Starting phenix.real_space_refine on Sun Jul 5 01:53:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p02_17324/07_2026/8p02_17324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p02_17324/07_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_17324/07_2026/8p02_17324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p02_17324/07_2026/8p02_17324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p02_17324/07_2026/8p02_17324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p02_17324/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 92 Ad-hoc single atom residues: {' FE': 2, ' CA': 1, ' K': 1} Unusual residues: {'BYC': 1, 'BYN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 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: 3.65, per 1000 atoms: 0.15 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 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: 0.60 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: 5.39 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 3.000 nonbonded pdb=" O9 BYN C 602 " pdb="FE FE C 603 " model vdw 2.015 3.000 nonbonded pdb=" O9 BYN A 602 " pdb="FE FE A 603 " model vdw 2.015 3.000 nonbonded pdb=" O9 BYN E 602 " pdb="FE FE E 603 " model vdw 2.015 3.000 nonbonded pdb=" O9 BYN F 602 " pdb="FE FE F 603 " model vdw 2.015 3.000 ... (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: 0.09 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.500 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- 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 : 0.996 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: 0.7479 time to fit residues: 197.8600 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 : 1.054 ------------------------------------------------------------------------------- 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: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 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: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.078429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058921 restraints weight = 51747.266| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.39 r_work: 0.2760 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25488 Z= 0.176 Angle : 0.670 7.127 34686 Z= 0.340 Chirality : 0.048 0.276 3678 Planarity : 0.005 0.059 4470 Dihedral : 14.924 111.436 4050 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.61 % Favored : 96.00 % Rotamer: Outliers : 0.85 % Allowed : 8.10 % Favored : 91.05 % 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: -1.61 (0.14), residues: 3072 helix: -0.79 (0.14), residues: 990 sheet: -1.10 (0.21), residues: 558 loop : -1.14 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 291 TYR 0.014 0.001 TYR C 218 PHE 0.017 0.001 PHE B 224 TRP 0.008 0.001 TRP A 518 HIS 0.006 0.001 HIS F 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (25488) covalent geometry : angle 0.66980 / 0.34 (34686) hydrogen bonds : bond 0.05691 / 3.78 ( 846) hydrogen bonds : angle 5.29257 / 3.76 ( 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 160 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.889 Fit side-chains REVERT: A 68 MET cc_start: 0.8938 (mmt) cc_final: 0.8728 (mmp) REVERT: A 318 MET cc_start: 0.8883 (ptp) cc_final: 0.8679 (ptp) REVERT: B 336 ASP cc_start: 0.8894 (t0) cc_final: 0.8680 (t0) REVERT: C 336 ASP cc_start: 0.8885 (t0) cc_final: 0.8673 (t0) REVERT: D 68 MET cc_start: 0.8932 (mmt) cc_final: 0.8722 (mmp) REVERT: E 370 MET cc_start: 0.8581 (mtp) cc_final: 0.8327 (mtt) REVERT: F 68 MET cc_start: 0.9010 (mmt) cc_final: 0.8760 (mmp) outliers start: 22 outliers final: 16 residues processed: 160 average time/residue: 0.5932 time to fit residues: 111.8732 Evaluate side-chains 142 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 2.9990 chunk 271 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.079216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059449 restraints weight = 51537.462| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.43 r_work: 0.2778 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25488 Z= 0.154 Angle : 0.614 7.086 34686 Z= 0.310 Chirality : 0.046 0.162 3678 Planarity : 0.004 0.056 4470 Dihedral : 13.850 124.552 4050 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.32 % Favored : 96.48 % Rotamer: Outliers : 2.12 % Allowed : 7.99 % Favored : 89.89 % 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: -0.87 (0.15), residues: 3072 helix: 0.06 (0.16), residues: 996 sheet: -0.91 (0.22), residues: 558 loop : -0.78 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 291 TYR 0.012 0.001 TYR B 218 PHE 0.013 0.001 PHE C 224 TRP 0.004 0.001 TRP B 462 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (25488) covalent geometry : angle 0.61445 / 0.31 (34686) hydrogen bonds : bond 0.04979 / 3.31 ( 846) hydrogen bonds : angle 4.97260 / 3.56 ( 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 195 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.057 Fit side-chains REVERT: A 68 MET cc_start: 0.8869 (mmt) cc_final: 0.8646 (mmp) REVERT: A 295 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.8093 (p90) REVERT: A 337 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 