chirality : 0.047 0.446 3507 Planarity : 0.005 0.047 4110 Dihedral : 19.718 179.312 3315 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.17 % Allowed : 6.62 % Favored : 92.21 % 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: 1.00 (0.15), residues: 2840 helix: 1.04 (0.14), residues: 1403 sheet: 0.42 (0.25), residues: 396 loop : 0.46 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.020 0.002 TYR E 141 PHE 0.024 0.002 PHE B 16 TRP 0.020 0.002 TRP A 484 HIS 0.009 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00446 (23776) covalent geometry : angle 0.67241 (32134) hydrogen bonds : bond 0.04455 ( 1210) hydrogen bonds : angle 4.77552 ( 3387) Misc. bond : bond 0.00251 ( 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 282 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.979 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: 0.8416 (mmm) cc_final: 0.8085 (mmm) REVERT: A 305 MET cc_start: 0.8599 (tpp) cc_final: 0.8380 (tpp) REVERT: A 648 MET cc_start: 0.9091 (mmp) cc_final: 0.8782 (mmm) REVERT: A 790 MET cc_start: 0.2031 (mmm) cc_final: 0.1787 (mmt) REVERT: C 82 MET cc_start: 0.9293 (tpt) cc_final: 0.8893 (tpt) REVERT: B 73 MET cc_start: 0.6120 (ptm) cc_final: 0.5610 (ppp) REVERT: B 93 PHE cc_start: 0.7777 (m-80) cc_final: 0.7267 (m-10) REVERT: D 135 MET cc_start: 0.7904 (mmt) cc_final: 0.7643 (mmm) REVERT: D 255 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 305 MET cc_start: 0.8354 (tpt) cc_final: 0.7542 (tpt) REVERT: D 367 ASP cc_start: 0.7658 (t0) cc_final: 0.7359 (t0) REVERT: F 82 MET cc_start: 0.8990 (tpp) cc_final: 0.8514 (tpt) REVERT: F 157 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: G 157 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7022 (m-30) outliers start: 29 outliers final: 15 residues processed: 271 average time/residue: 0.1498 time to fit residues: 64.5342 Evaluate side-chains 215 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 101 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 280 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 234 optimal weight: 0.3980 chunk 188 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3791 r_free = 0.3791 target = 0.118115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076621 restraints weight = 47879.349| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.41 r_work: 0.2951 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23777 Z= 0.128 Angle : 0.584 10.737 32134 Z= 0.289 Chirality : 0.044 0.303 3507 Planarity : 0.004 0.041 4110 Dihedral : 17.996 171.684 3315 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.05 % Allowed : 8.40 % Favored : 90.55 % 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: 1.66 (0.16), residues: 2840 helix: 1.64 (0.14), residues: 1385 sheet: 0.69 (0.25), residues: 400 loop : 0.73 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 110 TYR 0.019 0.001 TYR A 758 PHE 0.022 0.001 PHE D 553 TRP 0.016 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00291 (23776) covalent geometry : angle 0.58411 (32134) hydrogen bonds : bond 0.03705 ( 1210) hydrogen bonds : angle 4.37655 ( 3387) Misc. bond : bond 0.00134 ( 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 257 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8454 (mmm) cc_final: 0.7778 (mmm) REVERT: A 305 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8402 (tpp) REVERT: A 790 MET cc_start: 0.1731 (mmm) cc_final: 0.1490 (mmt) REVERT: C 157 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: C 325 MET cc_start: 0.8821 (tpp) cc_final: 0.8483 (mmm) REVERT: B 93 PHE cc_start: 0.7786 (m-80) cc_final: 0.7267 (m-10) REVERT: D 255 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8212 (tm-30) REVERT: D 299 ILE cc_start: 0.7706 (mm) cc_final: 0.7222 (tt) REVERT: D 305 MET cc_start: 0.8318 (tpt) cc_final: 0.7624 (tpt) REVERT: F 157 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: E 73 MET cc_start: 0.2101 (ptt) cc_final: 0.1272 (tmm) REVERT: E 120 MET cc_start: 0.2473 (ttm) cc_final: 0.1832 (tmm) outliers start: 26 outliers final: 16 residues processed: 248 average time/residue: 0.1536 time to fit residues: 61.4887 Evaluate side-chains 205 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE 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 310 GLN Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain F residue 157 ASP 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 Chi-restraints excluded: chain G residue 354 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 261 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN C 275 HIS D 88 ASN F 