Starting phenix.real_space_refine on Fri Aug 7 18:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7v_73882/08_2026/9z7v_73882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7v_73882/08_2026/9z7v_73882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z7v_73882/08_2026/9z7v_73882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7v_73882/08_2026/9z7v_73882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z7v_73882/08_2026/9z7v_73882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7v_73882/08_2026/9z7v_73882.map" } resolution = 3.0 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= 0.015 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 73 5.49 5 S 80 5.16 5 C 14350 2.51 5 N 3871 2.21 5 O 4427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22802 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4582 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 576} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 20, 'ASN:plan1': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 160 Chain: "B" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2664 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 19, 'TRANS': 340} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'TRP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASN:plan1': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2413 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2418 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 302} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1051 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1026 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 128} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2322 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 281} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 32 Chain: "J" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 742 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 22} Link IDs: {'rna2p': 6, 'rna3p': 29} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 819 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "I" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2330 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 3 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 14, 'PHE:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1277 SG CYS A 166 40.125 53.938 158.804 1.00103.39 S ATOM 1297 SG CYS A 169 42.881 56.389 159.266 1.00111.89 S ATOM 1708 SG CYS A 222 40.195 56.184 161.887 1.00102.70 S ATOM 1725 SG CYS A 225 39.299 57.719 158.599 1.00132.93 S Time building chain proxies: 5.00, per 1000 atoms: 0.22 Number of scatterers: 22802 At special positions: 0 Unit cell: (103.295, 112.356, 196.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 80 16.00 P 73 15.00 O 4427 8.00 N 3871 7.00 C 14350 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=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 222 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 169 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 166 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 225 " Number of angles added : 6 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5186 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 36 sheets defined 38.6% alpha, 18.0% beta 9 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 removed outlier: 3.550A pdb=" N ILE A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 49 removed outlier: 3.595A pdb=" N LEU A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 105 removed outlier: 3.972A pdb=" N VAL A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.598A pdb=" N SER A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.677A pdb=" N MET A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 263 through 271 removed outlier: 4.303A pdb=" N THR A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 removed outlier: 4.030A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.930A pdb=" N LYS A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.704A pdb=" N GLY A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 363 removed outlier: 3.728A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.403A pdb=" N ASP A 411 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 450 removed outlier: 3.665A pdb=" N VAL A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 removed outlier: 4.019A pdb=" N LEU A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.896A pdb=" N LYS A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.657A pdb=" N LEU A 516 " --> pdb=" O ILE A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.711A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.923A pdb=" N GLN A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 removed outlier: 3.809A pdb=" N LEU A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 591 removed outlier: 3.754A pdb=" N PHE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.577A pdb=" N ILE B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 58 removed outlier: 3.604A pdb=" N LEU B 55 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 327 through 334 removed outlier: 3.944A pdb=" N ILE B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'C' and resid 43 through 58 Processing helix chain 'C' and resid 73 through 81 Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.659A pdb=" N LEU C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.654A pdb=" N PHE C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.855A pdb=" N LYS C 203 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.528A pdb=" N PHE C 274 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.846A pdb=" N PHE C 288 " --> pdb=" O MET C 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.572A pdb=" N ALA D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 117 through 131 removed outlier: 4.053A pdb=" N LEU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N CYS D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 4.026A pdb=" N PHE D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 203 removed outlier: 3.884A pdb=" N LYS D 203 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 267 through 275 removed outlier: 