Starting phenix.real_space_refine on Fri Jul 3 20:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3g_42947/07_2026/8v3g_42947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3g_42947/07_2026/8v3g_42947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3g_42947/07_2026/8v3g_42947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3g_42947/07_2026/8v3g_42947.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3g_42947/07_2026/8v3g_42947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3g_42947/07_2026/8v3g_42947.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 Ca 8 9.91 5 K 4 8.98 5 S 124 5.16 5 C 10358 2.51 5 N 2728 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16210 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2883 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "D" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "F" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "G" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "H" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'Y7Z': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.98, per 1000 atoms: 0.25 Number of scatterers: 16210 At special positions: 0 Unit cell: (137.6, 136.74, 98.04, 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) Ca 8 19.99 K 4 19.00 S 124 16.00 O 2988 8.00 N 2728 7.00 C 10358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 371 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 754.4 milliseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 7 sheets defined 77.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 118 through 160 removed outlier: 3.605A pdb=" N SER A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 201 Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.632A pdb=" N ILE A 208 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 removed outlier: 3.874A pdb=" N ILE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.590A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 267 through 277 removed outlier: 4.414A pdb=" N ALA A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.641A pdb=" N LEU A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.884A pdb=" N VAL A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 335 removed outlier: 3.717A pdb=" N VAL A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 369 through 398 removed outlier: 3.878A pdb=" N GLY A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 436 removed outlier: 3.507A pdb=" N LEU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 478 removed outlier: 4.325A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 160 removed outlier: 3.602A pdb=" N SER B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 201 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.571A pdb=" N ILE B 208 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.531A pdb=" N PHE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.591A pdb=" N ILE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 277 removed outlier: 4.386A pdb=" N ALA B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.646A pdb=" N LEU B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.669A pdb=" N VAL B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 335 removed outlier: 3.710A pdb=" N VAL B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 369 through 398 removed outlier: 3.872A pdb=" N GLY B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 440 removed outlier: 3.525A pdb=" N PHE B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 478 Processing helix chain 'C' and resid 119 through 157 removed outlier: 3.634A pdb=" N SER C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 201 Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.539A pdb=" N ILE C 208 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 227 removed outlier: 3.528A pdb=" N PHE C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.620A pdb=" N ILE C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 267 through 277 removed outlier: 4.375A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.645A pdb=" N LEU C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.857A pdb=" N VAL C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 335 removed outlier: 3.702A pdb=" N VAL C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 369 through 398 removed