Starting phenix.real_space_refine on Sat Aug 8 00:24:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p02_17324/08_2026/8p02_17324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p02_17324/08_2026/8p02_17324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p02_17324/08_2026/8p02_17324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p02_17324/08_2026/8p02_17324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p02_17324/08_2026/8p02_17324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p02_17324/08_2026/8p02_17324.map" } resolution = 2.3 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= 0.001 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: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 K 6 8.98 5 Fe 12 7.16 5 P 24 5.49 5 S 174 5.16 5 C 15702 2.51 5 N 4260 2.21 5 O 4745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24929 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4049 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 29, 'TRANS': 484} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 96 Unusual residues: {' K': 1, ' CA': 1, ' FE': 2, 'BYC': 1, 'BYN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.75, per 1000 atoms: 0.19 Number of scatterers: 24929 At special positions: 0 Unit cell: (138.942, 144.801, 94.581, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 6 19.99 K 6 19.00 S 174 16.00 P 24 15.00 O 4745 8.00 N 4260 7.00 C 15702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 36.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.730A pdb=" N GLU A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.763A pdb=" N TRP A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.616A pdb=" N ASP A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.576A pdb=" N GLU A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 4.800A pdb=" N VAL A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.600A pdb=" N ASN A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.507A pdb=" N ARG A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.125A pdb=" N PHE A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 513 Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.680A pdb=" N ARG A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.730A pdb=" N GLU B 122 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.763A pdb=" N TRP B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.616A pdb=" N ASP B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.577A pdb=" N GLU B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 357 removed outlier: 4.799A pdb=" N VAL B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.600A pdb=" N ASN B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 430 Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.507A pdb=" N ARG B 454 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 removed outlier: 4.125A pdb=" N PHE B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.681A pdb=" N ARG B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.730A pdb=" N GLU C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.764A pdb=" N TRP C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 removed outlier: 3.617A pdb=" N ASP C 162 " --> pdb=" O PRO C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 188 through 197 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.576A pdb=" N GLU C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 357 removed outlier: 4.800A pdb=" N VAL C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 389 through 401 removed outlier: 3.600A pdb=" N ASN C 393 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 430 Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.507A pdb=" N ARG C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.125A pdb=" N PHE C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 513 Processing helix chain 'C' and resid 517 through 526 removed outlier: 3.680A pdb=" N ARG C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 525 " --> pdb=" O SER C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 80 through 88 Processing helix chain 'D' and resid 92 through 105 Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.729A pdb=" N GLU D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.763A pdb=" N TRP D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 162 removed outlier: 3.617A pdb=" N ASP D 162 " --> pdb=" O PRO D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 188 through 197 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.576A pdb=" N GLU D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 357 removed outlier: 4.799A pdb=" N VAL D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 389 through 401 removed outlier: 3.599A pdb=" N ASN D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 430 Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.506A pdb=" N ARG D 454 " --> pdb=" O MET D 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 removed outlier: 4.125A pdb=" N PHE D 502 " --> pdb=" O LYS D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 513 Processing helix chain 'D' and resid 517 through 526 removed outlier: 3.680A pdb=" N ARG D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 525 " --> pdb=" O