4.555A pdb=" N GLY D 272 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 274 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.811A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 57 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 117 through 131 removed outlier: 3.549A pdb=" N LEU E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS E 131 " --> pdb=" O ASP E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 removed outlier: 4.117A pdb=" N PHE E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 200 Processing helix chain 'E' and resid 210 through 221 Processing helix chain 'E' and resid 267 through 275 removed outlier: 3.522A pdb=" N GLU E 270 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 271 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY E 272 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE E 273 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 293 Processing helix chain 'F' and resid 7 through 29 removed outlier: 3.505A pdb=" N ALA F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 41 removed outlier: 3.573A pdb=" N LYS F 41 " --> pdb=" O LYS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.757A pdb=" N LYS F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.705A pdb=" N ASN F 98 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.911A pdb=" N VAL F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 136 removed outlier: 3.874A pdb=" N TRP F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.670A pdb=" N GLU G 25 " --> pdb=" O TYR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 41 removed outlier: 3.938A pdb=" N LYS G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 49 removed outlier: 4.032A pdb=" N LYS G 48 " --> pdb=" O PRO G 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 49 " --> pdb=" O MET G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 49' Processing helix chain 'G' and resid 52 through 63 Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.790A pdb=" N LYS G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.631A pdb=" N ASN G 98 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN G 99 " --> pdb=" O LYS G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 99' Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.604A pdb=" N VAL G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 136 removed outlier: 3.580A pdb=" N ARG G 115 " --> pdb=" O SER G 111 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.738A pdb=" N PHE H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 134 through 138' Processing helix chain 'H' and resid 141 through 161 removed outlier: 3.532A pdb=" N LEU H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 160 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 220 removed outlier: 3.635A pdb=" N VAL H 206 " --> pdb=" O PRO H 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY H 220 " --> pdb=" O THR H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 227 removed outlier: 3.699A pdb=" N ALA H 226 " --> pdb=" O ASP H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 237 Processing helix chain 'H' and resid 320 through 325 removed outlier: 3.675A pdb=" N VAL H 324 " --> pdb=" O GLN H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 336 removed outlier: 4.267A pdb=" N SER H 334 " --> pdb=" O SER H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 360 removed outlier: 3.545A pdb=" N LYS H 355 " --> pdb=" O SER H 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 44 removed outlier: 4.189A pdb=" N ILE I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA I 44 " --> pdb=" O ARG I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 60 removed outlier: 3.525A pdb=" N LYS I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 removed outlier: 3.924A pdb=" N HIS I 98 " --> pdb=" O PRO I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 105 removed outlier: 4.041A pdb=" N PHE I 103 " --> pdb=" O PHE I 99 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 145 removed outlier: 3.829A pdb=" N ILE I 133 " --> pdb=" O GLY I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 removed outlier: 4.047A pdb=" N ASP I 171 " --> pdb=" O LYS I 168 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP I 172 " --> pdb=" O ILE I 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 168 through 172' Processing helix chain 'I' and resid 183 through 203 removed outlier: 3.667A pdb=" N ASN I 194 " --> pdb=" O TRP I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 238 removed outlier: 3.514A pdb=" N ALA I 237 " --> pdb=" O ASP I 233 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA I 238 " --> pdb=" O ALA I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 247 removed outlier: 3.523A pdb=" N PHE I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 341 removed outlier: 3.714A pdb=" N LYS I 341 " --> pdb=" O ALA I 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 55 removed outlier: 6.980A pdb=" N CYS A 51 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASN A 72 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE A 53 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 70 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 55 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 71 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 8 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 125 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 123 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 12 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 116 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 removed outlier: 3.653A pdb=" N VAL A 202 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.834A pdb=" N LEU A 382 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA A 376 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 325 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 422 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA A 460 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 424 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA A 462 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 426 