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.115483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076740 restraints weight = 47877.859| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.62 r_work: 0.2882 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23777 Z= 0.213 Angle : 0.627 8.916 32134 Z= 0.312 Chirality : 0.046 0.398 3507 Planarity : 0.004 0.036 4110 Dihedral : 17.815 176.646 3315 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.82 % Allowed : 8.96 % Favored : 89.22 % 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: 1.55 (0.16), residues: 2840 helix: 1.58 (0.14), residues: 1391 sheet: 0.60 (0.25), residues: 400 loop : 0.63 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 343 TYR 0.022 0.002 TYR A 758 PHE 0.030 0.002 PHE D 553 TRP 0.029 0.002 TRP D 484 HIS 0.008 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00504 (23776) covalent geometry : angle 0.62740 (32134) hydrogen bonds : bond 0.04210 ( 1210) hydrogen bonds : angle 4.40347 ( 3387) Misc. bond : bond 0.00279 ( 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: 45 poor density : 194 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8216 (mmm) cc_final: 0.7956 (mmm) REVERT: A 305 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8480 (tpp) REVERT: C 157 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: C 259 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: C 276 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: C 325 MET cc_start: 0.8866 (tpp) cc_final: 0.8470 (mmm) REVERT: B 73 MET cc_start: 0.5505 (ppp) cc_final: 0.5036 (ppp) REVERT: B 93 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7156 (m-10) REVERT: D 135 MET cc_start: 0.7722 (mmm) cc_final: 0.7500 (mtt) REVERT: D 255 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 299 ILE cc_start: 0.7700 (mm) cc_final: 0.7207 (tt) REVERT: D 305 MET cc_start: 0.8457 (tpt) cc_final: 0.7674 (tpt) REVERT: D 323 MET cc_start: 0.8616 (mmm) cc_final: 0.8305 (mmm) REVERT: F 47 MET cc_start: 0.8509 (tpp) cc_final: 0.7962 (tpp) REVERT: E 120 MET cc_start: 0.2445 (ttm) cc_final: 0.1825 (tmm) outliers start: 45 outliers final: 21 residues processed: 225 average time/residue: 0.1437 time to fit residues: 53.5414 Evaluate side-chains 198 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 GLU 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 245 GLU Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 439 TYR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 261 optimal weight: 0.4980 chunk 143 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.117069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075513 restraints weight = 47441.527| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.37 r_work: 0.2931 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23777 Z= 0.126 Angle : 0.560 9.584 32134 Z= 0.275 Chirality : 0.043 0.318 3507 Planarity : 0.003 0.038 4110 Dihedral : 16.824 173.453 3315 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.41 % Allowed : 9.97 % Favored : 88.62 % 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: 1.70 (0.16), residues: 2840 helix: 1.79 (0.14), residues: 1383 sheet: 0.60 (0.25), residues: 400 loop : 0.61 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 110 TYR 0.020 0.001 TYR A 758 PHE 0.019 0.001 PHE D 553 TRP 0.032 0.002 TRP D 484 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00289 (23776) covalent geometry : angle 0.55973 (32134) hydrogen bonds : bond 0.03483 ( 1210) hydrogen bonds : angle 4.20952 ( 3387) Misc. bond : bond 0.00434 ( 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 232 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8112 (mmm) cc_final: 0.7896 (mmm) REVERT: A 305 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8596 (tpp) REVERT: C 157 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: C 276 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8576 (tp30) REVERT: C 325 MET cc_start: 0.8821 (tpp) cc_final: 0.8459 (mmm) REVERT: B 93 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: D 211 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7696 (p) REVERT: D 255 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 299 ILE cc_start: 0.7727 (mm) cc_final: 0.7198 (tt) REVERT: D 323 MET cc_start: 0.8536 (mmm) cc_final: 0.8234 (mmm) REVERT: E 73 MET cc_start: 0.1943 (ptt) cc_final: 0.0886 (tmm) REVERT: E 120 MET cc_start: 0.2962 (ttm) cc_final: 0.1992 (tmm) outliers start: 35 outliers final: 18 residues processed: 222 average time/residue: 0.1540 time to fit residues: 55.4683 Evaluate side-chains 198 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 