SER D 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 80 through 88 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.729A pdb=" N GLU E 122 " --> pdb=" O PRO E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.764A pdb=" N TRP E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 162 removed outlier: 3.616A pdb=" N ASP E 162 " --> pdb=" O PRO E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 188 through 197 Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 234 through 244 Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.576A pdb=" N GLU E 284 " --> pdb=" O THR E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 357 removed outlier: 4.799A pdb=" N VAL E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 389 through 401 removed outlier: 3.601A pdb=" N ASN E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 430 Processing helix chain 'E' and resid 450 through 458 removed outlier: 3.507A pdb=" N ARG E 454 " --> pdb=" O MET E 450 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 458 " --> pdb=" O ARG E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 removed outlier: 4.125A pdb=" N PHE E 502 " --> pdb=" O LYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 513 Processing helix chain 'E' and resid 517 through 526 removed outlier: 3.680A pdb=" N ARG E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 525 " --> pdb=" O SER E 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 80 through 88 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.730A pdb=" N GLU F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.763A pdb=" N TRP F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 162 removed outlier: 3.617A pdb=" N ASP F 162 " --> pdb=" O PRO F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 162' Processing helix chain 'F' and resid 188 through 197 Processing helix chain 'F' and resid 213 through 221 Processing helix chain 'F' and resid 234 through 244 Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.576A pdb=" N GLU F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 357 removed outlier: 4.799A pdb=" N VAL F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'F' and resid 389 through 401 removed outlier: 3.600A pdb=" N ASN F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 Processing helix chain 'F' and resid 450 through 458 removed outlier: 3.507A pdb=" N ARG F 454 " --> pdb=" O MET F 450 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY F 458 " --> pdb=" O ARG F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 503 removed outlier: 4.124A pdb=" N PHE F 502 " --> pdb=" O LYS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 513 Processing helix chain 'F' and resid 517 through 526 removed outlier: 3.681A pdb=" N ARG F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR F 525 " --> pdb=" O SER F 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 6.632A pdb=" N VAL A 35 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 112 removed outlier: 6.505A pdb=" N VAL A 111 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS A 251 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 125 removed outlier: 7.492A pdb=" N LYS A 307 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS A 276 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ARG A 274 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE A 311 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS A 272 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL A 313 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR A 270 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 157 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 207 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 125 Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.767A pdb=" N GLN A 379 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 364 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 377 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 408 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 477 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA A 410 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.632A pdb=" N VAL B 35 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.506A pdb=" N VAL B 111 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS B 251 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 125 removed outlier: 7.492A pdb=" N LYS B 307 " --> pdb=" O LYS B 276 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS B 276 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ARG B 274 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE B 311 " --> pdb=" O HIS B 272 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS B 272 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL B 313 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR B 270 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 157 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 207 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'B' and resid 361 through 365 removed outlier: 6.766A pdb=" N GLN B 379 " --> pdb=" O GLN B 362 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 364 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 377 