outlier: 3.877A pdb=" N GLY C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 440 removed outlier: 3.507A pdb=" N LEU C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 478 removed outlier: 3.768A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 160 removed outlier: 3.546A pdb=" N SER D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 201 Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 211 through 227 removed outlier: 3.531A pdb=" N PHE D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.579A pdb=" N ILE D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 267 through 277 removed outlier: 4.384A pdb=" N ALA D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.942A pdb=" N VAL D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 303 " --> pdb=" O THR D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 335 removed outlier: 3.704A pdb=" N VAL D 314 " --> pdb=" O CYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 369 through 397 removed outlier: 3.889A pdb=" N GLY D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 440 removed outlier: 3.502A pdb=" N LEU D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 478 Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.663A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.611A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.546A pdb=" N ASP E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 53 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.720A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.640A pdb=" N ILE E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.550A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.777A pdb=" N LEU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.570A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 39 " --> pdb=" O VAL F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 3.576A pdb=" N ASP F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 53 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.724A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 93 removed outlier: 3.564A pdb=" N VAL F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.538A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 141 through 147 removed outlier: 3.719A pdb=" N MET F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.751A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.531A pdb=" N VAL G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 56 removed outlier: 3.592A pdb=" N ASP G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN G 53 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 77 removed outlier: 3.688A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.728A pdb=" N VAL G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 removed outlier: 3.558A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 139 through 147 removed outlier: 3.817A pdb=" N GLN G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.702A pdb=" N LEU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 removed outlier: 3.709A pdb=" N VAL H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 removed outlier: 3.555A pdb=" N ASP H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.761A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 93 removed outlier: 3.527A pdb=" N ILE H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 112 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 140 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 241 Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 241 Processing sheet with id=AA3, first strand: chain 'C' and resid 235 through 241 Processing sheet with id=AA4, first strand: chain 'D' and resid 235 through 241 Processing sheet with id=AA5, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AA7, first strand: chain 'G' and resid 99 through 101 1103 hydrogen bonds defined for protein. 