Starting phenix.real_space_refine on Fri Sep 11 17:38:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tqf_10550/09_2026/6tqf_10550.map" } resolution = 3.5 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 P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 6718 2.51 5 N 1768 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 207 Unusual residues: {' MG': 1, 'ANP': 1, 'LMT': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 207 Unusual residues: {' MG': 1, 'ANP': 1, 'LMT': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10426 At special positions: 0 Unit cell: (87.7663, 76.689, 147.413, 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) S 24 16.00 P 6 15.00 Mg 2 11.99 O 1908 8.00 N 1768 7.00 C 6718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 373.8 milliseconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 44.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.915A pdb=" N GLY A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.688A pdb=" N TYR A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 removed outlier: 4.020A pdb=" N ILE A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 55' Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 72 through 102 removed outlier: 4.044A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.781A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 107' Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.724A pdb=" N ARG A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.968A pdb=" N GLY A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 4.027A pdb=" N VAL A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 3.598A pdb=" N TRP A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.932A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.675A pdb=" N LEU A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 236 " --> pdb=" O TRP A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 236' Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.719A pdb=" N VAL A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 removed outlier: 3.569A pdb=" N LEU A 272 " --> pdb=" O GLY A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.837A pdb=" N ARG A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.757A pdb=" N VAL A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 removed outlier: 3.560A pdb=" N ILE A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.542A pdb=" N ARG A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.298A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 344 removed outlier: 3.787A pdb=" N ASN A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.537A pdb=" N VAL A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.540A pdb=" N PHE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.994A pdb=" N THR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.527A pdb=" N LEU A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.812A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.701A pdb=" N CYS A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.742A pdb=" N THR A 567 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 568' Processing helix chain 'A' and resid 586 through 597 removed outlier: 3.641A pdb=" N TYR A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 35 removed outlier: 3.916A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 43 removed outlier: 3.687A pdb=" N TYR B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 4.020A pdb=" N ILE B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 72 through 102 removed outlier: 4.044A pdb=" N LEU B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.782A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 107' Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.724A pdb=" N ARG B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.967A pdb=" N GLY B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 4.027A pdb=" N VAL B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.599A pdb=" N TRP B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 163 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.931A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.675A pdb=" N LEU B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER B 236 " --> pdb=" O TRP B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.719A pdb=" N VAL B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 removed outlier: 3.569A pdb=" N LEU B 272 " --> pdb=" O GLY B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.837A pdb=" N ARG B 278 " --> pdb=" O TRP B 274 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.757A pdb=" N VAL B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.559A pdb=" N ILE B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.542A pdb=" N ARG B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.298A pdb=" N ALA B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 removed outlier: 3.787A pdb=" N ASN B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.536A pdb=" N VAL B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.541A pdb=" N PHE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.995A pdb=" N THR B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.526A pdb=" N LEU B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 