Starting phenix.real_space_refine on Sun May 3 21:55:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3g_42947/05_2026/8v3g_42947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3g_42947/05_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v3g_42947/05_2026/8v3g_42947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3g_42947/05_2026/8v3g_42947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v3g_42947/05_2026/8v3g_42947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3g_42947/05_2026/8v3g_42947.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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, 41 Unusual residues: {' K': 3, 'Y7Z': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 3.62, per 1000 atoms: 0.22 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: 1.26 Conformation dependent library (CDL) restraints added in 860.6 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: 2.49 Time building geometry restraints manager: 1.72 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: 11.290 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.580 Find NCS groups from input model: 0.340 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 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 covalent geometry : bond 0.00273 (16471) covalent geometry : angle 0.45694 (22236) SS BOND : bond 0.00645 ( 4) SS BOND : angle 1.38310 ( 8) hydrogen bonds : bond 0.18461 ( 1103) hydrogen bonds : angle 5.01531 ( 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 : 0.561 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: 0.8309 (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: 0.1646 time to fit residues: 71.8779 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 : 0.434 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.116041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.082278 restraints weight = 27907.972| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.62 r_work: 0.2859 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1150 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= 0.150 Angle : 0.497 9.884 22244 Z= 0.274 Chirality : 0.038 0.140 2564 Planarity : 0.004 0.031 2787 Dihedral : 5.012 89.264 2208 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 0.57 % Allowed : 5.38 % Favored : 94.05 % 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: 1.03 (0.72), residues: 48 loop : -0.96 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 241 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 covalent geometry : bond 0.00326 (16471) covalent geometry : angle 0.49362 (22236) SS BOND : bond 0.00722 ( 4) SS BOND : angle 3.06805 ( 8) hydrogen bonds : bond 0.06932 ( 1103) hydrogen bonds : angle 3.76776 ( 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 297 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 287 time to evaluate : 0.583 Fit side-chains REVERT: A 274 MET cc_start: 0.8953 (mtm) cc_final: 0.8547 (mmm) REVERT: A 469 GLU cc_start: 0.8961 (tp30) cc_final: 0.8603 (tt0) REVERT: B 274 MET cc_start: 0.8909 (mtm) cc_final: 0.8501 (mmm) REVERT: C 274 MET cc_start: 0.8966 (mtm) cc_final: 0.8575 (mmm) REVERT: C 469 GLU cc_start: 0.8914 (tp30) cc_final: 0.8527 (tt0) REVERT: D 274 MET cc_start: 0.8945 (mtm) cc_final: 0.8532 (mmm) REVERT: F 17 SER cc_start: 0.8985 (m) cc_final: 0.8677 (t) REVERT: F 94 LYS cc_start: 0.7932 (tppt) cc_final: 0.7715 (tppt) REVERT: G 37 ARG cc_start: 0.8678 (ttm110) cc_final: 0.8379 (ttm110) REVERT: G 86 ARG cc_start: 0.9200 (ttm170) cc_final: 0.8893 (mtm-85) REVERT: H 90 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8152 (ttm-80) outliers start: 10 outliers final: 6 residues processed: 292 average time/residue: 0.1553 time to fit residues: 62.6019 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.1980 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: 3.9990 chunk 60 optimal weight: 1.9990 chunk 192 optimal weight: 0.0060 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 462 GLN C 462 GLN D 462 GLN ** 