3261 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.93 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: 5239 1.34 - 1.46: 3686 1.46 - 1.58: 7330 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 16471 Sorted by residual: bond pdb=" C26 Y7Z A 504 " pdb=" N4 Y7Z A 504 " ideal model delta sigma weight residual 1.452 1.363 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C7 Y7Z A 504 " pdb=" N1 Y7Z A 504 " ideal model delta sigma weight residual 1.447 1.374 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 Y7Z A 504 " pdb=" N4 Y7Z A 504 " ideal model delta sigma weight residual 1.459 1.394 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" N VAL A 441 " pdb=" CA VAL A 441 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.24e+00 bond pdb=" N ILE A 434 " pdb=" CA ILE A 434 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.94e+00 ... (remaining 16466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 22171 2.89 - 5.78: 61 5.78 - 8.66: 3 8.66 - 11.55: 0 11.55 - 14.44: 1 Bond angle restraints: 22236 Sorted by residual: angle pdb=" C7 Y7Z A 504 " pdb=" N1 Y7Z A 504 " pdb=" C8 Y7Z A 504 " ideal model delta sigma weight residual 114.57 129.01 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C CYS A 371 " pdb=" CA CYS A 371 " pdb=" CB CYS A 371 " ideal model delta sigma weight residual 110.88 103.66 7.22 1.57e+00 4.06e-01 2.11e+01 angle pdb=" N CYS A 371 " pdb=" CA CYS A 371 " pdb=" C CYS A 371 " ideal model delta sigma weight residual 111.07 106.65 4.42 1.07e+00 8.73e-01 1.70e+01 angle pdb=" N ILE A 208 " pdb=" CA ILE A 208 " pdb=" C ILE A 208 " ideal model delta sigma weight residual 112.80 108.82 3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" N THR A 438 " pdb=" CA THR A 438 " pdb=" C THR A 438 " ideal model delta sigma weight residual 114.75 110.41 4.34 1.26e+00 6.30e-01 1.19e+01 ... (remaining 22231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9101 17.96 - 35.92: 604 35.92 - 53.88: 103 53.88 - 71.83: 93 71.83 - 89.79: 7 Dihedral angle restraints: 9908 sinusoidal: 4004 harmonic: 5904 Sorted by residual: dihedral pdb=" CB CYS D 333 " pdb=" SG CYS D 333 " pdb=" SG CYS D 371 " pdb=" CB CYS D 371 " ideal model delta sinusoidal sigma weight residual -86.00 -35.51 -50.49 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 371 " pdb=" CB CYS A 371 " ideal model delta sinusoidal sigma weight residual -86.00 -39.12 -46.88 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" C CYS A 371 " pdb=" N CYS A 371 " pdb=" CA CYS A 371 " pdb=" CB CYS A 371 " ideal model delta harmonic sigma weight residual -122.60 -112.64 -9.96 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 9905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2317 0.059 - 0.117: 239 0.117 - 0.176: 6 0.176 - 0.234: 1 0.234 - 0.293: 1 Chirality restraints: 2564 Sorted by residual: chirality pdb=" CA CYS A 371 " pdb=" N CYS A 371 " pdb=" C CYS A 371 " pdb=" CB CYS A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA TYR A 435 " pdb=" N TYR A 435 " pdb=" C TYR A 435 " pdb=" CB TYR A 435 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2561 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 430 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C GLU A 430 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU A 430 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A 431 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 261 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 262 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 261 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO B 262 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 262 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 262 " -0.018 5.00e-02 4.00e+02 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.83: 4977 2.83 - 3.41: 18397 3.41 - 3.99: 28698 3.99 - 4.56: 41673 4.56 - 5.14: 58958 Nonbonded interactions: 152703 Sorted by model distance: nonbonded pdb=" OG SER H 101 " pdb=" OE1 GLU H 104 " model vdw 2.258 3.040 nonbonded pdb=" OD2 ASP F 24 " pdb=" OG1 THR F 26 " model vdw 2.273 3.040 nonbonded pdb=" O HOH D1102 " pdb=" O HOH D1103 " model vdw 2.293 3.040 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 602 " model vdw 2.293 3.040 nonbonded pdb=" O HOH C 501 " pdb=" O HOH C 502 " model vdw 2.293 3.040 ... (remaining 152698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 478) selection = (chain 'B' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ ugh 478)) selection = (chain 'C' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ ugh 478)) selection = (chain 'D' and (resid 118 through 435 or (resid 436 and (name N or name CA or na \ me C or name CB or name CG or name CD or name CE or name NZ )) or resid 437 thro \ ugh 478)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 12.