407 removed outlier: 3.812A pdb=" N LEU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.701A pdb=" N CYS B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.744A pdb=" N THR B 567 " --> pdb=" O ARG B 563 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 568' Processing helix chain 'B' and resid 586 through 597 removed outlier: 3.642A pdb=" N TYR B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 592 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.647A pdb=" N LEU A 418 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG A 486 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG A 420 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 481 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 432 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR A 483 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 430 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 434 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.647A pdb=" N LEU A 418 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG A 486 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG A 420 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 481 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 432 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR A 483 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 430 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 427 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 573 through 575 removed outlier: 7.145A pdb=" N LEU A 574 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 456 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 455 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 619 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU A 621 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR A 459 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 240 Processing sheet with id=AA6, first strand: chain 'B' and resid 418 through 421 removed outlier: 6.646A pdb=" N LEU B 418 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG B 486 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG B 420 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER B 481 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 432 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR B 483 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 430 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 434 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 418 through 421 removed outlier: 6.646A pdb=" N LEU B 418 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG B 486 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG B 420 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER B 481 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 432 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR B 483 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 430 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 427 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 573 through 575 removed outlier: 7.146A pdb=" N LEU B 574 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B 456 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER B 455 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 619 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 457 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 621 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 459 " --> pdb=" O LEU B 621 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 570 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: 1.52 Time building geometry restraints manager: 1.02 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: 3258 1.34 - 1.46: 2303 1.46 - 1.57: 5075 1.57 - 1.69: 10 1.69 - 1.81: 40 Bond restraints: 10686 Sorted by residual: bond pdb=" N3B ANP B 807 " pdb=" PG ANP B 807 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N3B ANP A 807 " pdb=" PG ANP A 807 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" O3A ANP B 807 " pdb=" PB ANP B 807 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" O3A ANP A 807 " pdb=" PB ANP A 807 " ideal model delta sigma weight residual 1.700 1.604 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N VAL A 632 " pdb=" CA VAL A 632 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.09e+00 ... (remaining 10681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 14075 2.37 - 4.74: 362 4.74 - 7.12: 98 7.12 - 9.49: 20 9.49 - 11.86: 3 Bond angle restraints: 14558 Sorted by residual: angle pdb=" O GLU A 633 " pdb=" C GLU A 633 " pdb=" N ALA A 634 " ideal model delta sigma weight residual 121.65 125.95 -4.30 8.30e-01 1.45e+00 2.69e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 111.90 108.41 3.49 8.10e-01 1.52e+00 1.85e+01 angle pdb=" N ILE B 352 " pdb=" CA ILE B 352 " pdb=" C ILE B 352 " ideal model delta sigma weight residual 111.90 108.44 3.46 8.10e-01 1.52e+00 1.83e+01 angle pdb=" CA GLU A 633 " pdb=" C GLU A 633 " pdb=" N ALA A 634 " ideal model delta sigma weight residual 119.95 115.24 4.71 1.19e+00 7.06e-01 1.57e+01 angle pdb=" N VAL B 346 " pdb=" CA VAL B 346 " pdb=" C VAL B 346 " ideal model delta sigma weight residual 108.88 117.20 -8.32 2.16e+00 2.14e-01 1.49e+01 ... (remaining 14553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 5364 17.45 - 34.89: 573 34.89 - 52.34: 163 52.34 - 69.78: 26 69.78 - 87.23: 10 Dihedral angle restraints: 6136 sinusoidal: 2486 harmonic: 3650 Sorted by residual: dihedral pdb=" CA LEU A 429 " pdb=" C LEU A 429 " pdb=" N ASN A 430 " pdb=" CA ASN A 430 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEU B 429 " pdb=" C LEU B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ALA B 464 " pdb=" C ALA B 464 " pdb=" N GLY B 465 " pdb=" CA GLY B 465 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1283 0.058 - 0.116: 347 0.116 - 0.174: 52 0.174 - 0.232: 8 0.232 - 0.291: 2 Chirality restraints: 1692 Sorted by residual: chirality pdb=" C3' ANP A 807 " pdb=" C2' ANP A 807 " pdb=" C4' ANP A 807 " pdb=" O3' ANP A 807 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' ANP B 807 " pdb=" C2' ANP B 807 " pdb=" C4' ANP B 807 " pdb=" O3' ANP B 807 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1B LMT A 802 " pdb=" C2B LMT A 802 " pdb=" O1B LMT A 802 " pdb=" O5B LMT A 802 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1689 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 444 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 445 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 444 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO B 445 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 445 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 445 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 354 " 0.035 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 355 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.029 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 144 2.65 - 3.22: 8317 3.22 - 3.78: 13953 3.78 - 4.34: 19209 4.34 - 4.90: 32432 Nonbonded interactions: 74055 Sorted by model distance: nonbonded pdb=" OG1 THR B 467 " pdb="MG MG B 806 " model vdw 2.092 2.170 nonbonded pdb=" OG1 THR A 467 " pdb="MG MG A 806 " model vdw 2.092 2.170 nonbonded pdb=" OE1 GLN A 498 " pdb="MG MG A 806 " model vdw 2.141 2.170 nonbonded pdb=" OE1 GLN B 498 " pdb="MG MG B 806 " model vdw 2.141 2.170 nonbonded pdb=" O3' LMT A 804 " pdb=" O5B LMT A 804 " model vdw 2.183 3.040 ... (remaining 74050 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 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 : 0.007 0.161 10686 Z= 0.317 Angle : 0.991 11.860 14558 Z= 0.492 Chirality : 0.054 0.291 1692 Planarity : 0.006 0.058 1786 Dihedral : 15.746 87.227 3788 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 8.60 % Favored : 91.30 % 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: -6.53 (0.14), residues: 1264 helix: -4.79 (0.07), residues: 722 sheet: -1.47 (0.47), residues: 102 loop : -3.80 (0.20), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.008 0.001 TYR B 21 PHE 0.018 0.001 PHE A 317 TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.32 (10686) covalent geometry : angle 0.99092 / 0.49 (14558) hydrogen bonds : bond 0.25770 / 17.80 ( 192) hydrogen bonds : angle 7.92019 / 5.68 ( 570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.389 Fit side-chains REVERT: A 80 LEU cc_start: 0.9236 (tp) cc_final: 0.9034 (tp) REVERT: A 164 ASP cc_start: 0.8450 (t70) cc_final: 0.8105 (t0) REVERT: A 543 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 543 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7236 (mt-10) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1578 time to fit residues: 22.7517 Evaluate side-chains 74 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 ASN A 338 ASN A 430 ASN B 279 ASN B 338 ASN B 430 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.087936 restraints weight = 15024.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.088300 restraints weight = 10288.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.089128 restraints weight = 7808.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.089540 restraints weight = 7578.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.089908 restraints weight = 6630.223| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10686 Z= 0.092 Angle : 0.541 9.584 14558 Z= 0.263 Chirality : 0.039 0.151 1692 Planarity : 0.004 0.036 1786 Dihedral : 9.035 59.437 1524 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.66 % Allowed : 11.63 % Favored : 87.71 % 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: -5.43 (0.17), residues: 1264 helix: -4.06 (0.12), residues: 700 sheet: -1.52 (0.58), residues: 62 loop : -2.91 (0.22), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 486 TYR 0.006 0.001 TYR A 21 PHE 0.009 0.001 PHE B 573 TRP 0.006 0.001 TRP B 547 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (10686) covalent geometry : angle 0.54090 / 0.26 (14558) hydrogen bonds : bond 0.04288 / 2.76 ( 192) hydrogen bonds : angle 4.79740 / 3.31 ( 570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.381 Fit side-chains REVERT: A 543 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 543 GLU cc_start: 0.7229 (mt-10) cc_final: 0.7004 (mt-10) outliers start: 7 outliers final: 2 residues processed: 90 average time/residue: 0.1336 time to fit residues: 16.2582 Evaluate side-chains 76 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.082628 restraints weight = 15384.