Starting phenix.real_space_refine on Fri Feb 14 21:27:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tqf_10550/02_2025/6tqf_10550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tqf_10550/02_2025/6tqf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6tqf_10550/02_2025/6tqf_10550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tqf_10550/02_2025/6tqf_10550.map" model { file = "/net/cci-nas-00/data/ceres_data/6tqf_10550/02_2025/6tqf_10550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tqf_10550/02_2025/6tqf_10550.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.85, per 1000 atoms: 0.66 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: 2.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.17 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: 3.20 Time building geometry restraints manager: 2.92 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 - 26.39: 6092 26.39 - 52.78: 447 52.78 - 79.17: 62 79.17 - 105.56: 71 105.56 - 131.95: 20 Dihedral angle restraints: 6692 sinusoidal: 3042 harmonic: 3650 Sorted by residual: dihedral pdb=" C2B LMT A 801 " pdb=" C1B LMT A 801 " pdb=" O5B LMT A 801 " pdb=" C5B LMT A 801 " ideal model delta sinusoidal sigma weight residual -57.12 74.83 -131.95 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C2B LMT B 805 " pdb=" C1B LMT B 805 " pdb=" O5B LMT B 805 " pdb=" C5B LMT B 805 " ideal model delta sinusoidal sigma weight residual -57.12 74.78 -131.90 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C5B LMT B 805 " pdb=" C1B LMT B 805 " pdb=" O5B LMT B 805 " pdb=" O1B LMT B 805 " ideal model delta sinusoidal sigma weight residual 295.61 163.78 131.83 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 6689 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: 0.06 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.640 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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= 0.416 Angle : 0.991 11.860 14558 Z= 0.492 Chirality : 0.054 0.291 1692 Planarity : 0.006 0.058 1786 Dihedral : 22.161 131.947 4344 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS B 378 PHE 0.018 0.001 PHE A 317 TYR 0.008 0.001 TYR B 21 ARG 0.003 0.000 ARG A 270 *********************** 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 : 1.108 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: 0.3482 time to fit residues: 49.9510 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 : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.1980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.0040 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3276 r_free = 0.3276 target = 0.110891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.088089 restraints weight = 14716.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.089001 restraints weight = 10386.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.089271 restraints weight = 7862.987| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1347 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= 0.143 Angle : 0.645 9.360 14558 Z= 0.288 Chirality : 0.046 0.384 1692 Planarity : 0.004 0.036 1786 Dihedral : 14.483 101.155 2080 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 : 1.04 % Allowed : 11.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.17), residues: 1264 helix: -4.03 (0.12), residues: 698 sheet: -1.49 (0.59), residues: 62 loop : -2.90 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 547 HIS 0.001 0.000 HIS A 378 PHE 0.008 0.001 PHE B 573 TYR 0.006 0.001 TYR A 21 ARG 0.002 0.000 ARG A 486 *********************** 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 96 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.103 Fit side-chains REVERT: A 543 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7024 (mt-10) REVERT: B 543 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7012 (mt-10) outliers start: 11 outliers final: 2 residues processed: 94 average time/residue: 0.3127 time to fit residues: 39.2961 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 : 1.225 ------------------------------------------------------------------------------- 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 26 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.080510 restraints weight = 15668.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.083443 restraints weight = 9308.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085440 restraints weight = 6605.116| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10686 Z= 0.545 Angle : 0.786 10.881 14558 Z= 0.365 Chirality : 0.053 0.318 1692 Planarity : 0.005 0.033 1786 Dihedral : 12.659 80.584 2080 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.89 % Allowed : 14.18 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.17), residues: 1264 helix: -3.82 (0.13), residues: 726 sheet: -1.80 (0.50), residues: 90 loop : -2.94 (0.23), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 477 HIS 0.004 0.001 HIS B 159 PHE 0.019 0.002 PHE B 573 TYR 0.009 0.002 TYR B 90 ARG 0.003 0.000 ARG B 66 *********************** 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 84 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.093 Fit side-chains REVERT: A 166 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8388 (pp) REVERT: A 543 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 166 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 543 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7174 (mt-10) outliers start: 20 outliers final: 13 residues processed: 81 average time/residue: 0.2883 time to fit residues: 31.9113 Evaluate side-chains 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 129 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.085812 restraints weight = 14868.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088855 restraints weight = 8587.