Starting phenix.real_space_refine on Wed Mar 4 03:58:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tqf_10550/03_2026/6tqf_10550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tqf_10550/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6tqf_10550/03_2026/6tqf_10550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tqf_10550/03_2026/6tqf_10550.map" model { file = "/net/cci-nas-00/data/ceres_data/6tqf_10550/03_2026/6tqf_10550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tqf_10550/03_2026/6tqf_10550.cif" } 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-dev-5986/lib/python3.9/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: 2.44, 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: 0.84 Conformation dependent library (CDL) restraints added in 463.6 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: 0.35 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: 1.33 Time building geometry restraints manager: 1.10 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: 0.02 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: 1.460 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.060 Find NCS groups from input model: 0.080 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- 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= 0.317 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 : 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 covalent geometry : bond 0.00675 (10686) covalent geometry : angle 0.99092 (14558) hydrogen bonds : bond 0.25770 ( 192) hydrogen bonds : angle 7.92019 ( 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 : 0.376 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: 0.1702 time to fit residues: 24.1860 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 : 0.393 ------------------------------------------------------------------------------- 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... 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 = 0.3275 r_free = 0.3275 target = 0.110804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.087891 restraints weight = 15039.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.089007 restraints weight = 10097.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.089461 restraints weight = 7646.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.089750 restraints weight = 7505.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.090469 restraints weight = 6757.452| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1342 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= 0.103 Angle : 0.643 9.536 14558 Z= 0.287 Chirality : 0.047 0.426 1692 Planarity : 0.004 0.036 1786 Dihedral : 14.423 100.337 2080 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.04 % Allowed : 11.44 % Favored : 87.52 % 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: -5.41 (0.17), residues: 1264 helix: -4.04 (0.12), residues: 698 sheet: -1.50 (0.59), residues: 62 loop : -2.91 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 486 TYR 0.005 0.001 TYR A 21 PHE 0.008 0.001 PHE B 573 TRP 0.006 0.001 TRP A 337 HIS 0.001 0.000 HIS A 615 Details of bonding type rmsd covalent geometry : bond 0.00226 (10686) covalent geometry : angle 0.64262 (14558) hydrogen bonds : bond 0.04143 ( 192) hydrogen bonds : angle 4.76171 ( 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 97 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.407 Fit side-chains REVERT: A 543 GLU cc_start: 0.7227 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 543 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6998 (mt-10) outliers start: 11 outliers final: 2 residues processed: 95 average time/residue: 0.1375 time to fit residues: 17.5284 Evaluate side-chains 77 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 0.0050 chunk 120 optimal weight: 0.0060 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.6016 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.109985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.081298 restraints weight = 15320.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.084288 restraints weight = 9003.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.086302 restraints weight = 6358.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087636 restraints weight = 5058.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088431 restraints weight = 4350.713| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10686 Z= 0.233 Angle : 0.696 10.226 14558 Z= 0.321 Chirality : 0.049 0.358 1692 Planarity : 0.004 0.032 1786 Dihedral : 11.973 76.963 2080 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.32 % Allowed : 14.93 % Favored : 83.74 % 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: -5.14 (0.18), residues: 1264 helix: -3.73 (0.13), residues: 722 sheet: -1.67 (0.50), residues: 90 loop : -2.86 (0.23), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.007 0.001 TYR B 21 PHE 0.016 0.001 PHE A 573 TRP 0.008 0.001 TRP B 477 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00566 (10686) covalent geometry : angle 0.69628 (14558) hydrogen bonds : bond 0.06155 ( 192) hydrogen bonds : angle 4.72801 ( 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 86 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.370 Fit side-chains REVERT: A 166 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8419 (pp) REVERT: A 543 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 166 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 543 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7166 (mt-10) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.1343 time to fit residues: 15.0018 Evaluate side-chains 86 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 502 VAL 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 502 VAL 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: 0.6980 chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.114744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.086166 restraints weight = 15074.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.089281 restraints weight = 8648.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091430 restraints weight = 6031.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092810 restraints weight = 4739.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.093606 restraints weight = 4059.134| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1786 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= 0.088 Angle : 0.557 8.737 14558 Z= 0.257 Chirality : 0.043 0.390 1692 Planarity : 0.003 0.033 1786 Dihedral : 10.087 57.895 2080 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.89 % Allowed : 15.12 % 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: -4.50 (0.19), residues: 1264 helix: -3.26 (0.15), residues: 702 sheet: -1.08 (0.62), residues: 62 loop : -2.57 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.006 0.001 TYR A 257 PHE 0.011 0.001 PHE A 16 TRP 0.005 0.001 TRP B 547 HIS 0.001 0.000 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00195 (10686) covalent geometry : angle 0.55718 (14558) hydrogen bonds : bond 0.03437 ( 192) hydrogen bonds : angle 4.13739 ( 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 99 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.370 Fit side-chains REVERT: A 507 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 543 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 507 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7580 (tt) REVERT: B 543 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 20 outliers final: 4 residues processed: 95 average time/residue: 0.1277 time to fit residues: 16.5488 Evaluate side-chains 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 362 ILE 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: 4.