503 MET 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 211 THR Chi-restraints excluded: chain D residue 245 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 162 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 144 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS C 353 GLN D 125 ASN F 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076021 restraints weight = 47460.521| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.62 r_work: 0.2868 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23777 Z= 0.210 Angle : 0.612 9.693 32134 Z= 0.302 Chirality : 0.046 0.451 3507 Planarity : 0.004 0.038 4110 Dihedral : 16.873 177.272 3315 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.45 % Allowed : 10.70 % Favored : 87.85 % 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: 1.56 (0.16), residues: 2840 helix: 1.67 (0.14), residues: 1398 sheet: 0.51 (0.25), residues: 404 loop : 0.55 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 110 TYR 0.018 0.001 TYR A 758 PHE 0.039 0.001 PHE D 553 TRP 0.017 0.002 TRP D 484 HIS 0.008 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00496 (23776) covalent geometry : angle 0.61191 (32134) hydrogen bonds : bond 0.04068 ( 1210) hydrogen bonds : angle 4.31415 ( 3387) Misc. bond : bond 0.00658 ( 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 216 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8217 (mmm) cc_final: 0.7936 (mmm) REVERT: A 305 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8568 (tpp) REVERT: C 157 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: C 259 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: C 276 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: C 325 MET cc_start: 0.8850 (tpp) cc_final: 0.8467 (mmm) REVERT: B 93 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7160 (m-10) REVERT: D 48 LEU cc_start: 0.9369 (mt) cc_final: 0.9118 (tt) REVERT: D 211 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7754 (p) REVERT: D 255 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8186 (tm-30) REVERT: D 299 ILE cc_start: 0.7737 (mm) cc_final: 0.7222 (tt) REVERT: D 323 MET cc_start: 0.8621 (mmm) cc_final: 0.8326 (mmm) REVERT: D 671 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6678 (t80) REVERT: F 283 MET cc_start: 0.9007 (mmp) cc_final: 0.8785 (mmm) REVERT: E 120 MET cc_start: 0.2979 (ttm) cc_final: 0.2009 (tmm) outliers start: 36 outliers final: 23 residues processed: 206 average time/residue: 0.1473 time to fit residues: 50.3182 Evaluate side-chains 194 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 503 MET 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 259 GLU 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 95 ASP Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 690 THR 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: 20.0000 chunk 8 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 271 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075298 restraints weight = 47583.463| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.40 r_work: 0.2924 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23777 Z= 0.120 Angle : 0.560 10.936 32134 Z= 0.274 Chirality : 0.043 0.383 3507 Planarity : 0.003 0.043 4110 Dihedral : 16.385 172.488 3315 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.25 % Allowed : 11.63 % Favored : 87.12 % 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: 1.71 (0.16), residues: 2840 helix: 1.84 (0.14), residues: 1394 sheet: 0.43 (0.25), residues: 407 loop : 0.62 (0.19), residues: 1039 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 0.031 0.001 PHE D 553 TRP 0.032 0.002 TRP A 484 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00274 (23776) covalent geometry : angle 0.56033 (32134) hydrogen bonds : bond 0.03437 ( 1210) hydrogen bonds : angle 4.17068 ( 3387) Misc. bond : bond 0.00514 ( 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 217 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8698 (ppp) cc_final: 0.7066 (tpt) REVERT: A 305 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8607 (tpp) REVERT: A 671 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7562 (t80) REVERT: C 157 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: C 325 MET cc_start: 0.8814 (tpp) cc_final: 0.8447 (mmm) REVERT: B 93 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: D 211 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7789 (p) REVERT: D 299 ILE cc_start: 0.7776 (mm) cc_final: 0.7267 (tt) REVERT: D 323 MET cc_start: 0.8598 (mmm) cc_final: 0.8295 (mmm) REVERT: D 671 