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085625 restraints weight = 9020.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087653 restraints weight = 6369.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088901 restraints weight = 5059.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.089825 restraints weight = 4365.055| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10686 Z= 0.230 Angle : 0.629 10.111 14558 Z= 0.305 Chirality : 0.045 0.144 1692 Planarity : 0.004 0.031 1786 Dihedral : 8.678 56.837 1524 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.51 % Allowed : 14.37 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.15 (0.18), residues: 1264 helix: -3.72 (0.13), residues: 722 sheet: -1.70 (0.50), residues: 90 loop : -2.88 (0.23), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.007 0.001 TYR A 327 PHE 0.016 0.001 PHE A 573 TRP 0.009 0.001 TRP B 477 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (10686) covalent geometry : angle 0.62919 / 0.30 (14558) hydrogen bonds : bond 0.06127 / 4.02 ( 192) hydrogen bonds : angle 4.75532 / 3.26 ( 570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.431 Fit side-chains REVERT: A 166 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8428 (pp) REVERT: A 543 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7187 (mt-10) REVERT: B 166 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8434 (pp) REVERT: B 193 ASP cc_start: 0.8301 (t0) cc_final: 0.8089 (t0) REVERT: B 543 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7175 (mt-10) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.1269 time to fit residues: 15.0501 Evaluate side-chains 83 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085181 restraints weight = 15141.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.088251 restraints weight = 8751.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.090333 restraints weight = 6108.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091597 restraints weight = 4820.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.092509 restraints weight = 4145.741| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10686 Z= 0.098 Angle : 0.515 9.196 14558 Z= 0.250 Chirality : 0.039 0.119 1692 Planarity : 0.003 0.032 1786 Dihedral : 7.956 53.153 1524 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.51 % Allowed : 15.50 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.19), residues: 1264 helix: -3.33 (0.15), residues: 714 sheet: -1.14 (0.61), residues: 62 loop : -2.55 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.006 0.001 TYR A 257 PHE 0.011 0.001 PHE A 16 TRP 0.005 0.001 TRP A 477 HIS 0.001 0.000 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (10686) covalent geometry : angle 0.51541 / 0.25 (14558) hydrogen bonds : bond 0.03855 / 2.45 ( 192) hydrogen bonds : angle 4.24744 / 2.93 ( 570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.389 Fit side-chains REVERT: A 507 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 543 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7197 (mt-10) REVERT: B 193 ASP cc_start: 0.8253 (t0) cc_final: 0.8048 (t0) REVERT: B 507 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (tt) REVERT: B 543 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7116 (mt-10) outliers start: 16 outliers final: 7 residues processed: 94 average time/residue: 0.1188 time to fit residues: 15.6274 Evaluate side-chains 82 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.082759 restraints weight = 15418.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.085782 restraints weight = 9041.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087791 restraints weight = 6362.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.089034 restraints weight = 5063.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089989 restraints weight = 4365.518| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10686 Z= 0.228 Angle : 0.623 10.762 14558 Z= 0.299 Chirality : 0.045 0.147 1692 Planarity : 0.004 0.033 1786 Dihedral : 8.163 55.582 1524 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.70 % Allowed : 15.60 % Favored : 82.70 % 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: -4.54 (0.19), residues: 1264 helix: -3.26 (0.15), residues: 722 sheet: -1.46 (0.51), residues: 90 loop : -2.54 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.007 0.001 TYR B 21 PHE 0.014 0.001 PHE A 573 TRP 0.008 0.001 TRP B 477 HIS 0.002 0.001 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (10686) covalent geometry : angle 0.62295 / 0.30 (14558) hydrogen bonds : bond 0.05512 / 3.61 ( 192) hydrogen bonds : angle 4.51287 / 3.11 ( 570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.406 Fit side-chains REVERT: A 507 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7805 (tt) REVERT: A 543 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 193 ASP cc_start: 0.8333 (t0) cc_final: 0.8124 (t0) REVERT: B 507 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7808 (tt) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.1344 time to fit residues: 15.6972 Evaluate side-chains 83 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.085257 restraints weight = 15198.