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 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 0.089 16475 Z= 0.153 Angle : 0.458 14.441 22244 Z= 0.272 Chirality : 0.035 0.293 2564 Planarity : 0.003 0.032 2787 Dihedral : 14.030 89.793 6072 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 2012 helix: 2.27 (0.14), residues: 1482 sheet: 1.03 (0.83), residues: 40 loop : -0.85 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 90 TYR 0.014 0.001 TYR H 138 PHE 0.018 0.001 PHE A 456 TRP 0.014 0.001 TRP C 432 HIS 0.004 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (16471) covalent geometry : angle 0.45694 / 0.27 (22236) SS BOND : bond 0.00645 / 0.33 ( 4) SS BOND : angle 1.38310 / 0.80 ( 8) hydrogen bonds : bond 0.18461 / 12.41 ( 1103) hydrogen bonds : angle 5.01531 / 3.64 ( 3261) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.8704 (mtm) cc_final: 0.8349 (mmm) REVERT: B 274 MET cc_start: 0.8692 (mtm) cc_final: 0.8330 (mmm) REVERT: C 274 MET cc_start: 0.8648 (mtm) cc_final: 0.8300 (mmm) REVERT: D 274 MET cc_start: 0.8701 (mtm) cc_final: 0.8340 (mmm) REVERT: G 49 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8502 (tp40) REVERT: G 86 ARG cc_start: 0.8935 (ttm170) cc_final: 0.8308 (mtm-85) REVERT: H 86 ARG cc_start: 0.8303 (mtt90) cc_final: 0.8063 (mtt90) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.1666 time to fit residues: 73.5613 Evaluate side-chains 278 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN C 462 GLN D 462 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.079429 restraints weight = 27710.670| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.67 r_work: 0.2868 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16475 Z= 0.151 Angle : 0.497 10.445 22244 Z= 0.274 Chirality : 0.038 0.140 2564 Planarity : 0.004 0.031 2787 Dihedral : 5.009 89.176 2208 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 0.57 % Allowed : 5.43 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.19), residues: 2012 helix: 2.40 (0.14), residues: 1491 sheet: 1.02 (0.72), residues: 48 loop : -0.97 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 126 TYR 0.016 0.001 TYR H 138 PHE 0.018 0.002 PHE A 456 TRP 0.011 0.001 TRP C 432 HIS 0.007 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16471) covalent geometry : angle 0.49376 / 0.27 (22236) SS BOND : bond 0.00674 / 0.31 ( 4) SS BOND : angle 2.91598 / 1.68 ( 8) hydrogen bonds : bond 0.06920 / 4.62 ( 1103) hydrogen bonds : angle 3.76363 / 2.72 ( 3261) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 285 time to evaluate : 0.619 Fit side-chains REVERT: A 274 MET cc_start: 0.8960 (mtm) cc_final: 0.8553 (mmm) REVERT: A 469 GLU cc_start: 0.8957 (tp30) cc_final: 0.8595 (tt0) REVERT: B 274 MET cc_start: 0.8911 (mtm) cc_final: 0.8497 (mmm) REVERT: B 469 GLU cc_start: 0.8992 (tp30) cc_final: 0.8422 (tt0) REVERT: C 274 MET cc_start: 0.8960 (mtm) cc_final: 0.8566 (mmm) REVERT: C 469 GLU cc_start: 0.8917 (tp30) cc_final: 0.8526 (tt0) REVERT: D 274 MET cc_start: 0.8944 (mtm) cc_final: 0.8531 (mmm) REVERT: F 17 SER cc_start: 0.8978 (m) cc_final: 0.8670 (t) REVERT: F 94 LYS cc_start: 0.7954 (tppt) cc_final: 0.7740 (tppt) REVERT: G 37 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8351 (ttm110) REVERT: G 86 ARG cc_start: 0.9174 (ttm170) cc_final: 0.8880 (mtm-85) outliers start: 10 outliers final: 6 residues processed: 290 average time/residue: 0.1470 time to fit residues: 59.6515 Evaluate side-chains 279 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 273 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN C 462 GLN D 462 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.077453 restraints weight = 28349.815| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.73 r_work: 0.2828 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16475 Z= 0.154 Angle : 0.486 9.217 22244 Z= 0.266 Chirality : 0.038 0.141 2564 Planarity : 0.004 0.031 2787 Dihedral : 5.030 89.108 2208 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.47 % Rotamer: Outliers : 0.86 % Allowed : 7.15 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.19), residues: 2012 helix: 2.42 (0.14), residues: 1491 sheet: 0.83 (0.72), residues: 48 loop : -0.97 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 126 TYR 0.018 0.001 TYR H 138 PHE 0.018 