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 = 0.3585 r_free = 0.3585 target = 0.116340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081376 restraints weight = 28415.648| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.76 r_work: 0.2854 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16475 Z= 0.123 Angle : 0.448 8.408 22244 Z= 0.246 Chirality : 0.036 0.136 2564 Planarity : 0.003 0.031 2787 Dihedral : 4.842 86.642 2208 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Rotamer: Outliers : 0.63 % Allowed : 7.32 % Favored : 92.05 % 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: 2.65 (0.19), residues: 2012 helix: 2.57 (0.14), residues: 1491 sheet: 0.75 (0.86), residues: 40 loop : -0.88 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.007 0.001 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00255 (16471) covalent geometry : angle 0.44654 (22236) SS BOND : bond 0.00606 ( 4) SS BOND : angle 2.24294 ( 8) hydrogen bonds : bond 0.06077 ( 1103) hydrogen bonds : angle 3.50869 ( 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 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 0.620 Fit side-chains REVERT: A 274 MET cc_start: 0.8897 (mtm) cc_final: 0.8471 (mmm) REVERT: B 274 MET cc_start: 0.8883 (mtm) cc_final: 0.8457 (mmm) REVERT: C 274 MET cc_start: 0.8888 (mtm) cc_final: 0.8477 (mmm) REVERT: C 399 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7689 (pt0) REVERT: D 274 MET cc_start: 0.8941 (mtm) cc_final: 0.8522 (mmm) REVERT: E 13 LYS cc_start: 0.9059 (tppt) cc_final: 0.8854 (tppt) REVERT: E 111 ASN cc_start: 0.8607 (m110) cc_final: 0.8317 (m110) REVERT: F 17 SER cc_start: 0.8925 (m) cc_final: 0.8688 (t) REVERT: G 86 ARG cc_start: 0.9131 (ttm170) cc_final: 0.8771 (mtm-85) REVERT: G 111 ASN cc_start: 0.8543 (m-40) cc_final: 0.8277 (m110) REVERT: H 86 ARG cc_start: 0.8889 (ttm170) cc_final: 0.8506 (ttm170) outliers start: 11 outliers final: 6 residues processed: 283 average time/residue: 0.1498 time to fit residues: 58.4779 Evaluate side-chains 272 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 266 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 136 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3581 r_free = 0.3581 target = 0.116082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085683 restraints weight = 28258.076| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.68 r_work: 0.2787 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1489 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= 0.125 Angle : 0.449 8.042 22244 Z= 0.245 Chirality : 0.036 0.134 2564 Planarity : 0.003 0.044 2787 Dihedral : 4.793 85.543 2208 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 7.55 % Favored : 91.19 % 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: 2.74 (0.19), residues: 2012 helix: 2.63 (0.14), residues: 1491 sheet: 1.00 (0.73), residues: 48 loop : -0.88 (0.28), residues: 473 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 0.007 0.001 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00266 (16471) covalent geometry : angle 0.44755 (22236) SS BOND : bond 0.00621 ( 4) SS BOND : angle 2.18443 ( 8) hydrogen bonds : bond 0.06087 ( 1103) hydrogen bonds : angle 3.41082 ( 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 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.555 Fit side-chains REVERT: A 274 MET cc_start: 0.8956 (mtm) cc_final: 0.8535 (mmm) REVERT: A 469 GLU cc_start: 0.9071 (tp30) cc_final: 0.8491 (tt0) REVERT: B 274 MET cc_start: 0.8944 (mtm) cc_final: 0.8520 (mmm) REVERT: C 274 MET cc_start: 0.8945 (mtm) cc_final: 0.8531 (mmm) REVERT: C 399 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7918 (pt0) REVERT: D 274 MET cc_start: 0.8998 (mtm) cc_final: 0.8575 (mmm) REVERT: E 111 ASN cc_start: 0.8626 (m110) cc_final: 0.8310 (m110) REVERT: E 145 MET cc_start: 0.7436 (ptt) cc_final: 0.6751 (ptt) REVERT: F 17 SER cc_start: 0.8921 (m) cc_final: 0.8676 (t) REVERT: G 86 ARG cc_start: 0.9143 (ttm170) cc_final: 0.8856 (mtm-85) REVERT: G 111 ASN