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU A 464 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 428 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 471 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 removed outlier: 4.162A pdb=" N LEU B 80 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 12.902A pdb=" N ILE B 78 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE B 75 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP B 206 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 77 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR B 199 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ALA B 8 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 223 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 227 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 214 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 176 removed outlier: 11.275A pdb=" N LYS B 171 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LEU B 188 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N GLY B 173 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N SER B 186 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA B 175 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 5.776A pdb=" N LEU B 285 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU B 321 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 287 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 338 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.946A pdb=" N VAL C 253 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL C 207 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP C 114 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.577A pdb=" N THR C 260 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 4 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 64 Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB7, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 230 removed outlier: 3.904A pdb=" N LYS C 229 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 241 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 41 through 42 removed outlier: 6.825A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 253 through 260 current: chain 'D' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.825A pdb=" N VAL D 253 " --> pdb=" O LEU D 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 106 current: chain 'D' and resid 309 through 314 Processing sheet with id=AC2, first strand: chain 'D' and resid 61 through 64 Processing sheet with id=AC3, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 159 Processing sheet with id=AC5, first strand: chain 'D' and resid 223 through 230 removed outlier: 11.091A pdb=" N GLU D 223 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N THR D 244 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 11.312A pdb=" N ILE D 225 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N LEU D 242 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N ARG D 227 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N GLY D 240 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS D 229 " --> pdb=" O GLN D 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 41 through 42 removed outlier: 6.719A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 253 through 260 current: chain 'E' and resid 206 through 208 Processing sheet with id=AC7, first strand: chain 'E' and resid 93 through 95 removed outlier: 6.719A pdb=" N VAL E 253 " --> pdb=" O LEU E 101 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 98 through 106 current: chain 'E' and resid 309 through 314 Processing sheet with id=AC8, first strand: chain 'E' and resid 61 through 64 Processing sheet with id=AC9, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AD1, first strand: chain 'E' and resid 157 through 160 removed outlier: 3.775A pdb=" N TYR E 163 " --> pdb=" O LEU E 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 223 through 231 removed outlier: 11.121A pdb=" N GLU E 223 " --> pdb=" O THR E 244 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N THR E 244 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N ILE E 225 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N LEU E 242 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG E 227 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N GLY E 240 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS E 229 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 122 through 124 removed outlier: 6.413A pdb=" N LYS H 123 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 251 through 253 Processing sheet with id=AD5, first strand: chain 'H' and resid 264 through 269 Processing sheet with id=AD6, first strand: chain 'I' and resid 71 through 77 removed outlier: 6.951A pdb=" N GLY I 5 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL I 163 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR I 7 " --> pdb=" O ILE I 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 289 through 296 removed outlier: 3.506A pdb=" N ILE I 290 " --> pdb=" O LEU I 305 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TRP I 302 " --> pdb=" O GLY I 224 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG I 220 " --> pdb=" O ARG I 306 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER I 308 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE I 218 " --> pdb=" O SER I 308 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER I 219 " --> pdb=" O LEU I 348 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 261 through 263 removed outlier: 3.964A pdb=" N VAL I 261 " --> pdb=" O VAL I 273 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE I 271 " --> pdb=" O HIS I 263 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 261 through 263 removed outlier: 3.964A pdb=" N VAL I 261 " --> pdb=" O VAL I 273 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE I 271 " --> pdb=" O HIS I 263 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6759 1.34 - 1.46: 4551 1.46 - 1.58: 11805 1.58 - 1.70: 145 1.70 - 1.82: 129 Bond restraints: 23389 Sorted by residual: bond pdb=" C ASP C 283 " pdb=" N MET C 284 " ideal model delta sigma weight residual 1.335 1.291 0.044 