0.002 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.008 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (16471) covalent geometry : angle 0.48365 / 0.26 (22236) SS BOND : bond 0.00722 / 0.33 ( 4) SS BOND : angle 2.46603 / 1.36 ( 8) hydrogen bonds : bond 0.07001 / 4.67 ( 1103) hydrogen bonds : angle 3.60532 / 2.60 ( 3261) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.626 Fit side-chains REVERT: A 274 MET cc_start: 0.8935 (mtm) cc_final: 0.8507 (mmm) REVERT: A 469 GLU cc_start: 0.8987 (tp30) cc_final: 0.8545 (tt0) REVERT: B 274 MET cc_start: 0.8921 (mtm) cc_final: 0.8489 (mmm) REVERT: C 274 MET cc_start: 0.8913 (mtm) cc_final: 0.8494 (mmm) REVERT: C 399 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7727 (pt0) REVERT: D 274 MET cc_start: 0.8962 (mtm) cc_final: 0.8532 (mmm) REVERT: F 17 SER cc_start: 0.8947 (m) cc_final: 0.8679 (t) REVERT: G 111 ASN cc_start: 0.8593 (m-40) cc_final: 0.8324 (m110) outliers start: 15 outliers final: 10 residues processed: 273 average time/residue: 0.1416 time to fit residues: 53.9772 Evaluate side-chains 271 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 261 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain F residue 118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN C 415 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.078916 restraints weight = 28290.492| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.73 r_work: 0.2856 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16475 Z= 0.126 Angle : 0.449 7.848 22244 Z= 0.246 Chirality : 0.036 0.135 2564 Planarity : 0.003 0.044 2787 Dihedral : 4.847 86.688 2208 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.03 % Allowed : 8.41 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.19), residues: 2012 helix: 2.59 (0.14), residues: 1491 sheet: 0.76 (0.85), residues: 40 loop : -0.89 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 90 TYR 0.016 0.001 TYR H 138 PHE 0.017 0.002 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.008 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (16471) covalent geometry : angle 0.44707 / 0.25 (22236) SS BOND : bond 0.00657 / 0.30 ( 4) SS BOND : angle 2.15337 / 1.18 ( 8) hydrogen bonds : bond 0.06198 / 4.13 ( 1103) hydrogen bonds : angle 3.44222 / 2.49 ( 3261) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.604 Fit side-chains REVERT: A 274 MET cc_start: 0.8885 (mtm) cc_final: 0.8466 (mmm) REVERT: B 274 MET cc_start: 0.8856 (mtm) cc_final: 0.8436 (mmm) REVERT: C 274 MET cc_start: 0.8861 (mtm) cc_final: 0.8447 (mmm) REVERT: C 279 LYS cc_start: 0.7845 (mptt) cc_final: 0.7619 (mppt) REVERT: C 399 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7787 (pt0) REVERT: D 274 MET cc_start: 0.8917 (mtm) cc_final: 0.8494 (mmm) REVERT: E 111 ASN cc_start: 0.8605 (m110) cc_final: 0.8302 (m110) REVERT: E 145 MET cc_start: 0.7392 (ptt) cc_final: 0.6656 (ptt) REVERT: F 17 SER cc_start: 0.8950 (m) cc_final: 0.8722 (t) REVERT: F 72 MET cc_start: 0.8917 (mmp) cc_final: 0.8494 (mmp) REVERT: G 86 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8760 (mtm-85) REVERT: G 111 ASN cc_start: 0.8553 (m-40) cc_final: 0.8286 (m110) REVERT: H 86 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8589 (mtm-85) outliers start: 18 outliers final: 9 residues processed: 288 average time/residue: 0.1458 time to fit residues: 58.8968 Evaluate side-chains 269 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 296 ASN B 462 GLN C 415 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.079216 restraints weight = 28171.055| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.71 r_work: 0.2863 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16475 Z= 0.124 Angle : 0.453 8.187 22244 Z= 0.246 Chirality : 0.036 0.136 2564 Planarity : 0.003 0.031 2787 Dihedral : 4.770 86.072 2208 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 8.98 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.19), residues: 2012 helix: 2.66 (0.14), residues: 1491 sheet: 0.75 (0.86), residues: 40 loop : -0.85 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 90 TYR 0.016 0.001 TYR H 138 PHE 0.016 0.001 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.007 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (16471) covalent geometry : angle 0.45103 / 0.25 (22236) SS BOND : bond 0.00607 / 