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 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: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.111357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.082627 restraints weight = 15258.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.085700 restraints weight = 8861.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.087780 restraints weight = 6216.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089013 restraints weight = 4910.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090000 restraints weight = 4236.307| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10686 Z= 0.176 Angle : 0.615 10.232 14558 Z= 0.285 Chirality : 0.046 0.355 1692 Planarity : 0.004 0.034 1786 Dihedral : 9.790 59.736 2080 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.32 % Allowed : 15.78 % Favored : 82.89 % 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: -4.35 (0.20), residues: 1264 helix: -3.14 (0.16), residues: 718 sheet: -1.33 (0.51), residues: 90 loop : -2.43 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.007 0.001 TYR A 21 PHE 0.013 0.001 PHE B 573 TRP 0.007 0.001 TRP B 477 HIS 0.002 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00436 (10686) covalent geometry : angle 0.61503 (14558) hydrogen bonds : bond 0.04807 ( 192) hydrogen bonds : angle 4.29252 ( 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 91 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.426 Fit side-chains REVERT: A 507 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7755 (tt) REVERT: A 543 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 507 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7747 (tt) REVERT: B 543 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7172 (mt-10) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 0.1339 time to fit residues: 16.1038 Evaluate side-chains 84 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 82 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 35 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 110 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.116267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087646 restraints weight = 15086.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090864 restraints weight = 8625.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.093016 restraints weight = 5978.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094387 restraints weight = 4698.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.095213 restraints weight = 4021.944| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10686 Z= 0.084 Angle : 0.529 8.413 14558 Z= 0.247 Chirality : 0.041 0.317 1692 Planarity : 0.003 0.031 1786 Dihedral : 8.790 55.037 2080 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.66 % Allowed : 16.92 % Favored : 82.42 % 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: -3.87 (0.21), residues: 1264 helix: -2.76 (0.17), residues: 688 sheet: -0.64 (0.64), residues: 62 loop : -2.33 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.006 0.000 TYR A 21 PHE 0.012 0.001 PHE B 16 TRP 0.006 0.001 TRP B 547 HIS 0.001 0.000 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00184 (10686) covalent geometry : angle 0.52896 (14558) hydrogen bonds : bond 0.02907 ( 192) hydrogen bonds : angle 3.84253 ( 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 87 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.319 Fit side-chains REVERT: A 164 ASP cc_start: 0.8544 (t70) cc_final: 0.8088 (t0) REVERT: A 507 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 543 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 164 ASP cc_start: 0.8545 (t70) cc_final: 0.8085 (t0) REVERT: B 507 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 543 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7135 (mt-10) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.1398 time to fit residues: 16.2997 Evaluate side-chains 81 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR 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 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: 0.9980 chunk 110 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 49 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.114848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086140 restraints weight = 14964.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089273 restraints weight = 8706.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091402 restraints weight = 6090.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092771 restraints weight = 4803.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.093639 restraints weight = 4121.076| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2053 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= 0.104 Angle : 0.548 9.314 14558 Z= 0.253 Chirality : 0.042 0.318 1692 Planarity : 0.003 0.032 1786 Dihedral : 8.331 51.536 2080 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.95 % Allowed : 17.39 % Favored : 81.66 % 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: -3.63 (0.21), residues: 1264 helix: -2.58 (0.18), residues: 690 sheet: -0.64 (0.64), residues: 66 loop : -2.19 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.006 0.001 TYR A 21 PHE 0.009 0.001 PHE B 573 TRP 0.004 0.001 TRP B 477 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00250 (10686) covalent geometry : angle 0.54813 (14558) hydrogen bonds : bond 0.03540 ( 192) hydrogen bonds : angle 3.86294 ( 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 95 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.370 Fit side-chains REVERT: A 164 ASP cc_start: 0.8564 (t70) cc_final: 0.8137 (t0) REVERT: A 543 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7104 (mt-10) REVERT: B 164 ASP cc_start: 0.8568 (t70) cc_final: 0.8137 (t0) REVERT: B 507 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7682 (tt) REVERT: B 543 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7108 (mt-10) outliers start: 10 outliers final: 4 residues processed: 93 average time/residue: 0.1524 time to fit residues: 18.9617 Evaluate side-chains 84 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 90 TYR 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 57 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.113389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.084110 restraints weight = 15159.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087223 restraints weight = 8884.