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.088312 restraints weight = 8700.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090504 restraints weight = 6065.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091781 restraints weight = 4777.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092745 restraints weight = 4109.010| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10686 Z= 0.090 Angle : 0.513 9.267 14558 Z= 0.248 Chirality : 0.039 0.117 1692 Planarity : 0.003 0.031 1786 Dihedral : 7.724 53.730 1524 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.13 % Allowed : 16.35 % Favored : 82.51 % 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: -4.11 (0.20), residues: 1264 helix: -2.94 (0.16), residues: 702 sheet: -0.96 (0.62), residues: 66 loop : -2.40 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.006 0.001 TYR A 21 PHE 0.015 0.001 PHE A 16 TRP 0.005 0.001 TRP B 337 HIS 0.001 0.000 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (10686) covalent geometry : angle 0.51261 / 0.25 (14558) hydrogen bonds : bond 0.03581 / 2.26 ( 192) hydrogen bonds : angle 4.06997 / 2.82 ( 570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.390 Fit side-chains REVERT: A 507 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7678 (tt) REVERT: A 543 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 193 ASP cc_start: 0.8281 (t0) cc_final: 0.8073 (t0) REVERT: B 507 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7675 (tt) REVERT: B 543 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7092 (mt-10) outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 0.1391 time to fit residues: 15.4622 Evaluate side-chains 84 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 111 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.085847 restraints weight = 14964.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088932 restraints weight = 8650.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090876 restraints weight = 6057.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092349 restraints weight = 4805.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.093161 restraints weight = 4107.939| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10686 Z= 0.097 Angle : 0.510 9.677 14558 Z= 0.245 Chirality : 0.039 0.119 1692 Planarity : 0.003 0.030 1786 Dihedral : 7.507 54.908 1524 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.95 % Allowed : 17.01 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.21), residues: 1264 helix: -2.68 (0.17), residues: 702 sheet: -0.58 (0.64), residues: 64 loop : -2.24 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.006 0.001 TYR A 21 PHE 0.014 0.001 PHE B 16 TRP 0.005 0.001 TRP A 477 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10686) covalent geometry : angle 0.50991 / 0.24 (14558) hydrogen bonds : bond 0.03549 / 2.27 ( 192) hydrogen bonds : angle 3.96569 / 2.74 ( 570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.399 Fit side-chains REVERT: A 164 ASP cc_start: 0.8594 (t70) cc_final: 0.8164 (t0) REVERT: A 543 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7174 (mt-10) REVERT: B 164 ASP cc_start: 0.8603 (t70) cc_final: 0.8169 (t0) REVERT: B 193 ASP cc_start: 0.8325 (t0) cc_final: 0.8091 (t0) REVERT: B 543 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7061 (mt-10) outliers start: 10 outliers final: 3 residues processed: 91 average time/residue: 0.1403 time to fit residues: 17.2604 Evaluate side-chains 82 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.084422 restraints weight = 14974.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.087477 restraints weight = 8698.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089568 restraints weight = 6098.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090911 restraints weight = 4816.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091698 restraints weight = 4138.662| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10686 Z= 0.129 Angle : 0.541 9.850 14558 Z= 0.258 Chirality : 0.041 0.119 1692 Planarity : 0.003 0.031 1786 Dihedral : 7.618 55.156 1524 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.04 % Allowed : 16.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.21), residues: 1264 helix: -2.57 (0.17), residues: 704 sheet: -0.52 (0.65), residues: 64 loop : -2.27 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.007 0.001 TYR B 21 PHE 0.012 0.001 PHE A 16 TRP 0.005 0.001 TRP B 477 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (10686) covalent geometry : angle 0.54052 / 0.26 (14558) hydrogen bonds : bond 0.04110 / 2.66 ( 192) hydrogen bonds : angle 4.05657 / 2.80 ( 570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.409 Fit side-chains REVERT: A 507 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7731 (tt) REVERT: A 543 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 193 ASP cc_start: 0.8326 (t0) cc_final: 0.8106 (t0) REVERT: B 507 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 543 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7059 (mt-10) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1204 time to fit residues: 13.9590 Evaluate side-chains 85 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 0.0970 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.084868 restraints weight = 15038.