1.38e-02 5.25e+03 1.02e+01 bond pdb=" CA MET C 284 " pdb=" CB MET C 284 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.74e-02 3.30e+03 4.56e+00 bond pdb=" C3' A N 32 " pdb=" C2' A N 32 " ideal model delta sigma weight residual 1.525 1.547 -0.022 1.10e-02 8.26e+03 3.91e+00 bond pdb=" C1' G N 17 " pdb=" N9 G N 17 " ideal model delta sigma weight residual 1.483 1.458 0.025 1.50e-02 4.44e+03 2.73e+00 bond pdb=" C4' A N 32 " pdb=" O4' A N 32 " ideal model delta sigma weight residual 1.454 1.439 0.015 1.00e-02 1.00e+04 2.32e+00 ... (remaining 23384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 31587 2.48 - 4.95: 353 4.95 - 7.43: 30 7.43 - 9.90: 7 9.90 - 12.38: 1 Bond angle restraints: 31978 Sorted by residual: angle pdb=" O5' U J 20 " pdb=" C5' U J 20 " pdb=" C4' U J 20 " ideal model delta sigma weight residual 109.40 113.15 -3.75 8.00e-01 1.56e+00 2.20e+01 angle pdb=" C3' U J 1 " pdb=" O3' U J 1 " pdb=" P C J 2 " ideal model delta sigma weight residual 119.70 125.05 -5.35 1.20e+00 6.94e-01 1.99e+01 angle pdb=" N PHE C 214 " pdb=" CA PHE C 214 " pdb=" C PHE C 214 " ideal model delta sigma weight residual 113.51 106.76 6.75 1.52e+00 4.33e-01 1.97e+01 angle pdb=" N ARG C 215 " pdb=" CA ARG C 215 " pdb=" C ARG C 215 " ideal model delta sigma weight residual 108.90 101.72 7.18 1.63e+00 3.76e-01 1.94e+01 angle pdb=" C3' A N 32 " pdb=" O3' A N 32 " pdb=" P G N 33 " ideal model delta sigma weight residual 119.70 124.79 -5.09 1.20e+00 6.94e-01 1.80e+01 ... (remaining 31973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 13595 35.83 - 71.66: 476 71.66 - 107.49: 38 107.49 - 143.32: 1 143.32 - 179.15: 6 Dihedral angle restraints: 14116 sinusoidal: 6071 harmonic: 8045 Sorted by residual: dihedral pdb=" CA PHE I 259 " pdb=" C PHE I 259 " pdb=" N PRO I 260 " pdb=" CA PRO I 260 " ideal model delta harmonic sigma weight residual 0.00 44.67 -44.67 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" O4' C N 20 " pdb=" C1' C N 20 " pdb=" N1 C N 20 " pdb=" C2 C N 20 " ideal model delta sinusoidal sigma weight residual 232.00 52.85 179.15 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C N 14 " pdb=" C1' C N 14 " pdb=" N1 C N 14 " pdb=" C2 C N 14 " ideal model delta sinusoidal sigma weight residual -128.00 49.12 -177.12 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2616 0.043 - 0.086: 733 0.086 - 0.130: 272 0.130 - 0.173: 57 0.173 - 0.216: 6 Chirality restraints: 3684 Sorted by residual: chirality pdb=" CB ILE H 111 " pdb=" CA ILE H 111 " pdb=" CG1 ILE H 111 " pdb=" CG2 ILE H 111 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' A N 32 " pdb=" C4' A N 32 " pdb=" O3' A N 32 " pdb=" C2' A N 32 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3' A N 16 " pdb=" C4' A N 16 " pdb=" O3' A N 16 " pdb=" C2' A N 16 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 3681 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U J 20 " -0.026 2.00e-02 2.50e+03 2.86e-02 1.84e+01 pdb=" N1 U J 20 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U J 20 " -0.043 2.00e-02 2.50e+03 pdb=" O2 U J 20 " 0.011 2.00e-02 2.50e+03 pdb=" N3 U J 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U J 20 " -0.000 2.00e-02 2.50e+03 pdb=" O4 U J 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U J 20 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U J 20 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A N 23 " 0.031 2.00e-02 2.50e+03 2.26e-02 1.40e+01 pdb=" N9 A N 23 " -0.062 2.00e-02 2.50e+03 pdb=" C8 A N 23 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A N 23 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A N 23 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A N 23 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A N 23 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A N 23 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A N 23 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A N 23 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A N 23 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 45 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.24e+01 pdb=" C SER C 45 " -0.061 2.00e-02 2.50e+03 pdb=" O SER C 45 " 0.022 2.00e-02 2.50e+03 pdb=" N SER C 46 " 0.021 2.00e-02 2.50e+03 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 8553 2.89 - 3.39: 19749 3.39 - 3.90: 34383 3.90 - 4.40: 38489 4.40 - 4.90: 68504 Nonbonded interactions: 169678 Sorted by model distance: nonbonded pdb=" O2' A N 36 " pdb=" O PRO I 260 " model vdw 2.388 3.040 nonbonded pdb=" O2' U J 8 " pdb=" O5' U J 9 " model vdw 2.455 3.040 nonbonded pdb=" O GLU G 83 " pdb=" OE1 GLU G 83 " model vdw 2.468 3.040 nonbonded pdb=" O2' G N 15 " pdb=" OP2 A N 16 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP G 101 " pdb=" N MET G 102 " model vdw 2.509 3.120 ... (remaining 169673 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 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 56 or (resid 57 throug \ h 59 and (name N or name CA or name C or name O or name CB )) or resid 60 throug \ h 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or re \ sid 85 through 161 or (resid 162 and (name N or name CA or name C or name O or n \ ame CB )) or resid 163 through 170 or (resid 171 through 173 and (name N or name \ CA or name C or name O or name CB )) or resid 174 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 or (resid 195 \ and (name N or name CA or name C or name O or name CB )) or resid 196 through 2 \ 32 or (resid 233 and (name N or name CA or name C or name O or name CB )) or res \ id 234 through 265 or (resid 266 and (name N or name CA or name C or name O or n \ ame CB )) or resid 267 through 315)) selection = (chain 'D' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 37 or (resid 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 56 or (resid 57 throug \ h 59 and (name N or name CA or name C or name O or name CB )) or resid 60 throug \ h 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or re \ sid 75 through 83 or (resid 84 and (name N or name CA or name C or name O or nam \ e CB )) or resid 85 through 121 or (resid 122 and (name N or name CA or name C o \ r name O or name CB )) or resid 123 