0.28 ( 4) SS BOND : angle 2.17679 / 1.20 ( 8) hydrogen bonds : bond 0.06017 / 4.01 ( 1103) hydrogen bonds : angle 3.37239 / 2.43 ( 3261) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.656 Fit side-chains REVERT: A 274 MET cc_start: 0.8884 (mtm) cc_final: 0.8472 (mmm) REVERT: A 469 GLU cc_start: 0.8949 (tp30) cc_final: 0.8439 (tt0) REVERT: B 274 MET cc_start: 0.8865 (mtm) cc_final: 0.8444 (mmm) REVERT: C 274 MET cc_start: 0.8859 (mtm) cc_final: 0.8460 (mmm) REVERT: C 399 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7781 (pt0) REVERT: D 274 MET cc_start: 0.8914 (mtm) cc_final: 0.8491 (mmm) REVERT: E 111 ASN cc_start: 0.8604 (m110) cc_final: 0.8297 (m110) REVERT: F 17 SER cc_start: 0.8929 (m) cc_final: 0.8706 (t) REVERT: F 37 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8166 (ttm110) REVERT: F 72 MET cc_start: 0.8941 (mmp) cc_final: 0.8483 (mmp) REVERT: G 86 ARG cc_start: 0.8900 (mtm-85) cc_final: 0.8655 (mtm-85) REVERT: G 111 ASN cc_start: 0.8572 (m-40) cc_final: 0.8293 (m110) REVERT: G 119 GLU cc_start: 0.8752 (mp0) cc_final: 0.8430 (mp0) REVERT: H 37 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8174 (ttm110) outliers start: 26 outliers final: 16 residues processed: 287 average time/residue: 0.1531 time to fit residues: 61.6054 Evaluate side-chains 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN C 415 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.084658 restraints weight = 27948.542| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.60 r_work: 0.2774 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16475 Z= 0.143 Angle : 0.486 8.688 22244 Z= 0.261 Chirality : 0.037 0.135 2564 Planarity : 0.004 0.048 2787 Dihedral : 4.838 87.115 2208 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 1.37 % Allowed : 9.50 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.19), residues: 2012 helix: 2.60 (0.14), residues: 1475 sheet: 0.87 (0.73), residues: 48 loop : -0.84 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 90 TYR 0.017 0.001 TYR H 138 PHE 0.016 0.002 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.006 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16471) covalent geometry : angle 0.48361 / 0.26 (22236) SS BOND : bond 0.00741 / 0.34 ( 4) SS BOND : angle 2.41367 / 1.33 ( 8) hydrogen bonds : bond 0.06497 / 4.33 ( 1103) hydrogen bonds : angle 3.39914 / 2.45 ( 3261) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.762 Fit side-chains REVERT: A 274 MET cc_start: 0.8994 (mtm) cc_final: 0.8580 (mmm) REVERT: A 469 GLU cc_start: 0.9095 (tp30) cc_final: 0.8542 (tt0) REVERT: B 274 MET cc_start: 0.8980 (mtm) cc_final: 0.8563 (mmm) REVERT: C 274 MET cc_start: 0.8933 (mtm) cc_final: 0.8527 (mmm) REVERT: C 279 LYS cc_start: 0.7912 (mptt) cc_final: 0.7614 (mppt) REVERT: D 274 MET cc_start: 0.9004 (mtm) cc_final: 0.8581 (mmm) REVERT: E 111 ASN cc_start: 0.8629 (m110) cc_final: 0.8282 (m110) REVERT: F 17 SER cc_start: 0.8909 (m) cc_final: 0.8688 (t) REVERT: F 37 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8194 (ttm110) REVERT: F 72 MET cc_start: 0.9015 (mmp) cc_final: 0.8553 (mmp) REVERT: G 86 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8694 (mtm-85) REVERT: G 111 ASN cc_start: 0.8596 (m-40) cc_final: 0.8290 (m110) REVERT: H 37 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8236 (ttm110) outliers start: 24 outliers final: 19 residues processed: 285 average time/residue: 0.1497 time to fit residues: 59.8231 Evaluate side-chains 280 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 50 optimal weight: 0.0040 chunk 165 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN C 415 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.080081 restraints weight = 27814.152| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.70 r_work: 0.2880 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16475 Z= 0.115 Angle : 0.458 8.847 22244 Z= 0.245 Chirality : 0.036 0.136 2564 Planarity : 0.003 0.030 2787 Dihedral : 4.632 84.526 2208 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Rotamer: Outliers : 0.86 % Allowed : 9.84 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.19), residues: 2012 helix: 2.80 (0.14), residues: 1471 sheet: 0.75 (0.86), residues: 40 loop : -0.64 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 90 TYR 0.016 0.001 TYR H 138 PHE 