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090942 restraints weight = 6003.971| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1795 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= 0.137 Angle : 0.565 8.471 14558 Z= 0.261 Chirality : 0.043 0.387 1692 Planarity : 0.003 0.033 1786 Dihedral : 10.362 53.460 2080 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.27 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.19), residues: 1264 helix: -3.32 (0.15), residues: 702 sheet: -1.07 (0.62), residues: 62 loop : -2.60 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 547 HIS 0.002 0.000 HIS A 607 PHE 0.009 0.001 PHE A 317 TYR 0.006 0.001 TYR B 257 ARG 0.003 0.000 ARG B 66 *********************** 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 97 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 1.122 Fit side-chains REVERT: A 507 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7575 (tt) REVERT: A 543 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 507 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7573 (tt) REVERT: B 543 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7165 (mt-10) outliers start: 24 outliers final: 14 residues processed: 87 average time/residue: 0.2652 time to fit residues: 31.9838 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 : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 191 ASP 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 123 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 THR 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 32 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 60 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.084210 restraints weight = 14952.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087283 restraints weight = 8735.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.089371 restraints weight = 6143.669| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10686 Z= 0.191 Angle : 0.578 9.819 14558 Z= 0.267 Chirality : 0.044 0.344 1692 Planarity : 0.003 0.032 1786 Dihedral : 9.561 54.683 2080 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.42 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.20), residues: 1264 helix: -3.05 (0.16), residues: 704 sheet: -0.79 (0.58), residues: 76 loop : -2.48 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 477 HIS 0.001 0.001 HIS B 159 PHE 0.010 0.001 PHE A 573 TYR 0.006 0.001 TYR A 21 ARG 0.004 0.000 ARG B 66 *********************** 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 95 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.162 Fit side-chains REVERT: A 507 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 543 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 507 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7702 (tt) REVERT: B 543 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7136 (mt-10) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.2936 time to fit residues: 35.9284 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 : 1.083 ------------------------------------------------------------------------------- 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 459 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 123 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.0040 chunk 111 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 11 optimal weight: 0.0030 chunk 36 optimal weight: 4.9990 overall best weight: 0.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.086828 restraints weight = 14915.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089941 restraints weight = 8605.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092094 restraints weight = 6015.452| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10686 Z= 0.139 Angle : 0.536 8.499 14558 Z= 0.250 Chirality : 0.042 0.316 1692 Planarity : 0.003 0.032 1786 Dihedral : 8.680 57.845 2080 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.32 % Allowed : 16.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.21), residues: 1264 helix: -2.74 (0.17), residues: 688 sheet: -0.56 (0.66), residues: 62 loop : -2.33 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 337 HIS 0.001 0.000 HIS B 135 PHE 0.013 0.001 PHE A 16 TYR 0.006 0.000 TYR A 21 ARG 0.003 0.000 ARG A 66 *********************** 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 91 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.106 Fit side-chains REVERT: A 164 ASP cc_start: 0.8584 (t70) cc_final: 0.8130 (t0) REVERT: A 191 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8177 (t0) REVERT: A 507 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7613 (tt) REVERT: A 543 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7194 (mt-10) REVERT: B 164 ASP cc_start: 0.8591 (t70) cc_final: 0.8137 (t0) REVERT: B 191 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8176 (t0) REVERT: B 507 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7630 (tt) REVERT: B 543 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7162 (mt-10) outliers start: 14 outliers final: 4 residues processed: 88 average time/residue: 0.2913 time to fit residues: 34.6997 Evaluate side-chains 83 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 79 optimal weight: 0.0010 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.1980 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.084319 restraints weight = 15233.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087413 restraints weight = 8857.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089510 restraints weight = 6212.886| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10686 Z= 0.227 Angle : 0.576 9.807 14558 Z= 0.268 Chirality : 0.044 0.323 1692 Planarity : 0.003 0.033 1786 Dihedral : 8.634 55.669 2080 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.21), residues: 1264 helix: -2.66 (0.17), residues: 704 sheet: -0.57 (0.65), residues: 64 loop : -2.28 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 477 HIS 0.002 0.001 HIS A 135 PHE 0.011 0.001 PHE A 573 TYR 0.006 0.001 TYR A 21 ARG 0.004 0.000 ARG B 66 *********************** 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 89 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.104 Fit side-chains REVERT: A 166 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8485 (pp) REVERT: A 507 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7710 (tt) REVERT: A 543 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 164 ASP cc_start: 0.8655 (t70) cc_final: 0.8211 (t0) REVERT: B 166 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8509 (pp) REVERT: B 507 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7720 (tt) REVERT: B 543 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7203 (mt-10) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.3081 time to fit residues: 35.8844 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 : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 166 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.085664 restraints weight = 15095.