through 171 or (resid 172 through 173 and (n \ ame N or name CA or name C or name O or name CB )) or resid 174 through 268 or ( \ resid 269 and (name N or name CA or name C or name O or name CB )) or resid 270 \ through 315)) selection = (chain 'E' and (resid 1 through 21 or (resid 22 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 34 or (resid 35 and (n \ ame N or name CA or name C or name O or name CB )) or resid 36 through 37 or (re \ sid 38 and (name N or name CA or name C or name O or name CB )) or resid 39 thro \ ugh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or \ resid 75 through 121 or (resid 122 and (name N or name CA or name C or name O or \ name CB )) or resid 123 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 171 or (resid 172 through 173 a \ nd (name N or name CA or name C or name O or name CB )) or resid 174 through 192 \ or (resid 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 through 232 or (resid 233 and (name N or name CA or name C or name O or nam \ e CB )) or resid 234 through 315)) } ncs_group { reference = (chain 'F' and ((resid 7 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 98 or (resid 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 through 137)) selection = (chain 'G' and (resid 7 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB )) or resid 91 through 95 or (resid 96 and (name N or name \ CA or name C or name O or name CB )) or resid 97 through 137)) } 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: 14.090 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: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.740 Find NCS groups from input model: 0.320 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23393 Z= 0.155 Angle : 0.667 12.375 31984 Z= 0.421 Chirality : 0.048 0.216 3684 Planarity : 0.005 0.074 3814 Dihedral : 17.070 179.154 8930 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.89 % Favored : 94.93 % Rotamer: Outliers : 0.56 % Allowed : 19.21 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2761 helix: 1.35 (0.18), residues: 920 sheet: 0.31 (0.26), residues: 420 loop : -1.24 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 311 TYR 0.023 0.001 TYR I 299 PHE 0.020 0.001 PHE A 325 TRP 0.017 0.001 TRP I 302 HIS 0.006 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (23389) covalent geometry : angle 0.66603 / 0.42 (31978) hydrogen bonds : bond 0.21340 / 14.42 ( 870) hydrogen bonds : angle 6.16594 / 4.33 ( 2493) metal coordination : bond 0.00543 / 0.27 ( 4) metal coordination : angle 2.65116 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.870 Fit side-chains REVERT: B 63 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 277 GLU cc_start: 0.9042 (pt0) cc_final: 0.8648 (pp20) REVERT: C 60 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8473 (tttp) REVERT: G 102 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9068 (ttp) REVERT: G 108 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7905 (mp0) REVERT: G 133 GLU cc_start: 0.8054 (tp30) cc_final: 0.7844 (tt0) REVERT: I 63 ASP cc_start: 0.7554 (t0) cc_final: 0.7264 (t0) REVERT: I 203 ASN cc_start: 0.8092 (t0) cc_final: 0.7823 (t0) outliers start: 12 outliers final: 4 residues processed: 161 average time/residue: 0.7388 time to fit residues: 133.8898 Evaluate side-chains 142 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 102 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN E 196 GLN F 9 GLN H 109 ASN I 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.062960 restraints weight = 50298.914| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.78 r_work: 0.2756 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23393 Z= 0.186 Angle : 0.588 8.369 31984 Z= 0.323 Chirality : 0.046 0.561 3684 Planarity : 0.005 0.067 3814 Dihedral : 14.721 179.878 4096 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.14 % Allowed : 17.40 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2761 helix: 1.79 (0.17), residues: 937 sheet: 0.59 (0.24), residues: 440 loop : -1.26 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 311 TYR 0.018 0.001 TYR F 94 PHE 0.024 0.002 PHE A 325 TRP 0.016 0.001 TRP I 302 HIS 0.006 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (23389) covalent geometry : angle 0.58684 / 0.32 (31978) hydrogen bonds : bond 0.06829 / 4.57 ( 870) hydrogen bonds : angle 4.62061 / 3.25 ( 2493) metal coordination : bond 0.00877 / 0.43 ( 4) metal coordination : angle 2.27183 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.780 Fit side-chains REVERT: B 147 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8622 (tt0) REVERT: B 277 GLU cc_start: 0.8835 (pt0) cc_final: 0.8573 (pp20) REVERT: B 308 MET cc_start: 0.9096 (ttm) cc_final: 0.8801 (ttm) REVERT: C 162 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: D 269 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: E 108 MET cc_start: 0.8786 (mmt) cc_final: 0.8584 (mmt) REVERT: H 171 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8678 (t) REVERT: I 63 ASP cc_start: 0.7530 (t0) cc_final: 0.7136 (t0) REVERT: I 203 ASN cc_start: 0.7804 (t0) cc_final: 0.7533 (t0) outliers start: 46 outliers final: 9 residues processed: 181 average time/residue: 0.6801 time to fit residues: 139.0663 Evaluate side-chains 147 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 67 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 152 optimal weight: 0.0170 chunk 116 optimal weight: 0.6980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS F 9 GLN I 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.063502 restraints weight = 49958.525| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.81 r_work: 0.2788 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23393 Z= 0.114 Angle : 0.499 8.475 31984 Z= 0.273 Chirality : 0.043 0.536 3684 Planarity : 0.004 0.052 3814 Dihedral : 14.530 179.545 4089 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.23 % Allowed : 17.30 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2761 helix: 1.99 (0.17), residues: 952 sheet: 0.70 (0.24), residues: 444 loop : -1.22 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 292 TYR 0.012 0.001 TYR H 