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 408 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA B 477 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 410 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 37 removed outlier: 6.632A pdb=" N VAL C 35 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.505A pdb=" N VAL C 111 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS C 251 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 125 removed outlier: 7.491A pdb=" N LYS C 307 " --> pdb=" O LYS C 276 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS C 276 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG C 274 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE C 311 " --> pdb=" O HIS C 272 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N HIS C 272 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL C 313 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR C 270 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 157 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 207 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AB6, first strand: chain 'C' and resid 361 through 365 removed outlier: 6.767A pdb=" N GLN C 379 " --> pdb=" O GLN C 362 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 364 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 377 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 408 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA C 477 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 410 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.632A pdb=" N VAL D 35 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 111 through 112 removed outlier: 6.506A pdb=" N VAL D 111 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS D 251 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 125 removed outlier: 7.492A pdb=" N LYS D 307 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS D 276 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG D 274 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE D 311 " --> pdb=" O HIS D 272 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N HIS D 272 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL D 313 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR D 270 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 157 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 207 " --> pdb=" O CYS D 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AC2, first strand: chain 'D' and resid 361 through 365 removed outlier: 6.767A pdb=" N GLN D 379 " --> pdb=" O GLN D 362 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 364 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 377 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 408 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA D 477 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA D 410 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.631A pdb=" N VAL E 35 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 111 through 112 removed outlier: 6.505A pdb=" N VAL E 111 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS E 251 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 125 removed outlier: 7.491A pdb=" N LYS E 307 " --> pdb=" O LYS E 276 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS E 276 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG E 274 " --> pdb=" O PRO E 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE E 311 " --> pdb=" O HIS E 272 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS E 272 " --> pdb=" O PHE E 311 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL E 313 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR E 270 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL E 157 " --> pdb=" O PRO E 205 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 207 " --> pdb=" O CYS E 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AC7, first strand: chain 'E' and resid 361 through 365 removed outlier: 6.766A pdb=" N GLN E 379 " --> pdb=" O GLN E 362 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 364 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 377 " --> pdb=" O VAL E 364 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA E 408 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA E 477 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA E 410 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.632A pdb=" N VAL F 35 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 111 through 112 removed outlier: 6.505A pdb=" N VAL F 111 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS F 251 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 123 through 125 removed outlier: 7.492A pdb=" N LYS F 307 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS F 276 " --> pdb=" O LYS F 307 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG F 274 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE F 311 " --> pdb=" O HIS F 272 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS F 272 " --> pdb=" O PHE F 311 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL F 313 " --> pdb=" O TYR F 270 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR F 270 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL F 157 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 207 " --> pdb=" O CYS F 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AD3, first strand: chain 'F' and resid 361 through 365 removed outlier: 6.766A pdb=" N GLN F 379 " --> pdb=" O GLN F 362 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL F 364 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE F 377 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA F 408 " --> pdb=" O ILE F 475 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA F 477 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA F 410 " --> pdb=" O ALA F 477 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2448 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: 6.18 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4122 1.28 - 1.41: 6564 1.41 - 1.55: 14369 1.55 - 1.68: 127 1.68 - 1.82: 306 Bond restraints: 25488 Sorted by residual: bond pdb=" C ALA C 523 " pdb=" N ARG C 524 " ideal model delta sigma weight residual 1.334 1.687 -0.353 1.33e-02 5.65e+03 7.04e+02 bond pdb=" C ALA A 523 " pdb=" N ARG A 524 " ideal model delta sigma weight residual 1.334 1.687 -0.353 1.33e-02 5.65e+03 7.03e+02 bond pdb=" C ALA E 523 " pdb=" N ARG E 524 " ideal model delta sigma weight residual 1.334 1.687 -0.353 1.33e-02 5.65e+03 7.02e+02 bond pdb=" C ALA F 523 " pdb=" N ARG F 524 " ideal model delta sigma weight residual 1.334 1.687 -0.352 1.33e-02 5.65e+03 7.02e+02 bond pdb=" C ALA D 523 " pdb=" N ARG D 524 " ideal model delta sigma weight residual 1.334 1.687 -0.352 1.33e-02 5.65e+03 7.02e+02 ... (remaining 25483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 33705 3.01 - 6.02: 771 6.02 - 9.04: 156 9.04 - 12.05: 30 12.05 - 15.06: 24 Bond angle restraints: 34686 Sorted by residual: angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 128.18 -14.08 2.00e+00 2.50e-01 4.96e+01 angle pdb=" CA GLU D 91 " pdb=" CB GLU D 91 " pdb=" CG GLU D 91 " ideal model delta sigma weight residual 114.10 128.18 -14.08 2.00e+00 2.50e-01 4.95e+01 angle pdb=" CA GLU F 91 " pdb=" CB GLU F 91 " pdb=" CG GLU F 91 " ideal model delta sigma weight residual 114.10 128.17 -14.07 2.00e+00 2.50e-01 4.95e+01 angle pdb=" CA GLU B 91 " pdb=" CB GLU B 91 " pdb=" CG GLU B 91 " ideal model delta sigma weight residual 114.10 128.15 -14.05 2.00e+00 2.50e-01 4.93e+01 angle pdb=" CA GLU A 91 " pdb=" CB GLU A 91 " pdb=" CG GLU A 91 " ideal model delta sigma weight residual 114.10 128.13 -14.03 2.00e+00 2.50e-01 4.92e+01 ... (remaining 34681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.72: 14072 20.72 - 41.44: 1025 41.44 - 62.16: 323 62.16 - 82.88: 48 82.88 - 103.59: 24 Dihedral angle restraints: 15492 sinusoidal: 6672 harmonic: 8820 Sorted by residual: dihedral pdb=" CA GLY D 17 " pdb=" C GLY D 17 " pdb=" N GLU D 18 " pdb=" CA GLU D 18 " ideal model delta harmonic sigma weight residual -180.00 -135.09 -44.91 0 5.00e+00 4.00e-02 8.07e+01 dihedral pdb=" CA GLY F 17 " pdb=" C GLY F 17 " pdb=" N GLU F 18 " pdb=" CA GLU F 18 " ideal model delta harmonic sigma weight residual -180.00 -135.15 -44.85 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA GLY C 17 " pdb=" C GLY C 17 " pdb=" N GLU C 18 " pdb=" CA GLU C 18 " ideal model delta harmonic sigma weight residual 180.00 -135.18 -44.82 0 5.00e+00 4.00e-02 8.04e+01 ... (remaining 15489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 3666 0.988 - 1.976: 0 1.976 - 2.964: 0 2.964 - 3.953: 0 3.953 - 4.941: 12 Chirality restraints: 3678 Sorted by residual: chirality pdb=" CB THR F 371 " pdb=" CA THR F 371 " pdb=" OG1 THR F 371 " pdb=" CG2 THR F 371 " both_signs ideal model delta sigma weight residual False 2.55 -2.39 4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" CB THR E 371 " pdb=" CA THR E 371 " pdb=" OG1 THR E 371 " pdb=" CG2 THR E 371 " both_signs ideal model delta sigma weight residual False 2.55 -2.39 4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" CB THR D 371 " pdb=" CA THR D 371 " pdb=" OG1 THR D 371 " pdb=" CG2 THR D 371 " both_signs ideal model delta sigma weight residual False 2.55 -2.39 4.94 2.00e-01 2.50e+01 6.09e+02 ... (remaining 3675 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B BYC B 601 " -0.363 2.00e-02 2.50e+03 2.10e-01 4.40e+02 pdb=" C2B BYC B 601 " 0.124 2.00e-02 2.50e+03 pdb=" O57 BYC B 601 " 0.135 2.00e-02 2.50e+03 pdb=" S1P BYC B 601 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B BYC D 601 " -0.362 2.00e-02 2.50e+03 2.10e-01 4.39e+02 pdb=" C2B BYC D 601 " 0.125 2.00e-02 2.50e+03 pdb=" O57 BYC D 601 " 0.135 2.00e-02 2.50e+03 pdb=" S1P BYC D 601 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B BYC C 601 " -0.362 2.00e-02 2.50e+03 2.10e-01 4.39e+02 pdb=" C2B BYC C 601 " 0.124 2.00e-02 2.50e+03 pdb=" O57 BYC C 601 " 0.135 2.00e-02 2.50e+03 pdb=" S1P BYC C 601 " 0.103 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.64: 419 2.64 - 3.26: 24652 3.26 - 3.89: 53258 3.89 - 4.51: 74699 4.51 - 5.14: 117122 Nonbonded interactions: 270150 Sorted by model distance: nonbonded pdb=" O9 BYN B 602 " pdb="FE FE B 603 " model vdw 2.015 2.260 nonbonded pdb=" O9 BYN C 602 " pdb="FE FE C 603 " model vdw 2.015 2.260 nonbonded pdb=" O9 BYN A 602 " pdb="FE FE A 603 " model vdw 