0.016 0.001 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (16471) covalent geometry : angle 0.45613 / 0.24 (22236) SS BOND : bond 0.00628 / 0.29 ( 4) SS BOND : angle 2.18347 / 1.23 ( 8) hydrogen bonds : bond 0.05620 / 3.75 ( 1103) hydrogen bonds : angle 3.29592 / 2.38 ( 3261) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 0.521 Fit side-chains REVERT: A 274 MET cc_start: 0.8885 (mtm) cc_final: 0.8471 (mmm) REVERT: A 469 GLU cc_start: 0.8935 (tp30) cc_final: 0.8442 (tt0) REVERT: B 274 MET cc_start: 0.8857 (mtm) cc_final: 0.8444 (mmm) REVERT: C 274 MET cc_start: 0.8853 (mtm) cc_final: 0.8457 (mmm) REVERT: C 279 LYS cc_start: 0.7875 (mptt) cc_final: 0.7627 (mppt) REVERT: D 274 MET cc_start: 0.8902 (mtm) cc_final: 0.8480 (mmm) REVERT: E 111 ASN cc_start: 0.8617 (m110) cc_final: 0.8310 (m110) REVERT: F 37 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8176 (ttm110) REVERT: F 72 MET cc_start: 0.8906 (mmp) cc_final: 0.8419 (mmp) REVERT: G 86 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8651 (mtm-85) REVERT: G 111 ASN cc_start: 0.8555 (m-40) cc_final: 0.8320 (m110) REVERT: H 37 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8202 (ttm110) outliers start: 15 outliers final: 12 residues processed: 284 average time/residue: 0.1478 time to fit residues: 58.7137 Evaluate side-chains 281 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 130 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086969 restraints weight = 28130.925| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.62 r_work: 0.2817 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16475 Z= 0.115 Angle : 0.475 9.947 22244 Z= 0.249 Chirality : 0.036 0.139 2564 Planarity : 0.003 0.034 2787 Dihedral : 4.517 82.460 2208 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.14 % Allowed : 9.67 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.19), residues: 2012 helix: 2.86 (0.14), residues: 1471 sheet: 0.74 (0.85), residues: 40 loop : -0.58 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 90 TYR 0.015 0.001 TYR H 138 PHE 0.016 0.001 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16471) covalent geometry : angle 0.47313 / 0.25 (22236) SS BOND : bond 0.00636 / 0.29 ( 4) SS BOND : angle 2.27190 / 1.29 ( 8) hydrogen bonds : bond 0.05420 / 3.62 ( 1103) hydrogen bonds : angle 3.24544 / 2.34 ( 3261) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.631 Fit side-chains REVERT: A 274 MET cc_start: 0.8944 (mtm) cc_final: 0.8531 (mmm) REVERT: B 274 MET cc_start: 0.8945 (mtm) cc_final: 0.8533 (mmm) REVERT: B 469 GLU cc_start: 0.9017 (tp30) cc_final: 0.8426 (tt0) REVERT: C 274 MET cc_start: 0.8906 (mtm) cc_final: 0.8515 (mmm) REVERT: C 279 LYS cc_start: 0.7839 (mptt) cc_final: 0.7594 (mppt) REVERT: D 274 MET cc_start: 0.8962 (mtm) cc_final: 0.8542 (mmm) REVERT: D 469 GLU cc_start: 0.8942 (tp30) cc_final: 0.8389 (tt0) REVERT: E 111 ASN cc_start: 0.8615 (m110) cc_final: 0.8296 (m110) REVERT: F 37 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8233 (ttm110) REVERT: F 72 MET cc_start: 0.8987 (mmp) cc_final: 0.8476 (mmp) REVERT: G 111 ASN cc_start: 0.8558 (m-40) cc_final: 0.8294 (m110) REVERT: H 37 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.8204 (ttm110) outliers start: 20 outliers final: 16 residues processed: 283 average time/residue: 0.1491 time to fit residues: 59.4181 Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN C 408 HIS C 462 GLN D 462 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.075907 restraints weight = 27779.713| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.69 r_work: 0.2798 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16475 Z= 0.203 Angle : 0.566 10.163 22244 Z= 0.300 Chirality : 0.040 0.150 2564 Planarity : 0.004 0.042 2787 Dihedral : 4.992 89.589 2208 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.26 % Allowed : 9.84 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.19), residues: 2012 helix: 2.46 (0.13), residues: 1468 sheet: 0.67 (0.72), residues: 48 loop : -0.72 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 90 TYR 0.021 0.002 TYR G 138 PHE 0.016 0.002 PHE D 456 TRP 0.009 0.002 TRP C 158 HIS 0.007 0.002 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (16471) covalent geometry : angle 0.56327 / 0.30 (22236) SS BOND : bond 0.00809 / 0.37 ( 4) SS BOND : angle 