cc_start: 0.8567 (m-40) cc_final: 0.8293 (m110) REVERT: G 119 GLU cc_start: 0.8951 (mp0) cc_final: 0.8665 (mp0) REVERT: H 37 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8212 (ttm110) outliers start: 22 outliers final: 12 residues processed: 285 average time/residue: 0.1616 time to fit residues: 63.9997 Evaluate side-chains 274 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 262 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 391 VAL 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 62 THR 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: 1.9990 chunk 137 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 130 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 296 ASN B 462 GLN C 415 GLN 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 = 0.3564 r_free = 0.3564 target = 0.114963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.078027 restraints weight = 28113.855| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.73 r_work: 0.2836 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1594 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= 0.144 Angle : 0.477 8.564 22244 Z= 0.259 Chirality : 0.037 0.134 2564 Planarity : 0.003 0.032 2787 Dihedral : 4.873 87.112 2208 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.54 % Allowed : 9.10 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.19), residues: 2012 helix: 2.56 (0.14), residues: 1491 sheet: 0.86 (0.72), residues: 48 loop : -0.93 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 90 TYR 0.018 0.001 TYR H 138 PHE 0.016 0.002 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00323 (16471) covalent geometry : angle 0.47524 (22236) SS BOND : bond 0.00685 ( 4) SS BOND : angle 2.39212 ( 8) hydrogen bonds : bond 0.06578 ( 1103) hydrogen bonds : angle 3.42126 ( 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 289 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.602 Fit side-chains REVERT: A 274 MET cc_start: 0.8932 (mtm) cc_final: 0.8508 (mmm) REVERT: A 469 GLU cc_start: 0.8999 (tp30) cc_final: 0.8546 (tt0) REVERT: B 274 MET cc_start: 0.8898 (mtm) cc_final: 0.8472 (mmm) REVERT: C 274 MET cc_start: 0.8926 (mtm) cc_final: 0.8514 (mmm) REVERT: C 399 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7800 (pt0) REVERT: D 274 MET cc_start: 0.8960 (mtm) cc_final: 0.8525 (mmm) REVERT: E 86 ARG cc_start: 0.8578 (mmt90) cc_final: 0.8311 (mmt90) REVERT: E 111 ASN cc_start: 0.8619 (m110) cc_final: 0.8302 (m110) REVERT: F 17 SER cc_start: 0.8923 (m) cc_final: 0.8687 (t) REVERT: F 37 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8170 (ttm110) REVERT: G 86 ARG cc_start: 0.9098 (ttm170) cc_final: 0.8774 (mtm-85) REVERT: G 111 ASN cc_start: 0.8566 (m-40) cc_final: 0.8287 (m110) REVERT: H 37 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8192 (ttm110) REVERT: H 86 ARG cc_start: 0.8949 (ttm170) cc_final: 0.8703 (mtm-85) outliers start: 27 outliers final: 13 residues processed: 282 average time/residue: 0.1557 time to fit residues: 60.6824 Evaluate side-chains 276 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 263 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 462 GLN C 408 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.076710 restraints weight = 27981.943| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.72 r_work: 0.2811 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16475 Z= 0.171 Angle : 0.511 9.443 22244 Z= 0.277 Chirality : 0.038 0.137 2564 Planarity : 0.004 0.048 2787 Dihedral : 4.998 89.170 2208 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 1.54 % Allowed : 9.15 % 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: 2.47 (0.19), residues: 2012 helix: 2.47 (0.14), residues: 1475 sheet: 0.75 (0.73), residues: 48 loop : -0.94 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 90 TYR 0.020 0.002 TYR H 138 PHE 0.016 0.002 PHE A 456 TRP 0.010 0.002 TRP C 432 HIS 0.006 0.001 HIS C 408 Details of bonding type rmsd covalent geometry : bond 0.00396 (16471) covalent geometry : angle 0.50869 (22236) SS BOND : bond 0.00693 ( 4) SS BOND : angle 2.61129 ( 8) hydrogen bonds : bond 0.07254 ( 1103) hydrogen bonds : angle 3.49185 ( 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 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.554 Fit side-chains REVERT: A 274 MET cc_start: 0.8974 (mtm) cc_final: 0.8551 (mmm) REVERT: A 469 GLU cc_start: 0.9016 (tp30) cc_final: 0.8589 (tt0) REVERT: B 274 MET cc_start: 0.8924 (mtm) cc_final: 0.8497 (mmm) REVERT: C 274 MET cc_start: 0.8942 (mtm) cc_final: 0.8523 (mmm) REVERT: D 274 MET cc_start: 0.8977 (mtm) cc_final: 0.8543 (mmm) REVERT: D 387 THR cc_start: 0.8832 (p) cc_final: 0.8579 (p) REVERT: D 469 GLU cc_start: 0.8889 (tp30) cc_final: 0.8358 (tt0) REVERT: F 17 SER cc_start: 0.8924 (m) cc_final: 0.8678 (t) REVERT: F 37 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8178 (ttm110) REVERT: F 72 MET cc_start: 0.8935 (mmp) cc_final: 0.8457 (mmp) REVERT: G 86 ARG cc_start: 0.9104 (ttm170) cc_final: 0.8772 (mtm-85) REVERT: G 111 ASN cc_start: 0.8582 (m-40) cc_final: 0.8348 (m110) REVERT: H 37 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8215 (ttm110) outliers start: 27 outliers final: 20 residues processed: 282 average time/residue: 0.1481 time to fit residues: 58.4236 Evaluate side-chains 288 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 391 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 223 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 50 optimal weight: 0.0040 chunk 165 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 462 GLN ** 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 = 0.3584 r_free = 0.3584 target = 0.116733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.079992 restraints weight = 27971.423| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.72 r_work: 0.2870 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16475 Z= 0.116 Angle : 0.456 8.135 22244 Z= 0.247 Chirality : 0.036 0.137 2564 Planarity : 0.003 0.030 2787 Dihedral : 4.665 85.421 2208 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 0.63 % Allowed : 10.47 % 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: 2.87 (0.19), residues: 2012 helix: 2.75 (0.14), residues: 1471 sheet: 0.80 (0.88), residues: 40 loop : -0.73 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 90 TYR 0.016 0.001 TYR H 138 PHE 0.016 0.001 PHE A 456 TRP 0.011 0.001 TRP C 432 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00234 (16471) covalent geometry : angle 0.45439 (22236) SS BOND : bond 0.00572 ( 4) SS BOND : angle 2.25573 ( 8) hydrogen bonds : bond 0.05730 ( 1103) hydrogen bonds : angle 3.32475 ( 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 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 0.680 Fit side-chains REVERT: A 274 MET cc_start: 0.8893 (mtm) cc_final: 0.8476 (mmm) REVERT: B 274 MET cc_start: 0.8856 (mtm) cc_final: 0.8437 (mmm) REVERT: C 274 MET cc_start: 0.8877 (mtm) cc_final: 0.8469 (mmm) REVERT: D 274 MET cc_start: 0.8909 (mtm) cc_final: 0.8483 (mmm) REVERT: E 13 LYS cc_start: 0.8998 (tppt) cc_final: 0.8770 (mttp) REVERT: E 111 ASN cc_start: 0.8614 (m110) cc_final: 0.8305 (m110) REVERT: F 37 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8206 (ttm110) REVERT: F 72 MET cc_start: 0.8914 (mmp) cc_final: 0.8452 (mmp) REVERT: F 76 MET cc_start: 0.8365 (mmt) cc_final: 0.8157 (mmt) REVERT: G 86 ARG cc_start: 0.9072 (ttm170) cc_final: 0.8748 (mtm-85) REVERT: G 111 ASN cc_start: 0.8575 (m-40) cc_final: 0.8338 (m110) REVERT: H 37 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.8217 (ttm110) outliers start: 11 outliers final: 8 residues processed: 284 average time/residue: 0.1588 time to fit residues: 62.1950 Evaluate side-chains 274 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 163 optimal weight: 0.0980 chunk 130 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 462 GLN E 49 GLN G 49 GLN ** 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 = 0.3590 r_free = 0.3590 target = 