2.015 2.260 nonbonded pdb=" O9 BYN E 602 " pdb="FE FE E 603 " model vdw 2.015 2.260 nonbonded pdb=" O9 BYN F 602 " pdb="FE FE F 603 " model vdw 2.015 2.260 ... (remaining 270145 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.450 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 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 : 0.015 0.353 25488 Z= 0.768 Angle : 1.193 15.061 34686 Z= 0.595 Chirality : 0.286 4.941 3678 Planarity : 0.011 0.210 4470 Dihedral : 16.482 103.595 9852 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.71 % Favored : 95.70 % Rotamer: Outliers : 2.31 % Allowed : 3.01 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -3.07 (0.13), residues: 3072 helix: -2.59 (0.11), residues: 996 sheet: -1.68 (0.21), residues: 534 loop : -1.68 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 345 TYR 0.017 0.002 TYR A 265 PHE 0.023 0.002 PHE D 224 TRP 0.033 0.002 TRP A 518 HIS 0.006 0.002 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.01472 / 0.77 (25488) covalent geometry : angle 1.19277 / 0.60 (34686) hydrogen bonds : bond 0.17890 / 11.78 ( 846) hydrogen bonds : angle 6.85058 / 4.86 ( 2448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.977 Fit side-chains REVERT: A 68 MET cc_start: 0.9120 (mmt) cc_final: 0.8910 (mmp) REVERT: B 336 ASP cc_start: 0.8676 (t0) cc_final: 0.8453 (t0) REVERT: B 515 MET cc_start: 0.9383 (mtp) cc_final: 0.9077 (mtp) REVERT: C 336 ASP cc_start: 0.8654 (t0) cc_final: 0.8427 (t0) REVERT: C 515 MET cc_start: 0.9422 (mtp) cc_final: 0.9076 (mtp) REVERT: D 68 MET cc_start: 0.9127 (mmt) cc_final: 0.8916 (mmp) REVERT: E 302 MET cc_start: 0.8496 (tpp) cc_final: 0.8289 (tpp) REVERT: F 68 MET cc_start: 0.9140 (mmt) cc_final: 0.8919 (mmp) outliers start: 60 outliers final: 12 residues processed: 232 average time/residue: 0.7592 time to fit residues: 200.3233 Evaluate side-chains 143 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 465 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 461 GLN B 293 HIS ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN B 461 GLN C 293 HIS ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 461 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN D 461 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 ASN E 461 GLN F 293 HIS ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN F 461 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059161 restraints weight = 51666.811| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.41 r_work: 0.2765 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25488 Z= 0.163 Angle : 0.648 7.097 34686 Z= 0.331 Chirality : 0.048 0.226 3678 Planarity : 0.005 0.057 4470 Dihedral : 14.704 120.031 4050 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.55 % Favored : 96.06 % Rotamer: Outliers : 0.96 % Allowed : 7.60 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -1.56 (0.14), residues: 3072 helix: -0.71 (0.15), residues: 990 sheet: -1.12 (0.21), residues: 558 loop : -1.12 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 291 TYR 0.014 0.001 TYR C 218 PHE 0.013 0.001 PHE B 224 TRP 0.009 0.001 TRP A 518 HIS 0.006 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (25488) covalent geometry : angle 0.64824 / 0.33 (34686) hydrogen bonds : bond 0.05576 / 3.71 ( 846) hydrogen bonds : angle 5.19465 / 3.69 ( 2448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.931 Fit side-chains REVERT: A 68 MET cc_start: 0.8925 (mmt) cc_final: 0.8710 (mmp) REVERT: B 336 ASP cc_start: 0.8851 (t0) cc_final: 0.8640 (t0) REVERT: C 336 ASP cc_start: 0.8846 (t0) cc_final: 0.8637 (t0) REVERT: D 68 MET cc_start: 0.8927 (mmt) cc_final: 0.8713 (mmp) REVERT: E 370 MET cc_start: 0.8557 (mtp) cc_final: 0.8337 (mtt) REVERT: F 68 MET cc_start: 0.9008 (mmt) cc_final: 0.8749 (mmp) outliers start: 25 outliers final: 16 residues processed: 161 average time/residue: 0.5954 time to fit residues: 112.7080 Evaluate side-chains 143 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 465 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 259 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 204 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058535 restraints weight = 51644.766| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.39 r_work: 0.2757 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25488 Z= 0.181 Angle : 0.617 7.059 34686 Z= 0.315 Chirality : 0.046 0.166 3678 Planarity : 0.004 0.058 4470 Dihedral : 13.960 132.901 4050 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.78 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 7.95 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.83 (0.15), residues: 3072 helix: 0.14 (0.16), residues: 990 sheet: -1.07 (0.21), residues: 600 loop : -0.67 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.013 0.001 TYR E 226 PHE 0.015 0.001 PHE D 224 TRP 0.005 0.001 TRP C 134 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (25488) covalent geometry : angle 0.61705 / 0.31 (34686) hydrogen bonds : bond 0.05281 / 3.52 ( 846) hydrogen bonds : angle 4.95655 / 3.55 ( 2448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.653 Fit side-chains REVERT: A 68 MET cc_start: 0.8891 (mmt) cc_final: 0.8672 (mmp) REVERT: A 