273 PHE 0.025 0.001 PHE A 325 TRP 0.018 0.001 TRP I 302 HIS 0.004 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (23389) covalent geometry : angle 0.49829 / 0.27 (31978) hydrogen bonds : bond 0.05020 / 3.35 ( 870) hydrogen bonds : angle 4.12758 / 2.92 ( 2493) metal coordination : bond 0.00466 / 0.23 ( 4) metal coordination : angle 1.96181 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.890 Fit side-chains REVERT: A 565 HIS cc_start: 0.8328 (m90) cc_final: 0.7973 (m90) REVERT: B 109 MET cc_start: 0.8937 (mtp) cc_final: 0.8693 (mtm) REVERT: B 147 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8646 (tt0) REVERT: B 277 GLU cc_start: 0.8829 (pt0) cc_final: 0.8527 (pp20) REVERT: B 308 MET cc_start: 0.9128 (ttm) cc_final: 0.8793 (ttm) REVERT: D 13 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: D 269 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: G 88 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: G 108 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7765 (mt-10) REVERT: I 63 ASP cc_start: 0.7573 (t0) cc_final: 0.7198 (t0) REVERT: I 203 ASN cc_start: 0.7750 (t0) cc_final: 0.7454 (t0) outliers start: 48 outliers final: 12 residues processed: 177 average time/residue: 0.7387 time to fit residues: 147.8565 Evaluate side-chains 146 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 239 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 140 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 264 optimal weight: 0.0470 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 9 GLN I 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.060992 restraints weight = 50133.344| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.81 r_work: 0.2690 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23393 Z= 0.170 Angle : 0.538 10.189 31984 Z= 0.294 Chirality : 0.045 0.549 3684 Planarity : 0.004 0.061 3814 Dihedral : 14.470 179.340 4089 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.42 % Allowed : 16.98 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2761 helix: 1.96 (0.17), residues: 962 sheet: 0.82 (0.26), residues: 416 loop : -1.34 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 322 TYR 0.011 0.001 TYR E 247 PHE 0.025 0.002 PHE A 325 TRP 0.020 0.001 TRP I 302 HIS 0.005 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (23389) covalent geometry : angle 0.53753 / 0.29 (31978) hydrogen bonds : bond 0.05799 / 3.89 ( 870) hydrogen bonds : angle 4.08100 / 2.89 ( 2493) metal coordination : bond 0.00664 / 0.32 ( 4) metal coordination : angle 2.30203 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.952 Fit side-chains REVERT: A 446 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: A 565 HIS cc_start: 0.8392 (m90) cc_final: 0.8179 (m170) REVERT: B 277 GLU cc_start: 0.8902 (pt0) cc_final: 0.8527 (pp20) REVERT: B 308 MET cc_start: 0.9172 (ttm) cc_final: 0.8867 (ttm) REVERT: D 269 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: E 157 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8840 (mttm) REVERT: G 83 GLU cc_start: 0.8749 (tp30) cc_final: 0.8457 (mt-10) REVERT: G 88 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: H 101 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8588 (mm) REVERT: H 171 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8613 (t) REVERT: I 63 ASP cc_start: 0.7764 (t0) cc_final: 0.7387 (t0) REVERT: I 203 ASN cc_start: 0.7845 (t0) cc_final: 0.7558 (t0) outliers start: 52 outliers final: 16 residues processed: 171 average time/residue: 0.7599 time to fit residues: 147.0676 Evaluate side-chains 151 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 68 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 170 optimal weight: 0.3980 chunk 104 optimal weight: 0.0040 chunk 76 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 280 optimal weight: 9.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 GLN F 9 GLN F 50 ASN I 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063166 restraints weight = 49885.288| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.84 r_work: 0.2775 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23393 Z= 0.097 Angle : 0.477 9.054 31984 Z= 0.260 Chirality : 0.042 0.487 3684 Planarity : 0.004 0.050 3814 Dihedral : 14.414 178.968 4089 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.05 % Allowed : 17.81 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2761 helix: 2.11 (0.17), residues: 963 sheet: 0.90 (0.25), residues: 421 loop : -1.28 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 322 TYR 0.010 0.001 TYR G 114 PHE 0.024 0.001 PHE A 325 TRP 0.021 0.001 TRP I 302 HIS 0.004 0.000 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (23389) covalent geometry : angle 0.47613 / 0.26 (31978) hydrogen bonds : bond 0.04485 / 3.00 ( 870) hydrogen bonds : angle 3.88307 / 2.75 ( 2493) metal coordination : bond 0.00320 / 0.16 ( 4) metal coordination : angle 1.85737 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.902 Fit side-chains REVERT: B 226 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7999 (p) REVERT: B 277 GLU cc_start: 0.8858 (pt0) cc_final: 0.8571 (pp20) REVERT: B 308 MET cc_start: 0.9174 (ttm) cc_final: 0.8944 (ttm) REVERT: D 269 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: E 157 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8856 (mttm) REVERT: G 88 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: I 63 ASP cc_start: 0.7743 (t0) cc_final: 0.7379 (t0) REVERT: I 203 ASN cc_start: 0.7791 (t0) cc_final: 0.7484 (t0) outliers start: 44 outliers final: 16 residues processed: 167 average time/residue: 0.7253 time to fit residues: 137.5817 Evaluate side-chains 146 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 86 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 180 optimal weight: 0.0010 overall best weight: 0.5448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 565 HIS D 141 GLN F 9 GLN I 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063437 restraints weight = 50279.284| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.89 r_work: 0.2785 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23393 Z= 0.098 Angle : 0.468 9.225 31984 Z= 0.254 Chirality : 0.041 0.422 3684 Planarity : 0.004 0.050 3814 Dihedral : 14.337 178.911 4089 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.86 % Allowed : 18.