166 HIS cc_start: 0.9303 (OUTLIER) cc_final: 0.9017 (t70) REVERT: B 295 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.8127 (p90) REVERT: C 166 HIS cc_start: 0.9309 (OUTLIER) cc_final: 0.9015 (t70) REVERT: C 302 MET cc_start: 0.8657 (tpp) cc_final: 0.8345 (tpp) REVERT: D 68 MET cc_start: 0.8868 (mmt) cc_final: 0.8644 (mmp) REVERT: D 295 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.8097 (p90) REVERT: D 337 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8109 (t0) REVERT: E 370 MET cc_start: 0.8455 (mtp) cc_final: 0.8245 (mtt) REVERT: F 166 HIS cc_start: 0.9290 (OUTLIER) cc_final: 0.9084 (t70) outliers start: 55 outliers final: 19 residues processed: 195 average time/residue: 0.5559 time to fit residues: 128.0335 Evaluate side-chains 155 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 344 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 344 VAL 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 344 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 344 VAL 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: 0.1980 chunk 3 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 187 optimal weight: 0.0870 chunk 238 optimal weight: 0.4980 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN C 76 ASN 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 = 0.3368 r_free = 0.3368 target = 0.080486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060840 restraints weight = 51302.969| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.44 r_work: 0.2816 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25488 Z= 0.124 Angle : 0.580 7.165 34686 Z= 0.293 Chirality : 0.045 0.152 3678 Planarity : 0.004 0.053 4470 Dihedral : 13.361 140.591 4046 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 1.66 % Allowed : 8.95 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.51 (0.15), residues: 3072 helix: 0.45 (0.17), residues: 996 sheet: -0.90 (0.22), residues: 558 loop : -0.54 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 320 TYR 0.012 0.001 TYR C 218 PHE 0.012 0.001 PHE D 224 TRP 0.005 0.001 TRP D 191 HIS 0.010 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (25488) covalent geometry : angle 0.58013 / 0.29 (34686) hydrogen bonds : bond 0.04316 / 2.87 ( 846) hydrogen bonds : angle 4.82259 / 3.46 ( 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 181 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.722 Fit side-chains REVERT: A 68 MET cc_start: 0.8843 (mmt) cc_final: 0.8613 (mmp) REVERT: A 337 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7741 (t0) REVERT: B 76 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8570 (m110) REVERT: B 166 HIS cc_start: 0.9240 (OUTLIER) cc_final: 0.8966 (t70) REVERT: B 295 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.8093 (p90) REVERT: B 302 MET cc_start: 0.8690 (tpp) cc_final: 0.8312 (tpp) REVERT: C 76 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8574 (m110) REVERT: C 166 HIS cc_start: 0.9241 (OUTLIER) cc_final: 0.8963 (t70) REVERT: C 302 MET cc_start: 0.8755 (tpp) cc_final: 0.8393 (tpp) REVERT: D 68 MET cc_start: 0.8840 (mmt) cc_final: 0.8610 (mmp) REVERT: D 337 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7725 (t0) REVERT: E 68 MET cc_start: 0.8813 (mmt) cc_final: 0.8564 (mmp) REVERT: F 68 MET cc_start: 0.8859 (mmt) cc_final: 0.8619 (mmp) REVERT: F 166 HIS cc_start: 0.9212 (OUTLIER) cc_final: 0.8999 (t70) outliers start: 43 outliers final: 11 residues processed: 179 average time/residue: 0.6329 time to fit residues: 132.5325 Evaluate side-chains 153 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 371 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 166 HIS 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 166 HIS Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 371 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 371 THR Chi-restraints excluded: chain F residue 166 HIS 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: 0.9980 chunk 152 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 254 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN C 76 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.060246 restraints weight = 51206.827| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.43 r_work: 0.2804 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25488 Z= 0.145 Angle : 0.584 7.108 34686 Z= 0.295 Chirality : 0.045 0.153 3678 Planarity : 0.004 0.056 4470 Dihedral : 13.160 142.811 4038 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 1.77 % Allowed : 9.53 % Favored : 88.70 % 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: -0.37 (0.15), residues: 3072 helix: 0.58 (0.17), residues: 1002 sheet: -0.86 (0.22), residues: 558 loop : -0.46 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 291 TYR 0.011 0.001 TYR B 218 PHE 0.012 0.001 PHE D 224 TRP 0.005 0.001 TRP A 462 HIS 0.009 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (25488) covalent geometry : angle 0.58419 / 0.29 (34686) hydrogen bonds : bond 0.04414 / 2.94 ( 846) hydrogen bonds : angle 4.79285 / 3.45 ( 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 180 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.775 Fit side-chains REVERT: A 