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.087960 restraints weight = 8674.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090059 restraints weight = 6051.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.091322 restraints weight = 4770.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092266 restraints weight = 4109.033| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10686 Z= 0.118 Angle : 0.530 9.912 14558 Z= 0.253 Chirality : 0.041 0.118 1692 Planarity : 0.003 0.031 1786 Dihedral : 7.598 55.396 1524 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.95 % Allowed : 17.30 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.22), residues: 1264 helix: -2.43 (0.18), residues: 716 sheet: -0.47 (0.67), residues: 64 loop : -2.10 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.007 0.001 TYR A 21 PHE 0.014 0.001 PHE B 16 TRP 0.005 0.001 TRP B 477 HIS 0.001 0.001 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10686) covalent geometry : angle 0.53005 / 0.25 (14558) hydrogen bonds : bond 0.03873 / 2.49 ( 192) hydrogen bonds : angle 3.99704 / 2.76 ( 570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.459 Fit side-chains REVERT: A 164 ASP cc_start: 0.8625 (t70) cc_final: 0.8222 (t0) REVERT: A 507 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 543 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 164 ASP cc_start: 0.8643 (t70) cc_final: 0.8233 (t0) REVERT: B 193 ASP cc_start: 0.8334 (t0) cc_final: 0.8103 (t0) REVERT: B 507 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7683 (tt) REVERT: B 543 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7066 (mt-10) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.1352 time to fit residues: 15.6134 Evaluate side-chains 87 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.085320 restraints weight = 14954.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088411 restraints weight = 8635.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090374 restraints weight = 6023.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091820 restraints weight = 4781.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092640 restraints weight = 4100.264| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10686 Z= 0.110 Angle : 0.526 9.595 14558 Z= 0.252 Chirality : 0.040 0.118 1692 Planarity : 0.003 0.031 1786 Dihedral : 7.590 59.972 1524 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.85 % Allowed : 17.67 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.22), residues: 1264 helix: -2.28 (0.18), residues: 716 sheet: -0.41 (0.68), residues: 64 loop : -2.07 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.007 0.001 TYR B 21 PHE 0.013 0.001 PHE A 16 TRP 0.006 0.001 TRP B 337 HIS 0.001 0.000 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (10686) covalent geometry : angle 0.52608 / 0.25 (14558) hydrogen bonds : bond 0.03706 / 2.38 ( 192) hydrogen bonds : angle 3.93271 / 2.72 ( 570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.417 Fit side-chains REVERT: A 164 ASP cc_start: 0.8572 (t70) cc_final: 0.8205 (t0) REVERT: A 507 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 543 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 164 ASP cc_start: 0.8577 (t70) cc_final: 0.8206 (t0) REVERT: B 193 ASP cc_start: 0.8337 (t0) cc_final: 0.8102 (t0) REVERT: B 507 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7680 (tt) REVERT: B 543 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7060 (mt-10) REVERT: B 544 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7916 (tp30) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.1383 time to fit residues: 15.6581 Evaluate side-chains 84 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 47 optimal weight: 0.0030 chunk 112 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087818 restraints weight = 15164.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.091033 restraints weight = 8691.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093233 restraints weight = 6041.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.094659 restraints weight = 4735.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095563 restraints weight = 4054.824| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10686 Z= 0.092 Angle : 0.509 9.521 14558 Z= 0.243 Chirality : 0.039 0.117 1692 Planarity : 0.003 0.030 1786 Dihedral : 7.356 56.561 1524 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.76 % Allowed : 18.05 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.22), residues: 1264 helix: -2.10 (0.19), residues: 702 sheet: -0.28 (0.70), residues: 64 loop : -2.04 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 613 TYR 0.006 0.001 TYR A 21 PHE 0.016 0.001 PHE B 16 TRP 0.007 0.001 TRP A 337 HIS 0.001 0.000 HIS A 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.09 (10686) covalent geometry : angle 0.50878 / 0.24 (14558) hydrogen bonds : bond 0.03229 / 2.05 ( 192) hydrogen bonds : angle 3.81296 / 2.64 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.74 seconds wall clock time: 27 minutes 59.08 seconds (1679.08 seconds total)