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2761 helix: 2.21 (0.18), residues: 965 sheet: 0.93 (0.26), residues: 419 loop : -1.24 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 322 TYR 0.010 0.001 TYR D 247 PHE 0.024 0.001 PHE A 325 TRP 0.021 0.001 TRP I 302 HIS 0.004 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (23389) covalent geometry : angle 0.46709 / 0.25 (31978) hydrogen bonds : bond 0.04178 / 2.80 ( 870) hydrogen bonds : angle 3.75990 / 2.68 ( 2493) metal coordination : bond 0.00336 / 0.16 ( 4) metal coordination : angle 1.97347 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.931 Fit side-chains REVERT: B 226 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7942 (p) REVERT: B 277 GLU cc_start: 0.8877 (pt0) cc_final: 0.8577 (pp20) REVERT: D 269 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: E 157 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8873 (mttm) REVERT: G 83 GLU cc_start: 0.8699 (tp30) cc_final: 0.8460 (mt-10) REVERT: G 88 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: G 108 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7675 (mt-10) REVERT: H 171 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8675 (t) REVERT: H 323 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: I 63 ASP cc_start: 0.7785 (t0) cc_final: 0.7497 (t0) REVERT: I 203 ASN cc_start: 0.7758 (t0) cc_final: 0.7414 (t0) outliers start: 40 outliers final: 17 residues processed: 165 average time/residue: 0.7257 time to fit residues: 136.0978 Evaluate side-chains 151 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 287 SER Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 55 optimal weight: 0.6980 chunk 192 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 264 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 GLN E 154 ASN F 9 GLN I 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.063654 restraints weight = 50040.628| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.87 r_work: 0.2789 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23393 Z= 0.098 Angle : 0.465 9.099 31984 Z= 0.252 Chirality : 0.041 0.363 3684 Planarity : 0.004 0.050 3814 Dihedral : 14.296 178.896 4089 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.77 % Allowed : 18.70 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2761 helix: 2.19 (0.17), residues: 972 sheet: 0.77 (0.24), residues: 449 loop : -1.21 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 322 TYR 0.009 0.001 TYR G 114 PHE 0.024 0.001 PHE A 325 TRP 0.022 0.001 TRP I 302 HIS 0.004 0.000 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (23389) covalent geometry : angle 0.46453 / 0.25 (31978) hydrogen bonds : bond 0.04112 / 2.76 ( 870) hydrogen bonds : angle 3.72957 / 2.66 ( 2493) metal coordination : bond 0.00354 / 0.17 ( 4) metal coordination : angle 1.99243 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.785 Fit side-chains REVERT: B 226 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7929 (p) REVERT: B 277 GLU cc_start: 0.8838 (pt0) cc_final: 0.8534 (pp20) REVERT: D 269 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: E 157 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8866 (mttm) REVERT: G 83 GLU cc_start: 0.8769 (tp30) cc_final: 0.8461 (mt-10) REVERT: G 88 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: G 108 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7705 (mt-10) REVERT: H 137 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8381 (mtp-110) REVERT: H 171 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8676 (t) REVERT: H 323 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: I 63 ASP cc_start: 0.7796 (t0) cc_final: 0.7526 (t0) REVERT: I 203 ASN cc_start: 0.7746 (t0) cc_final: 0.7390 (t0) outliers start: 38 outliers final: 20 residues processed: 163 average time/residue: 0.7801 time to fit residues: 143.4117 Evaluate side-chains 153 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 287 SER Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 218 optimal weight: 0.0980 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 GLN F 9 GLN I 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.063569 restraints weight = 49819.777| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.82 r_work: 0.2787 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23393 Z= 0.104 Angle : 0.463 8.366 31984 Z= 0.251 Chirality : 0.041 0.280 3684 Planarity : 0.004 0.050 3814 Dihedral : 14.236 179.066 4089 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.72 % Allowed : 18.60 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2761 helix: 2.27 (0.17), residues: 971 sheet: 0.83 (0.25), residues: 439 loop : -1.20 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 322 TYR 0.011 0.001 TYR D 163 PHE 0.024 0.001 PHE A 325 TRP 0.027 0.001 TRP I 302 HIS 0.004 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (23389) covalent geometry : angle 0.46261 / 0.25 (31978) hydrogen bonds : bond 0.04206 / 2.82 ( 870) hydrogen bonds : angle 3.68370 / 2.63 ( 2493) metal coordination : bond 0.00396 / 0.19 ( 4) metal coordination : angle 2.05302 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.852 Fit side-chains REVERT: B 63 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 226 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7970 (p) REVERT: B 277 GLU cc_start: 0.8832 (pt0) cc_final: 0.8527 (pp20) REVERT: D 269 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: E 157 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8876 (mttm) REVERT: G 88 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: G 108 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7750 (mt-10) REVERT: H 171 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8684 (t) REVERT: H 323 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: I 63 ASP cc_start: 0.7851 (t0) cc_final: 0.7579 (t0) REVERT: I 203 ASN cc_start: 0.7788 (t0) cc_final: 0.7458 (t0) outliers start: 37 outliers final: 20 residues processed: 162 average time/residue: 