68 MET cc_start: 0.8840 (mmt) cc_final: 0.8608 (mmp) REVERT: A 337 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7682 (OUTLIER) REVERT: B 302 MET cc_start: 0.8741 (tpp) cc_final: 0.8317 (tpp) REVERT: C 302 MET cc_start: 0.8764 (tpp) cc_final: 0.8416 (tpp) REVERT: D 68 MET cc_start: 0.8847 (mmt) cc_final: 0.8616 (mmp) REVERT: D 337 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7719 (t0) REVERT: E 68 MET cc_start: 0.8874 (mmt) cc_final: 0.8624 (mmp) REVERT: F 68 MET cc_start: 0.8862 (mmt) cc_final: 0.8621 (mmp) outliers start: 46 outliers final: 15 residues processed: 180 average time/residue: 0.6117 time to fit residues: 127.7438 Evaluate side-chains 148 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 21 optimal weight: 0.5980 chunk 173 optimal weight: 0.5980 chunk 225 optimal weight: 0.7980 chunk 242 optimal weight: 0.7980 chunk 260 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN 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 = 0.3382 r_free = 0.3382 target = 0.081017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.061350 restraints weight = 51111.655| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.44 r_work: 0.2832 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25488 Z= 0.115 Angle : 0.573 7.678 34686 Z= 0.288 Chirality : 0.044 0.159 3678 Planarity : 0.004 0.055 4470 Dihedral : 13.022 144.409 4038 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 1.20 % Allowed : 10.69 % Favored : 88.12 % 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: -0.24 (0.15), residues: 3072 helix: 0.67 (0.17), residues: 1002 sheet: -0.77 (0.22), residues: 546 loop : -0.38 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 291 TYR 0.011 0.001 TYR B 218 PHE 0.010 0.001 PHE A 224 TRP 0.004 0.001 TRP D 462 HIS 0.009 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (25488) covalent geometry : angle 0.57295 / 0.29 (34686) hydrogen bonds : bond 0.04092 / 2.72 ( 846) hydrogen bonds : angle 4.73201 / 3.40 ( 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 174 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.066 Fit side-chains REVERT: A 68 MET cc_start: 0.8827 (mmt) cc_final: 0.8583 (mmp) REVERT: A 337 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7547 (t0) REVERT: B 166 HIS cc_start: 0.9200 (OUTLIER) cc_final: 0.8893 (t70) REVERT: B 302 MET cc_start: 0.8702 (tpp) cc_final: 0.8303 (tpp) REVERT: C 166 HIS cc_start: 0.9192 (OUTLIER) cc_final: 0.8886 (t70) REVERT: C 302 MET cc_start: 0.8699 (tpp) cc_final: 0.8418 (tpp) REVERT: D 68 MET cc_start: 0.8827 (mmt) cc_final: 0.8586 (mmp) REVERT: D 337 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7576 (OUTLIER) REVERT: D 450 MET cc_start: 0.8223 (tpp) cc_final: 0.7970 (mmm) REVERT: E 68 MET cc_start: 0.8831 (mmt) cc_final: 0.8576 (mmp) outliers start: 31 outliers final: 14 residues processed: 170 average time/residue: 0.6705 time to fit residues: 132.8421 Evaluate side-chains 159 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 166 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 371 THR 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 F residue 295 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 163 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 208 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 403 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062302 restraints weight = 51001.277| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.42 r_work: 0.2847 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25488 Z= 0.115 Angle : 0.569 7.497 34686 Z= 0.285 Chirality : 0.044 0.197 3678 Planarity : 0.004 0.084 4470 Dihedral : 12.804 144.524 4038 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.27 % Allowed : 11.38 % Favored : 87.35 % 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: -0.02 (0.15), residues: 3072 helix: 0.81 (0.17), residues: 1002 sheet: -0.15 (0.24), residues: 468 loop : -0.43 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 320 TYR 0.010 0.001 TYR B 218 PHE 0.010 0.001 PHE B 224 TRP 0.005 0.001 TRP D 134 HIS 0.009 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (25488) covalent geometry : angle 0.56909 / 0.29 (34686) hydrogen bonds : bond 0.03949 / 2.63 ( 846) hydrogen bonds : angle 4.64850 / 3.33 ( 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 182 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.166 Fit side-chains REVERT: A 68 MET cc_start: 0.8815 (mmt) cc_final: 0.8561 (mmp) REVERT: A 295 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8236 (p90) REVERT: A 337 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7468 (t0) REVERT: A 403 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: B 166 HIS cc_start: 0.9224 (OUTLIER) cc_final: 0.8921 (t70) REVERT: B 302 MET cc_start: 0.8653 (tpp) cc_final: 0.8420 (tpp) REVERT: B 448 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8492 (t) REVERT: C 166 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8854 (t70) REVERT: C 302 MET cc_start: 0.8723 (tpp) cc_final: 0.8393 (tpp) REVERT: C 448 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (t) REVERT: D 68 MET cc_start: 0.8815 (mmt) cc_final: 0.8560 (mmp) REVERT: D 295 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8256 (p90) REVERT: D 337 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7492 (t0) REVERT: D 403 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: D 450 MET cc_start: 0.8191 (tpp) cc_final: 0.7943 (mmm) REVERT: E 68 MET cc_start: 0.8846 (mmt) cc_final: 0.8581 (mmp) REVERT: E 448 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8413 (t) outliers start: 33 outliers final: 8 residues processed: 179 average time/residue: 0.6549 time to fit residues: 136.5423 Evaluate side-chains 162 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 403 GLN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 166 HIS 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 403 GLN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain E residue 448 THR 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: 1.9990 chunk 224 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 258 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 214 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 403 GLN 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 = 0.3386 r_free = 0.3386 target = 0.080958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061420 restraints weight = 51126.621| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.44 r_work: 0.2826 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25488 Z= 0.132 Angle : 0.587 8.950 34686 Z= 0.292 Chirality : 0.044 0.191 3678 Planarity : 0.004 0.087 4470 Dihedral : 12.628 143.505 4038 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 1.16 % Allowed : 11.77 % Favored : 87.08 % 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: 0.87 (0.17), residues: 1002 sheet: -0.40 (0.23), residues: 540 loop : -0.26 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 320 TYR 0.011 0.001 TYR B 218 PHE 0.012 0.001 PHE D 224 TRP 0.005 0.001 TRP A 462 HIS 0.009 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (25488) covalent geometry : angle 0.58656 / 0.29 (34686) hydrogen bonds : bond 0.04154 / 2.76 ( 846) hydrogen bonds : angle 4.62519 / 3.31 ( 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 174 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.059 Fit side-chains REVERT: A 68 MET cc_start: 0.8817 (mmt) cc_final: 0.8560 (mmp) REVERT: A 295 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.8274 (p90) REVERT: A 337 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7546 (OUTLIER) REVERT: B 166 HIS cc_start: 0.9288 (OUTLIER) cc_final: 0.8893 (t70) REVERT: B 302 MET cc_start: 0.8706 (tpp) cc_final: 0.8325 (tpp) REVERT: B 448 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8533 (t) REVERT: C 68 MET cc_start: 0.8830 (mmp) cc_final: 0.8623 (mmp) REVERT: C 166 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8889 (t70) REVERT: C 302 MET cc_start: 0.8720 (tpp) cc_final: 0.8281 (tpp) REVERT: C 448 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8545 (t) REVERT: D 68 MET cc_start: 0.8823 (mmt) cc_final: 0.8567 (mmp) REVERT: D 337 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7561 (OUTLIER) REVERT: D 450 MET cc_start: 0.8198 (tpp) cc_final: 0.7945 (mmm) REVERT: E 68 MET cc_start: 0.8856 (mmt) cc_final: 0.8592 (mmp) REVERT: E 448 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8456 (t) outliers start: 30 outliers final: 14 residues processed: 170 average time/residue: 0.6635 time to fit residues: 131.5417 Evaluate side-chains 164 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 166 HIS Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 371 THR 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 448 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060650 restraints weight = 51281.824| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.44 r_work: 0.2807 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25488 Z= 0.156 Angle : 0.598 8.830 34686 Z= 0.298 Chirality : 0.045 0.170 3678 Planarity : 0.004 0.087 4470 Dihedral : 12.587 143.558 4038 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.45 % Favored : 96.42 % Rotamer: Outliers : 1.00 % Allowed : 11.73 % Favored : 87.27 % 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: 0.14 (0.15), residues: 3072 helix: 0.87 (0.17), residues: 1002 sheet: -0.01 (0.24), residues: 468 loop : -0.29 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.011 0.001 TYR B 218 PHE 0.013 0.001 PHE D 224 TRP 0.005 0.001 TRP A 134 HIS 0.009 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (25488) covalent geometry : angle 0.59793 / 0.30 (34686) hydrogen bonds : bond 0.04381 / 2.92 ( 846) hydrogen bonds : angle 4.65686 / 3.33 ( 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 168 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.019 Fit side-chains REVERT: A 68 MET cc_start: 0.8825 (mmt) cc_final: 0.8570 (mmp) REVERT: A 337 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7623 (OUTLIER) REVERT: B 166 HIS cc_start: 0.9340 (OUTLIER) cc_final: 0.8924 (t70) REVERT: B 302 MET cc_start: 0.8749 (tpp) cc_final: 0.8352 (tpp) REVERT: B 448 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8580 (t) REVERT: C 166 HIS cc_start: 0.9323 (OUTLIER) cc_final: 0.8908 (t70) REVERT: C 448 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8582 (t) REVERT: D 68 MET cc_start: 0.8836 (mmt) cc_final: 0.8582 (mmp) REVERT: D 337 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7647 (OUTLIER) REVERT: D 450 MET cc_start: 0.8229 (tpp) cc_final: 0.7965 (mmm) REVERT: E 448 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8517 (t) outliers start: 26 outliers final: 14 residues processed: 167 average time/residue: 0.6302 time to fit residues: 122.5844 Evaluate side-chains 159 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL 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 166 HIS 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 166 HIS 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 235 GLU Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain F residue 295 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 39 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 403 GLN 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 = 0.3390 r_free = 0.3390 target = 0.081127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.061585 restraints weight = 51162.905| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.44 r_work: 0.2830 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2030 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= 0.127 Angle : 0.585 9.211 34686 Z= 0.291 Chirality : 0.044 0.169 3678 Planarity : 0.004 0.080 4470 Dihedral : 12.465 143.736 4038 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.00 % Allowed : 11.69 % Favored : 87.31 % 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: 0.14 (0.15), residues: 3072 helix: 0.90 (0.17), residues: 1002 sheet: -0.35 (0.23), residues: 498 loop : -0.19 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.011 0.001 TYR C 218 PHE 0.011 0.001 PHE D 224 TRP 0.006 0.001 TRP A 134 HIS 0.008 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (25488) covalent geometry : angle 0.58544 / 0.29 (34686) hydrogen bonds : bond 0.04083 / 2.72 ( 846) hydrogen bonds : angle 4.60359 / 3.29 ( 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 171 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.066 Fit side-chains REVERT: A 68 MET cc_start: 0.8817 (mmt) cc_final: 0.8556 (mmp) REVERT: A 295 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (p90) REVERT: A 337 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7533 (OUTLIER) REVERT: B 68 MET cc_start: 0.8836 (mmp) cc_final: 0.8626 (mmp) REVERT: B 166 HIS cc_start: 0.9230 (OUTLIER) cc_final: 0.8867 (t70) REVERT: B 302 MET cc_start: 0.8715 (tpp) cc_final: 0.8307 (tpp) REVERT: B 337 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7749 (OUTLIER) REVERT: B 403 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8833 (tm-30) REVERT: B 448 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8584 (t) REVERT: C 166 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8871 (t70) REVERT: C 337 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7733 (OUTLIER) REVERT: C 403 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8811 (tm-30) REVERT: C 448 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8588 (t) REVERT: D 68 MET cc_start: 0.8826 (mmt) cc_final: 0.8567 (mmp) REVERT: D 295 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8310 (p90) REVERT: D 337 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7559 (OUTLIER) REVERT: D 450 MET cc_start: 0.8195 (tpp) cc_final: 0.7943 (mmm) REVERT: E 448 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8511 (t) outliers start: 26 outliers final: 12 residues processed: 167 average time/residue: 0.6741 time to fit residues: 131.0722 Evaluate side-chains 162 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL 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 166 HIS Chi-restraints excluded: chain B residue 295 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 295 HIS Chi-restraints excluded: chain C residue 337 ASP 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 83 VAL Chi-restraints excluded: chain E residue 295 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain F residue 295 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 93 optimal weight: 0.4980 chunk 181 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061541 restraints weight = 50961.656| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.44 r_work: 0.2829 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 25488 Z= 0.242 Angle : 0.822 65.884 34686 Z= 0.471 Chirality : 0.045 0.163 3678 Planarity : 0.007 0.266 4470 Dihedral : 12.465 143.735 4038 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 0.85 % Allowed : 11.88 % Favored : 87.27 % 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: 0.14 (0.15), residues: 3072 helix: 0.90 (0.17), residues: 1002 sheet: -0.34 (0.23), residues: 498 loop : -0.19 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.011 0.001 TYR C 218 PHE 0.011 0.001 PHE D 224 TRP 0.005 0.001 TRP A 134 HIS 0.008 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (25488) covalent geometry : angle 0.82225 / 0.47 (34686) hydrogen bonds : bond 0.04118 / 2.74 ( 846) hydrogen bonds : angle 4.60089 / 3.29 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9977.45 seconds wall clock time: 170 minutes 35.89 seconds (10235.89 seconds total)