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089310 restraints weight = 6249.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090602 restraints weight = 4953.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091547 restraints weight = 4272.512| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 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 : 0.004 0.040 10686 Z= 0.179 Angle : 0.619 9.902 14558 Z= 0.287 Chirality : 0.046 0.330 1692 Planarity : 0.004 0.036 1786 Dihedral : 8.660 49.416 2080 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.95 % Allowed : 17.39 % Favored : 81.66 % 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: -3.63 (0.21), residues: 1264 helix: -2.62 (0.17), residues: 720 sheet: -0.48 (0.60), residues: 78 loop : -2.10 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.006 0.001 TYR B 327 PHE 0.014 0.001 PHE B 573 TRP 0.006 0.001 TRP B 274 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00439 (10686) covalent geometry : angle 0.61857 (14558) hydrogen bonds : bond 0.04880 ( 192) hydrogen bonds : angle 4.19210 ( 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 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.384 Fit side-chains REVERT: A 507 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7747 (tt) REVERT: A 543 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 507 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7755 (tt) REVERT: B 543 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7193 (mt-10) outliers start: 10 outliers final: 2 residues processed: 80 average time/residue: 0.1396 time to fit residues: 14.8822 Evaluate side-chains 76 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU 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: 3.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.113970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.084828 restraints weight = 15189.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087922 restraints weight = 8897.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.089933 restraints weight = 6273.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091342 restraints weight = 4988.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092148 restraints weight = 4282.245| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10686 Z= 0.153 Angle : 0.596 10.081 14558 Z= 0.277 Chirality : 0.044 0.323 1692 Planarity : 0.003 0.032 1786 Dihedral : 8.491 50.876 2080 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 17.58 % 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 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: -3.57 (0.22), residues: 1264 helix: -2.50 (0.18), residues: 718 sheet: -0.45 (0.67), residues: 64 loop : -2.16 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.007 0.001 TYR A 21 PHE 0.017 0.001 PHE B 16 TRP 0.006 0.001 TRP B 274 HIS 0.002 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00373 (10686) covalent geometry : angle 0.59557 (14558) hydrogen bonds : bond 0.04396 ( 192) hydrogen bonds : angle 4.09162 ( 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 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.384 Fit side-chains REVERT: A 507 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7712 (tt) REVERT: A 543 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 507 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7723 (tt) REVERT: B 543 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 544 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7918 (tp30) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.1479 time to fit residues: 15.1450 Evaluate side-chains 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 241 ILE 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: 2.9990 chunk 35 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085443 restraints weight = 14969.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088516 restraints weight = 8694.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.090605 restraints weight = 6101.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091884 restraints weight = 4836.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092882 restraints weight = 4164.245| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2232 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= 0.114 Angle : 0.565 9.187 14558 Z= 0.264 Chirality : 0.043 0.311 1692 Planarity : 0.003 0.031 1786 Dihedral : 8.141 56.553 2080 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.85 % Allowed : 18.05 % Favored : 81.10 % 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: -3.34 (0.22), residues: 1264 helix: -2.30 (0.18), residues: 716 sheet: -0.38 (0.68), residues: 64 loop : -2.09 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 613 TYR 0.006 0.001 TYR A 21 PHE 0.009 0.001 PHE B 573 TRP 0.006 0.001 TRP B 337 HIS 0.001 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00276 (10686) covalent geometry : angle 0.56493 (14558) hydrogen bonds : bond 0.03734 ( 192) hydrogen bonds : angle 3.90389 ( 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 82 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.378 Fit side-chains REVERT: A 140 MET cc_start: 0.8313 (tpp) cc_final: 0.8081 (tpp) REVERT: A 507 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 543 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7173 (mt-10) REVERT: B 507 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7661 (tt) REVERT: B 543 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7141 (mt-10) REVERT: B 544 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7922 (tp30) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.1450 time to fit residues: 15.5275 Evaluate side-chains 77 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 0.2980 chunk 3 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.115242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.085812 restraints weight = 15298.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088967 restraints weight = 8895.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091065 restraints weight = 6229.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.092444 restraints weight = 4938.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093230 restraints weight = 4244.848| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10686 Z= 0.135 Angle : 0.585 9.965 14558 Z= 0.272 Chirality : 0.044 0.315 1692 Planarity : 0.003 0.032 1786 Dihedral : 8.181 56.555 2080 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.76 % Allowed : 18.53 % Favored : 80.72 % 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: -3.31 (0.22), residues: 1264 helix: -2.27 (0.18), residues: 716 sheet: -0.30 (0.70), residues: 64 loop : -2.09 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 613 TYR 0.006 0.001 TYR A 21 PHE 0.016 0.001 PHE B 16 TRP 0.006 0.001 TRP B 274 HIS 0.001 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00331 (10686) covalent geometry : angle 0.58520 (14558) hydrogen bonds : bond 0.04109 ( 192) hydrogen bonds : angle 3.96913 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.51 seconds wall clock time: 28 minutes 7.88 seconds (1687.88 seconds total)