0.7907 time to fit residues: 144.0643 Evaluate side-chains 153 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 287 SER Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 112 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 259 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 GLN F 9 GLN I 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062568 restraints weight = 50802.925| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.88 r_work: 0.2761 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23393 Z= 0.126 Angle : 0.491 11.810 31984 Z= 0.265 Chirality : 0.042 0.292 3684 Planarity : 0.004 0.060 3814 Dihedral : 14.208 179.225 4089 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.67 % Allowed : 18.88 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2761 helix: 2.24 (0.17), residues: 971 sheet: 0.80 (0.25), residues: 439 loop : -1.21 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 137 TYR 0.010 0.001 TYR E 247 PHE 0.024 0.001 PHE A 325 TRP 0.028 0.001 TRP I 302 HIS 0.005 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (23389) covalent geometry : angle 0.49035 / 0.26 (31978) hydrogen bonds : bond 0.04578 / 3.08 ( 870) hydrogen bonds : angle 3.71582 / 2.65 ( 2493) metal coordination : bond 0.00476 / 0.23 ( 4) metal coordination : angle 2.05455 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.847 Fit side-chains REVERT: B 63 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7953 (mt-10) REVERT: B 132 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: B 226 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 277 GLU cc_start: 0.8858 (pt0) cc_final: 0.8525 (pp20) REVERT: E 157 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8872 (mttm) REVERT: G 83 GLU cc_start: 0.8717 (tp30) cc_final: 0.8487 (mt-10) REVERT: G 88 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: G 108 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7797 (mt-10) REVERT: G 133 GLU cc_start: 0.8037 (tp30) cc_final: 0.7822 (tt0) REVERT: H 137 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7987 (mpt180) REVERT: H 171 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8677 (t) REVERT: H 323 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: I 203 ASN cc_start: 0.7796 (t0) cc_final: 0.7478 (t0) outliers start: 36 outliers final: 19 residues processed: 158 average time/residue: 0.7780 time to fit residues: 138.8290 Evaluate side-chains 153 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 204 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 287 SER Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 59 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 163 optimal weight: 0.0470 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 GLN F 9 GLN I 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.062199 restraints weight = 50309.227| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.83 r_work: 0.2715 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23393 Z= 0.140 Angle : 0.497 9.461 31984 Z= 0.269 Chirality : 0.042 0.297 3684 Planarity : 0.004 0.050 3814 Dihedral : 14.202 179.282 4089 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.49 % Allowed : 19.02 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2761 helix: 2.23 (0.17), residues: 970 sheet: 0.78 (0.25), residues: 439 loop : -1.22 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 137 TYR 0.010 0.001 TYR D 163 PHE 0.025 0.001 PHE A 325 TRP 0.031 0.001 TRP I 302 HIS 0.005 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (23389) covalent geometry : angle 0.49628 / 0.27 (31978) hydrogen bonds : bond 0.04760 / 3.20 ( 870) hydrogen bonds : angle 3.73506 / 2.66 ( 2493) metal coordination : bond 0.00523 / 0.26 ( 4) metal coordination : angle 2.08540 / 1.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 132 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: B 226 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7980 (p) REVERT: B 277 GLU cc_start: 0.8904 (pt0) cc_final: 0.8521 (pp20) REVERT: E 35 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7432 (ttm-80) REVERT: E 157 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8832 (mttm) REVERT: G 83 GLU cc_start: 0.8739 (tp30) cc_final: 0.8420 (mt-10) REVERT: G 88 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: G 108 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7902 (mt-10) REVERT: G 133 GLU cc_start: 0.8064 (tp30) cc_final: 0.7822 (tt0) REVERT: H 171 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8631 (t) REVERT: H 323 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: I 63 ASP cc_start: 0.7666 (t0) cc_final: 0.7413 (t0) REVERT: I 203 ASN cc_start: 0.7784 (t0) cc_final: 0.7472 (t0) outliers start: 32 outliers final: 18 residues processed: 153 average time/residue: 0.7708 time to fit residues: 133.0477 Evaluate side-chains 151 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 287 SER Chi-restraints excluded: chain I residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 GLN F 9 GLN I 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.063057 restraints weight = 50062.272| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.84 r_work: 0.2732 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23393 Z= 0.104 Angle : 0.475 11.603 31984 Z= 0.256 Chirality : 0.041 0.272 3684 Planarity : 0.004 0.056 3814 Dihedral : 14.187 179.114 4089 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.40 % Allowed : 18.98 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2761 helix: 2.28 (0.17), residues: 970 sheet: 0.78 (0.25), residues: 440 loop : -1.19 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 137 TYR 0.009 0.001 TYR G 114 PHE 0.024 0.001 PHE A 325 TRP 0.035 0.001 TRP I 302 HIS 0.003 0.001 HIS H 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (23389) covalent geometry : angle 0.47445 / 0.26 (31978) hydrogen bonds : bond 0.04266 / 2.86 ( 870) hydrogen bonds : angle 3.67585 / 2.62 ( 2493) metal coordination : bond 0.00386 / 0.19 ( 4) metal coordination : angle 1.95028 / 1.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5869.75 seconds wall clock time: 101 minutes 17.29 seconds (6077.29 seconds total)