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6506 (t80) REVERT: E 73 MET cc_start: 0.1697 (ptt) cc_final: 0.0885 (tmm) REVERT: E 120 MET cc_start: 0.2913 (ttm) cc_final: 0.1897 (tmm) outliers start: 31 outliers final: 20 residues processed: 206 average time/residue: 0.1340 time to fit residues: 45.5215 Evaluate side-chains 194 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 305 MET 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 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 565 LEU Chi-restraints excluded: chain D residue 671 PHE 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 G residue 14 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 30 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 144 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073800 restraints weight = 47483.121| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.39 r_work: 0.2893 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23777 Z= 0.178 Angle : 0.597 9.972 32134 Z= 0.294 Chirality : 0.045 0.425 3507 Planarity : 0.004 0.045 4110 Dihedral : 16.614 176.708 3315 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.37 % Allowed : 11.43 % Favored : 87.20 % 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: 1.73 (0.14), residues: 1398 sheet: 0.44 (0.25), residues: 407 loop : 0.56 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.014 0.001 TYR A 758 PHE 0.029 0.001 PHE D 553 TRP 0.032 0.002 TRP A 484 HIS 0.007 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00420 (23776) covalent geometry : angle 0.59709 (32134) hydrogen bonds : bond 0.03824 ( 1210) hydrogen bonds : angle 4.25596 ( 3387) Misc. bond : bond 0.00611 ( 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 205 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8741 (ppp) cc_final: 0.7185 (tpt) REVERT: A 305 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8585 (tpp) REVERT: A 339 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 671 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7611 (t80) REVERT: C 157 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: C 325 MET cc_start: 0.8809 (tpp) cc_final: 0.8451 (mmm) REVERT: B 93 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: B 125 VAL cc_start: 0.7321 (t) cc_final: 0.7113 (m) REVERT: D 211 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7859 (p) REVERT: D 299 ILE cc_start: 0.7731 (mm) cc_final: 0.7224 (tt) REVERT: D 323 MET cc_start: 0.8639 (mmm) cc_final: 0.8337 (mmm) REVERT: D 671 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6748 (t80) REVERT: E 73 MET cc_start: 0.1748 (ptt) cc_final: 0.0945 (tmm) REVERT: E 120 MET cc_start: 0.3213 (ttm) cc_final: 0.2071 (tmm) outliers start: 34 outliers final: 23 residues processed: 197 average time/residue: 0.1485 time to fit residues: 47.9328 Evaluate side-chains 189 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 LEU 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 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 671 PHE 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 G residue 14 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 136 optimal weight: 0.0030 chunk 276 optimal weight: 0.9980 chunk 69 optimal weight: 0.0070 chunk 84 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS C 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076332 restraints weight = 47922.224| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.39 r_work: 0.2940 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23777 Z= 0.109 Angle : 0.560 11.316 32134 Z= 0.273 Chirality : 0.042 0.363 3507 Planarity : 0.003 0.044 4110 Dihedral : 16.297 173.327 3315 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.09 % Allowed : 11.83 % Favored : 87.08 % 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: 1.78 (0.16), residues: 2840 helix: 1.89 (0.14), residues: 1390 sheet: 0.47 (0.25), residues: 407 loop : 0.66 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 110 TYR 0.014 0.001 TYR A 758 PHE 0.022 0.001 PHE D 553 TRP 0.032 0.002 TRP A 484 HIS 0.006 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00249 (23776) covalent geometry : angle 0.55962 (32134) hydrogen bonds : bond 0.03219 ( 1210) hydrogen bonds : angle 4.09942 ( 3387) Misc. bond : bond 0.00388 ( 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 214 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8721 (ppp) cc_final: 0.7176 (tpt) REVERT: A 671 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7438 (t80) REVERT: C 157 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: C 325 MET cc_start: 0.8767 (tpp) cc_final: 0.8408 (mmm) REVERT: B 36 MET cc_start: 0.7040 (tpp) cc_final: 0.6538 (tpp) REVERT: B 93 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7154 (m-10) REVERT: D 211 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7826 (p) REVERT: D 299 ILE cc_start: 0.7749 (mm) cc_final: 0.7246 (tt) REVERT: D 648 MET cc_start: 0.9084 (mmm) cc_final: 0.8883 (mmm) REVERT: D 671 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6586 (t80) REVERT: E 73 MET cc_start: 0.1793 (ptt) cc_final: 0.0974 (tmm) REVERT: E 120 MET cc_start: 0.3177 (ttm) cc_final: 0.2038 (tmm) REVERT: G 119 MET cc_start: 0.8755 (ttm) cc_final: 0.8540 (ttm) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 0.1521 time to fit residues: 50.9534 Evaluate side-chains 195 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 439 TYR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 671 PHE 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 77 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain G residue 14 SER 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: 1.9990 chunk 243 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** F 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.117114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075631 restraints weight = 47697.733| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.37 r_work: 0.2929 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4279 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= 0.130 Angle : 0.590 13.590 32134 Z= 0.289 Chirality : 0.043 0.385 3507 Planarity : 0.003 0.044 4110 Dihedral : 16.345 174.846 3315 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.01 % Allowed : 12.07 % Favored : 86.92 % 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: 1.74 (0.16), residues: 2840 helix: 1.83 (0.14), residues: 1396 sheet: 0.50 (0.26), residues: 407 loop : 0.66 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 110 TYR 0.014 0.001 TYR A 758 PHE 0.020 0.001 PHE D 553 TRP 0.032 0.002 TRP A 484 HIS 0.005 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00302 (23776) covalent geometry : angle 0.59020 (32134) hydrogen bonds : bond 0.03450 ( 1210) hydrogen bonds : angle 4.14499 ( 3387) Misc. bond : bond 0.00442 ( 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 203 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8731 (ppp) cc_final: 0.7216 (tpt) REVERT: A 671 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 157 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: C 325 MET cc_start: 0.8773 (tpp) cc_final: 0.8414 (mmm) REVERT: B 36 MET cc_start: 0.7197 (tpp) cc_final: 0.6725 (tpp) REVERT: B 93 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7129 (m-10) REVERT: D 211 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7748 (p) REVERT: D 299 ILE cc_start: 0.7755 (mm) cc_final: 0.7272 (tt) REVERT: D 671 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.6741 (t80) REVERT: D 790 MET cc_start: 0.2900 (mmm) cc_final: 0.1925 (ppp) REVERT: E 73 MET cc_start: 0.1650 (ptt) cc_final: 0.0799 (tmm) REVERT: E 120 MET cc_start: 0.3210 (ttm) cc_final: 0.2056 (tmm) outliers start: 25 outliers final: 19 residues processed: 195 average time/residue: 0.1469 time to fit residues: 47.1324 Evaluate side-chains 192 residues out of total 2499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 671 PHE 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 77 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain G residue 14 SER 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 132 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075371 restraints weight = 47492.854| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.38 r_work: 0.2923 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23777 Z= 0.138 Angle : 0.593 13.033 32134 Z= 0.290 Chirality : 0.043 0.387 3507 Planarity : 0.004 0.043 4110 Dihedral : 16.404 175.095 3315 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.09 % Allowed : 11.99 % Favored : 86.92 % 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: 1.70 (0.16), residues: 2840 helix: 1.79 (0.14), residues: 1398 sheet: 0.47 (0.26), residues: 407 loop : 0.65 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 110 TYR 0.015 0.001 TYR A 758 PHE 0.023 0.001 PHE D 553 TRP 0.029 0.002 TRP A 484 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00321 (23776) covalent geometry : angle 0.59262 (32134) hydrogen bonds : bond 0.03504 ( 1210) hydrogen bonds : angle 4.15882 ( 3387) Misc. bond : bond 0.00427 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8913.48 seconds wall clock time: 152 minutes 14.27 seconds (9134.27 seconds total)