295 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.8079 (p90) REVERT: A 337 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8159 (t0) REVERT: C 302 MET cc_start: 0.8618 (tpp) cc_final: 0.8188 (tpp) REVERT: D 68 MET cc_start: 0.8887 (mmt) cc_final: 0.8669 (mmp) REVERT: D 295 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.8089 (p90) REVERT: D 337 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8183 (t0) REVERT: E 370 MET cc_start: 0.8515 (mtp) cc_final: 0.8294 (mtt) outliers start: 48 outliers final: 13 residues processed: 187 average time/residue: 0.5516 time to fit residues: 120.3480 Evaluate side-chains 146 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 465 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 238 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN C 76 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060816 restraints weight = 50973.611| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.41 r_work: 0.2806 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25488 Z= 0.125 Angle : 0.578 6.979 34686 Z= 0.293 Chirality : 0.045 0.147 3678 Planarity : 0.004 0.056 4470 Dihedral : 13.411 137.393 4046 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 1.54 % Allowed : 8.95 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.48 (0.15), residues: 3072 helix: 0.45 (0.17), residues: 996 sheet: -0.93 (0.22), residues: 558 loop : -0.49 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.013 0.001 TYR B 218 PHE 0.011 0.001 PHE D 224 TRP 0.006 0.001 TRP A 134 HIS 0.003 0.001 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (25488) covalent geometry : angle 0.57847 / 0.29 (34686) hydrogen bonds : bond 0.04382 / 2.92 ( 846) hydrogen bonds : angle 4.77494 / 3.43 ( 2448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.686 Fit side-chains REVERT: A 68 MET cc_start: 0.8839 (mmt) cc_final: 0.8613 (mmp) REVERT: A 337 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7725 (OUTLIER) REVERT: B 76 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8625 (m110) REVERT: C 76 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: C 302 MET cc_start: 0.8618 (tpp) cc_final: 0.8249 (tpp) REVERT: D 68 MET cc_start: 0.8838 (mmt) cc_final: 0.8614 (mmp) REVERT: D 337 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7751 (t0) REVERT: E 68 MET cc_start: 0.8852 (mmt) cc_final: 0.8607 (mmp) REVERT: F 68 MET cc_start: 0.8852 (mmt) cc_final: 0.8606 (mmp) outliers start: 40 outliers final: 12 residues processed: 176 average time/residue: 0.5814 time to fit residues: 118.8767 Evaluate side-chains 150 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 295 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 172 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN C 76 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 76 ASN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.057698 restraints weight = 51355.141| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.41 r_work: 0.2739 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25488 Z= 0.245 Angle : 0.636 7.277 34686 Z= 0.322 Chirality : 0.047 0.154 3678 Planarity : 0.004 0.062 4470 Dihedral : 13.307 138.107 4038 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 1.81 % Allowed : 8.95 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.32 (0.15), residues: 3072 helix: 0.54 (0.17), residues: 1002 sheet: -0.79 (0.22), residues: 558 loop : -0.38 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.012 0.001 TYR F 226 PHE 0.018 0.001 PHE D 224 TRP 0.006 0.001 TRP C 390 HIS 0.004 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (25488) covalent geometry : angle 0.63565 / 0.32 (34686) hydrogen bonds : bond 0.05319 / 3.54 ( 846) hydrogen bonds : angle 4.89699 / 3.53 ( 2448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.985 Fit side-chains REVERT: A 68 MET cc_start: 0.8868 (mmt) cc_final: 0.8646 (mmp) REVERT: A 337 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7969 (t0) REVERT: B 302 MET cc_start: 0.8814 (tpp) cc_final: 0.8312 (tpp) REVERT: C 302 MET cc_start: 0.8696 (tpp) cc_final: 0.8331 (tpp) REVERT: D 68 MET cc_start: 0.8872 (mmt) cc_final: 0.8648 (mmp) REVERT: D 337 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8010 (t0) outliers start: 47 outliers final: 14 residues processed: 183 average time/residue: 0.5994 time to fit residues: 127.7279 Evaluate side-chains 149 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 403 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 304 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 225 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 241 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN C 76 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059666 restraints weight = 51087.386| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.41 r_work: 0.2780 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25488 Z= 0.140 Angle : 0.596 7.075 34686 Z= 0.301 Chirality : 0.045 0.150 3678 Planarity : 0.004 0.062 4470 Dihedral : 13.146 137.084 4038 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.48 % Favored : 96.32 % Rotamer: Outliers : 1.31 % Allowed : 10.22 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.22 (0.15), residues: 3072 helix: 0.67 (0.17), residues: 1002 sheet: -0.88 (0.22), residues: 558 loop : -0.29 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.013 0.001 TYR C 218 PHE 0.012 0.001 PHE D 224 TRP 0.005 0.001 TRP F 462 HIS 0.002 0.001 HIS E 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (25488) covalent geometry : angle 0.59573 / 0.30 (34686) hydrogen bonds : bond 0.04658 / 3.10 ( 846) hydrogen bonds : angle 4.79927 / 3.45 ( 2448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.609 Fit side-chains REVERT: A 68 MET cc_start: 0.8847 (mmt) cc_final: 0.8596 (mmp) REVERT: A 337 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 302 MET cc_start: 0.8767 (tpp) cc_final: 0.8284 (tpp) REVERT: B 448 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8467 (t) REVERT: C 302 MET cc_start: 0.8624 (tpp) cc_final: 0.8284 (tpp) REVERT: C 448 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8454 (t) REVERT: D 68 MET cc_start: 0.8849 (mmt) cc_final: 0.8615 (mmp) REVERT: D 337 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7841 (t0) REVERT: F 68 MET cc_start: 0.8855 (mmt) cc_final: 0.8621 (mmp) outliers start: 34 outliers final: 13 residues processed: 171 average time/residue: 0.5703 time to fit residues: 113.4298 Evaluate side-chains 154 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 448 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 163 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.060680 restraints weight = 50879.515| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.40 r_work: 0.2809 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25488 Z= 0.123 Angle : 0.587 7.283 34686 Z= 0.294 Chirality : 0.045 0.164 3678 Planarity : 0.004 0.059 4470 Dihedral : 12.939 138.008 4038 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.42 % Favored : 96.45 % Rotamer: Outliers : 1.00 % Allowed : 11.15 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.12 (0.15), residues: 3072 helix: 0.78 (0.17), residues: 1002 sheet: -0.92 (0.22), residues: 558 loop : -0.20 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.012 0.001 TYR C 218 PHE 0.011 0.001 PHE B 224 TRP 0.004 0.001 TRP F 462 HIS 0.003 0.001 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (25488) covalent geometry : angle 0.58709 / 0.29 (34686) hydrogen bonds : bond 0.04253 / 2.83 ( 846) hydrogen bonds : angle 4.70585 / 3.38 ( 2448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.825 Fit side-chains REVERT: A 68 MET cc_start: 0.8832 (mmt) cc_final: 0.8599 (mmp) REVERT: A 337 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7617 (t0) REVERT: B 302 MET cc_start: 0.8752 (tpp) cc_final: 0.8315 (tpp) REVERT: B 448 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8426 (t) REVERT: C 302 MET cc_start: 0.8721 (tpp) cc_final: 0.8392 (tpp) REVERT: C 448 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8489 (t) REVERT: D 68 MET cc_start: 0.8823 (mmt) cc_final: 0.8591 (mmp) REVERT: D 337 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7652 (OUTLIER) REVERT: E 68 MET cc_start: 0.8826 (mmt) cc_final: 0.8572 (mmp) REVERT: F 68 MET cc_start: 0.8824 (mmt) cc_final: 0.8574 (mmp) outliers start: 26 outliers final: 13 residues processed: 168 average time/residue: 0.5843 time to fit residues: 114.1534 Evaluate side-chains 155 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 295 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 36 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 291 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058872 restraints weight = 51279.035| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.39 r_work: 0.2752 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25488 Z= 0.218 Angle : 0.629 7.417 34686 Z= 0.315 Chirality : 0.047 0.158 3678 Planarity : 0.004 0.062 4470 Dihedral : 12.933 138.137 4038 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 1.50 % Allowed : 10.53 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.05 (0.15), residues: 3072 helix: 0.75 (0.17), residues: 1002 sheet: -0.82 (0.22), residues: 558 loop : -0.11 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.012 0.001 TYR B 218 PHE 0.016 0.001 PHE A 224 TRP 0.006 0.001 TRP F 390 HIS 0.004 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (25488) covalent geometry : angle 0.62894 / 0.32 (34686) hydrogen bonds : bond 0.05051 / 3.36 ( 846) hydrogen bonds : angle 4.80208 / 3.45 ( 2448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.841 Fit side-chains REVERT: A 68 MET cc_start: 0.8840 (mmt) cc_final: 0.8603 (mmp) REVERT: A 337 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7884 (t0) REVERT: B 302 MET cc_start: 0.8764 (tpp) cc_final: 0.8295 (tpp) REVERT: B 448 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 302 MET cc_start: 0.8707 (tpp) cc_final: 0.8356 (tpp) REVERT: C 448 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8575 (t) REVERT: D 68 MET cc_start: 0.8853 (mmt) cc_final: 0.8614 (mmp) REVERT: D 337 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7894 (t0) REVERT: E 68 MET cc_start: 0.8908 (mmt) cc_final: 0.8680 (mmp) REVERT: F 68 MET cc_start: 0.8898 (mmt) cc_final: 0.8668 (mmp) outliers start: 39 outliers final: 22 residues processed: 