0.116742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.080154 restraints weight = 28134.270| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.72 r_work: 0.2876 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16475 Z= 0.117 Angle : 0.484 10.041 22244 Z= 0.253 Chirality : 0.036 0.143 2564 Planarity : 0.003 0.033 2787 Dihedral : 4.568 83.739 2208 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 0.97 % Allowed : 10.30 % Favored : 88.73 % 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: 2.97 (0.19), residues: 2012 helix: 2.82 (0.14), residues: 1471 sheet: 0.70 (0.86), residues: 40 loop : -0.63 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 126 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 covalent geometry : bond 0.00245 (16471) covalent geometry : angle 0.48183 (22236) SS BOND : bond 0.00645 ( 4) SS BOND : angle 2.27076 ( 8) hydrogen bonds : bond 0.05599 ( 1103) hydrogen bonds : angle 3.27154 ( 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 287 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.623 Fit side-chains REVERT: A 274 MET cc_start: 0.8883 (mtm) cc_final: 0.8476 (mmm) REVERT: A 469 GLU cc_start: 0.8908 (tp30) cc_final: 0.8370 (tt0) REVERT: B 274 MET cc_start: 0.8852 (mtm) cc_final: 0.8441 (mmm) REVERT: B 469 GLU cc_start: 0.8890 (tp30) cc_final: 0.8392 (tt0) REVERT: C 274 MET cc_start: 0.8857 (mtm) cc_final: 0.8455 (mmm) REVERT: D 274 MET cc_start: 0.8915 (mtm) cc_final: 0.8504 (mmm) REVERT: D 469 GLU cc_start: 0.8827 (tp30) cc_final: 0.8368 (tt0) REVERT: E 111 ASN cc_start: 0.8603 (m110) cc_final: 0.8291 (m110) REVERT: F 37 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8209 (ttm110) REVERT: F 72 MET cc_start: 0.8915 (mmp) cc_final: 0.8446 (mmp) REVERT: G 86 ARG cc_start: 0.9047 (ttm170) cc_final: 0.8777 (mtm-85) REVERT: G 111 ASN cc_start: 0.8576 (m-40) cc_final: 0.8339 (m110) REVERT: H 37 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8219 (ttm110) outliers start: 17 outliers final: 12 residues processed: 281 average time/residue: 0.1532 time to fit residues: 59.8672 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.077499 restraints weight = 27808.555| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.71 r_work: 0.2826 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16475 Z= 0.159 Angle : 0.527 9.535 22244 Z= 0.277 Chirality : 0.038 0.163 2564 Planarity : 0.004 0.032 2787 Dihedral : 4.822 87.656 2208 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.14 % Allowed : 10.30 % Favored : 88.56 % 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: 2.72 (0.19), residues: 2012 helix: 2.62 (0.14), residues: 1471 sheet: 0.79 (0.72), residues: 48 loop : -0.72 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 126 TYR 0.018 0.001 TYR G 138 PHE 0.016 0.002 PHE A 456 TRP 0.009 0.001 TRP C 432 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00365 (16471) covalent geometry : angle 0.52483 (22236) SS BOND : bond 0.00795 ( 4) SS BOND : angle 2.61957 ( 8) hydrogen bonds : bond 0.06850 ( 1103) hydrogen bonds : angle 3.39538 ( 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 284 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.625 Fit side-chains REVERT: A 274 MET cc_start: 0.8957 (mtm) cc_final: 0.8546 (mmm) REVERT: A 469 GLU cc_start: 0.8916 (tp30) cc_final: 0.8472 (tt0) REVERT: B 274 MET cc_start: 0.8904 (mtm) cc_final: 0.8486 (mmm) REVERT: C 274 MET cc_start: 0.8923 (mtm) cc_final: 0.8516 (mmm) REVERT: D 274 MET cc_start: 0.8965 (mtm) cc_final: 0.8547 (mmm) REVERT: D 387 THR cc_start: 0.8843 (p) cc_final: 0.8584 (p) REVERT: D 469 GLU cc_start: 0.8841 (tp30) cc_final: 0.8326 (tt0) REVERT: F 37 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8147 (ttm110) REVERT: F 72 MET cc_start: 0.8917 (mmp) cc_final: 0.8455 (mmp) REVERT: G 86 ARG cc_start: 0.9074 (ttm170) cc_final: 0.8748 (mtm-85) REVERT: G 111 ASN cc_start: 0.8616 (m-40) cc_final: 0.8363 (m110) REVERT: H 37 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8240 (ttm110) outliers start: 20 outliers final: 