2.82375 / 1.53 ( 8) hydrogen bonds : bond 0.07727 / 5.16 ( 1103) hydrogen bonds : angle 3.50087 / 2.53 ( 3261) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 0.645 Fit side-chains REVERT: A 274 MET cc_start: 0.8976 (mtm) cc_final: 0.8564 (mmm) REVERT: A 469 GLU cc_start: 0.8923 (tp30) cc_final: 0.8514 (tt0) REVERT: B 274 MET cc_start: 0.8943 (mtm) cc_final: 0.8529 (mmm) REVERT: B 469 GLU cc_start: 0.8949 (tp30) cc_final: 0.8438 (tt0) REVERT: C 274 MET cc_start: 0.8938 (mtm) cc_final: 0.8534 (mmm) REVERT: D 274 MET cc_start: 0.8970 (mtm) cc_final: 0.8551 (mmm) REVERT: D 387 THR cc_start: 0.8848 (p) cc_final: 0.8613 (p) REVERT: D 469 GLU cc_start: 0.8872 (tp30) cc_final: 0.8370 (tt0) REVERT: F 37 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8157 (ttm110) REVERT: G 111 ASN cc_start: 0.8619 (m-40) cc_final: 0.8343 (m110) REVERT: H 37 ARG cc_start: 0.8748 (mtm-85) cc_final: 0.8190 (ttm110) outliers start: 22 outliers final: 19 residues processed: 284 average time/residue: 0.1505 time to fit residues: 59.4866 Evaluate side-chains 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN D 462 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086406 restraints weight = 28017.577| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.57 r_work: 0.2792 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16475 Z= 0.127 Angle : 0.495 8.897 22244 Z= 0.262 Chirality : 0.037 0.156 2564 Planarity : 0.003 0.034 2787 Dihedral : 4.693 86.254 2208 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.76 % Rotamer: Outliers : 1.03 % Allowed : 10.58 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.19), residues: 2012 helix: 2.70 (0.14), residues: 1471 sheet: 0.69 (0.74), residues: 46 loop : -0.70 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 126 TYR 0.016 0.001 TYR H 138 PHE 0.015 0.001 PHE A 456 TRP 0.011 0.001 TRP B 432 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (16471) covalent geometry : angle 0.49287 / 0.26 (22236) SS BOND : bond 0.00655 / 0.30 ( 4) SS BOND : angle 2.51685 / 1.43 ( 8) hydrogen bonds : bond 0.06057 / 4.04 ( 1103) hydrogen bonds : angle 3.33903 / 2.41 ( 3261) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 0.634 Fit side-chains REVERT: A 274 MET cc_start: 0.8989 (mtm) cc_final: 0.8576 (mmm) REVERT: A 469 GLU cc_start: 0.8981 (tp30) cc_final: 0.8512 (tt0) REVERT: B 274 MET cc_start: 0.8967 (mtm) cc_final: 0.8550 (mmm) REVERT: C 274 MET cc_start: 0.8941 (mtm) cc_final: 0.8535 (mmm) REVERT: C 279 LYS cc_start: 0.7912 (mptt) cc_final: 0.7674 (mppt) REVERT: D 274 MET cc_start: 0.8994 (mtm) cc_final: 0.8560 (mmm) REVERT: E 13 LYS cc_start: 0.9006 (tppt) cc_final: 0.8791 (mttp) REVERT: F 37 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8221 (ttm110) REVERT: F 72 MET cc_start: 0.9022 (mmp) cc_final: 0.8530 (mmp) REVERT: G 111 ASN cc_start: 0.8621 (m-40) cc_final: 0.8339 (m110) REVERT: H 37 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8335 (ttm110) outliers start: 18 outliers final: 18 residues processed: 284 average time/residue: 0.1469 time to fit residues: 57.8744 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 107 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN B 462 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079261 restraints weight = 27866.829| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.70 r_work: 0.2864 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16475 Z= 0.126 Angle : 0.499 8.806 22244 Z= 0.261 Chirality : 0.037 0.152 2564 Planarity : 0.003 0.033 2787 Dihedral : 4.619 85.019 2208 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.09 % Allowed : 10.76 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.19), residues: 2012 helix: 2.77 (0.14), residues: 1471 sheet: 0.69 (0.73), residues: 46 loop : -0.65 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 126 TYR 0.016 0.001 TYR H 138 PHE 0.016 0.001 PHE A 456 TRP 0.010 0.001 TRP B 432 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (16471) covalent geometry : angle 0.49676 / 0.26 (22236) SS BOND : bond 0.00669 / 0.30 ( 4) SS BOND : angle 2.40926 / 1.36 ( 8) hydrogen bonds : bond 0.05934 / 3.96 ( 1103) hydrogen bonds : angle 3.29882 / 2.38 ( 3261) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4409.14 seconds wall clock time: 76 minutes 5.06 seconds (4565.06 seconds total)