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088805 restraints weight = 8739.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090926 restraints weight = 6106.673| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10686 Z= 0.171 Angle : 0.549 9.173 14558 Z= 0.256 Chirality : 0.043 0.314 1692 Planarity : 0.003 0.032 1786 Dihedral : 8.246 51.449 2080 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.13 % Allowed : 17.01 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.22), residues: 1264 helix: -2.49 (0.18), residues: 702 sheet: -0.46 (0.66), residues: 64 loop : -2.08 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 477 HIS 0.001 0.001 HIS B 135 PHE 0.009 0.001 PHE B 573 TYR 0.006 0.001 TYR A 21 ARG 0.004 0.000 ARG B 66 *********************** 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 89 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.153 Fit side-chains REVERT: A 164 ASP cc_start: 0.8617 (t70) cc_final: 0.8193 (t0) REVERT: A 166 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8504 (pp) REVERT: A 507 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7656 (tt) REVERT: A 543 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 164 ASP cc_start: 0.8625 (t70) cc_final: 0.8202 (t0) REVERT: B 166 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8516 (pp) REVERT: B 507 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 543 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7212 (mt-10) outliers start: 12 outliers final: 5 residues processed: 87 average time/residue: 0.3021 time to fit residues: 35.7525 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 : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 166 LEU 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 166 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.082147 restraints weight = 15531.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.085188 restraints weight = 9137.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.087235 restraints weight = 6440.579| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10686 Z= 0.380 Angle : 0.674 11.327 14558 Z= 0.315 Chirality : 0.048 0.337 1692 Planarity : 0.004 0.034 1786 Dihedral : 9.083 56.291 2080 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.85 % Allowed : 17.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.21), residues: 1264 helix: -2.71 (0.17), residues: 714 sheet: -0.65 (0.53), residues: 102 loop : -2.35 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.003 0.001 HIS B 159 PHE 0.016 0.001 PHE A 573 TYR 0.009 0.001 TYR B 327 ARG 0.004 0.000 ARG B 66 *********************** 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 72 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.206 Fit side-chains REVERT: A 166 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8420 (pp) REVERT: A 507 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 166 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8420 (pp) REVERT: B 507 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7851 (tt) outliers start: 9 outliers final: 3 residues processed: 72 average time/residue: 0.3080 time to fit residues: 29.8368 Evaluate side-chains 68 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 166 LEU 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 82 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.087097 restraints weight = 15132.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.090274 restraints weight = 8767.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.092367 restraints weight = 6119.359| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10686 Z= 0.147 Angle : 0.554 8.946 14558 Z= 0.260 Chirality : 0.042 0.308 1692 Planarity : 0.003 0.030 1786 Dihedral : 8.284 52.968 2080 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.66 % Allowed : 17.77 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.22), residues: 1264 helix: -2.36 (0.18), residues: 712 sheet: -0.46 (0.68), residues: 64 loop : -2.06 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 337 HIS 0.001 0.000 HIS A 159 PHE 0.017 0.001 PHE B 16 TYR 0.006 0.001 TYR A 21 ARG 0.004 0.000 ARG B 66 ********************** 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 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.127 Fit side-chains REVERT: A 140 MET cc_start: 0.8318 (tpp) cc_final: 0.8067 (tpp) REVERT: A 166 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8478 (pp) REVERT: A 507 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 543 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 140 MET cc_start: 0.8308 (tpp) cc_final: 0.8052 (tpp) REVERT: B 166 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8495 (pp) REVERT: B 507 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7630 (tt) outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.3205 time to fit residues: 34.3607 Evaluate side-chains 76 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU 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 166 LEU 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 51 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.085161 restraints weight = 15155.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.088292 restraints weight = 8839.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090357 restraints weight = 6192.273| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10686 Z= 0.231 Angle : 0.593 10.240 14558 Z= 0.276 Chirality : 0.044 0.318 1692 Planarity : 0.003 0.031 1786 Dihedral : 8.349 53.419 2080 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.57 % Allowed : 18.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.22), residues: 1264 helix: -2.33 (0.18), residues: 714 sheet: -0.40 (0.69), residues: 64 loop : -2.02 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 477 HIS 0.001 0.001 HIS B 159 PHE 0.011 0.001 PHE A 573 TYR 0.006 0.001 TYR A 21 ARG 0.007 0.000 ARG B 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.55 seconds wall clock time: 50 minutes 34.48 seconds (3034.48 seconds total)