16 residues processed: 278 average time/residue: 0.1568 time to fit residues: 60.3097 Evaluate side-chains 279 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 371 CYS 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 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 G residue 144 MET Chi-restraints excluded: chain H residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 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: 3.9990 chunk 23 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 172 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3560 r_free = 0.3560 target = 0.114709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.077890 restraints weight = 28019.883| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.73 r_work: 0.2832 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16475 Z= 0.146 Angle : 0.520 9.549 22244 Z= 0.272 Chirality : 0.038 0.161 2564 Planarity : 0.003 0.034 2787 Dihedral : 4.798 87.841 2208 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 0.86 % Allowed : 10.81 % Favored : 88.33 % 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: 2.73 (0.19), residues: 2012 helix: 2.63 (0.14), residues: 1471 sheet: 0.71 (0.72), residues: 48 loop : -0.73 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 126 TYR 0.018 0.001 TYR H 138 PHE 0.016 0.002 PHE A 456 TRP 0.010 0.001 TRP C 432 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00329 (16471) covalent geometry : angle 0.51813 (22236) SS BOND : bond 0.00702 ( 4) SS BOND : angle 2.57382 ( 8) hydrogen bonds : bond 0.06618 ( 1103) hydrogen bonds : angle 3.38439 ( 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 282 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 0.432 Fit side-chains REVERT: A 274 MET cc_start: 0.8943 (mtm) cc_final: 0.8530 (mmm) REVERT: A 469 GLU cc_start: 0.8937 (tp30) cc_final: 0.8510 (tt0) REVERT: B 274 MET cc_start: 0.8900 (mtm) cc_final: 0.8481 (mmm) REVERT: B 469 GLU cc_start: 0.8901 (tp30) cc_final: 0.8358 (tt0) REVERT: C 274 MET cc_start: 0.8921 (mtm) cc_final: 0.8509 (mmm) REVERT: D 274 MET cc_start: 0.8965 (mtm) cc_final: 0.8536 (mmm) REVERT: D 469 GLU cc_start: 0.8847 (tp30) cc_final: 0.8346 (tt0) REVERT: E 13 LYS cc_start: 0.9016 (tppt) cc_final: 0.8782 (mttp) REVERT: F 37 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8189 (ttm110) REVERT: F 72 MET cc_start: 0.8918 (mmp) cc_final: 0.8467 (mmp) REVERT: G 86 ARG cc_start: 0.9071 (ttm170) cc_final: 0.8745 (mtm-85) REVERT: G 111 ASN cc_start: 0.8617 (m-40) cc_final: 0.8358 (m110) REVERT: H 37 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8228 (ttm110) outliers start: 15 outliers final: 14 residues processed: 279 average time/residue: 0.1565 time to fit residues: 60.0458 Evaluate side-chains 280 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 371 CYS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 107 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN B 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.078035 restraints weight = 27875.011| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.72 r_work: 0.2835 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16475 Z= 0.143 Angle : 0.517 9.398 22244 Z= 0.271 Chirality : 0.038 0.165 2564 Planarity : 0.003 0.033 2787 Dihedral : 4.779 87.887 2208 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.09 % Allowed : 10.70 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.19), residues: 2012 helix: 2.65 (0.14), residues: 1471 sheet: 0.72 (0.71), residues: 48 loop : -0.71 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 126 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 0.005 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00321 (16471) covalent geometry : angle 0.51442 (22236) SS BOND : bond 0.00680 ( 4) SS BOND : angle 2.53241 ( 8) hydrogen bonds : bond 0.06539 ( 1103) hydrogen bonds : angle 3.37131 ( 3261) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.87 seconds wall clock time: 75 minutes 32.87 seconds (4532.87 seconds total)