181 average time/residue: 0.5587 time to fit residues: 118.7427 Evaluate side-chains 166 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 448 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.060762 restraints weight = 51120.279| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.42 r_work: 0.2803 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25488 Z= 0.122 Angle : 0.596 8.600 34686 Z= 0.298 Chirality : 0.045 0.152 3678 Planarity : 0.004 0.060 4470 Dihedral : 12.761 137.227 4038 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 0.96 % Allowed : 11.42 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.05 (0.15), residues: 3072 helix: 0.81 (0.17), residues: 1002 sheet: -0.51 (0.23), residues: 510 loop : -0.18 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.013 0.001 TYR D 218 PHE 0.013 0.001 PHE B 224 TRP 0.004 0.001 TRP F 462 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25488) covalent geometry : angle 0.59583 / 0.30 (34686) hydrogen bonds : bond 0.04318 / 2.88 ( 846) hydrogen bonds : angle 4.68945 / 3.36 ( 2448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.052 Fit side-chains REVERT: A 68 MET cc_start: 0.8820 (mmt) cc_final: 0.8591 (mmp) REVERT: A 337 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7645 (OUTLIER) REVERT: B 302 MET cc_start: 0.8733 (tpp) cc_final: 0.8287 (tpp) REVERT: B 448 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8544 (t) REVERT: C 302 MET cc_start: 0.8734 (tpp) cc_final: 0.8388 (tpp) REVERT: C 448 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8529 (t) REVERT: D 68 MET cc_start: 0.8808 (mmt) cc_final: 0.8575 (mmp) REVERT: D 337 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7654 (OUTLIER) REVERT: E 68 MET cc_start: 0.8841 (mmt) cc_final: 0.8597 (mmp) REVERT: F 68 MET cc_start: 0.8846 (mmt) cc_final: 0.8601 (mmp) outliers start: 25 outliers final: 14 residues processed: 163 average time/residue: 0.5964 time to fit residues: 112.9372 Evaluate side-chains 157 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 39 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 290 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059550 restraints weight = 51394.865| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.38 r_work: 0.2767 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25488 Z= 0.186 Angle : 0.625 9.245 34686 Z= 0.312 Chirality : 0.046 0.165 3678 Planarity : 0.004 0.062 4470 Dihedral : 12.706 137.615 4038 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.96 % Rotamer: Outliers : 0.73 % Allowed : 11.57 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.05 (0.15), residues: 3072 helix: 0.81 (0.17), residues: 1002 sheet: -0.83 (0.22), residues: 558 loop : -0.01 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.012 0.001 TYR D 218 PHE 0.015 0.001 PHE A 224 TRP 0.006 0.001 TRP B 390 HIS 0.003 0.001 HIS E 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (25488) covalent geometry : angle 0.62480 / 0.31 (34686) hydrogen bonds : bond 0.04811 / 3.20 ( 846) hydrogen bonds : angle 4.72539 / 3.39 ( 2448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.888 Fit side-chains REVERT: A 68 MET cc_start: 0.8855 (mmt) cc_final: 0.8627 (mmp) REVERT: A 337 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 302 MET cc_start: 0.8779 (tpp) cc_final: 0.8326 (tpp) REVERT: B 448 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8616 (t) REVERT: C 302 MET cc_start: 0.8742 (tpp) cc_final: 0.8399 (tpp) REVERT: C 448 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8602 (t) REVERT: D 68 MET cc_start: 0.8842 (mmt) cc_final: 0.8581 (mmp) REVERT: D 337 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7838 (t0) REVERT: E 68 MET cc_start: 0.8881 (mmt) cc_final: 0.8647 (mmp) outliers start: 19 outliers final: 12 residues processed: 160 average time/residue: 0.6184 time to fit residues: 115.0873 Evaluate side-chains 160 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain D residue 295 HIS Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 448 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN D 76 ASN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058780 restraints weight = 51328.291| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.40 r_work: 0.2755 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25488 Z= 0.213 Angle : 0.635 9.323 34686 Z= 0.318 Chirality : 0.047 0.170 3678 Planarity : 0.004 0.062 4470 Dihedral : 12.677 137.507 4038 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.42 % Favored : 96.39 % Rotamer: Outliers : 0.89 % Allowed : 11.42 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.06 (0.15), residues: 3072 helix: 0.78 (0.17), residues: 1002 sheet: -0.78 (0.22), residues: 558 loop : 0.01 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.012 0.001 TYR C 218 PHE 0.016 0.001 PHE B 224 TRP 0.005 0.001 TRP E 390 HIS 0.004 0.001 HIS D 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (25488) covalent geometry : angle 0.63497 / 0.32 (34686) hydrogen bonds : bond 0.04971 / 3.30 ( 846) hydrogen bonds : angle 4.74119 / 3.41 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8128.76 seconds wall clock time: 139 minutes 14.36 seconds (8354.36 seconds total)