Starting phenix.real_space_refine on Fri Feb 6 17:06:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4h_31711/02_2026/7v4h_31711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4h_31711/02_2026/7v4h_31711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v4h_31711/02_2026/7v4h_31711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4h_31711/02_2026/7v4h_31711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v4h_31711/02_2026/7v4h_31711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4h_31711/02_2026/7v4h_31711.map" } resolution = 2.9 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= 0.018 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 17300 2.51 5 N 4750 2.21 5 O 5210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27340 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "H" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "I" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Time building chain proxies: 5.93, per 1000 atoms: 0.22 Number of scatterers: 27340 At special positions: 0 Unit cell: (134.33, 136.35, 107.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 5210 8.00 N 4750 7.00 C 17300 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 32.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.529A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 removed outlier: 3.591A pdb=" N ALA J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 123 Processing helix chain 'J' and resid 168 through 183 removed outlier: 3.567A pdb=" N VAL J 172 " --> pdb=" O GLY J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 229 removed outlier: 3.902A pdb=" N TYR J 219 " --> pdb=" O TRP J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 276 through 284 Processing helix chain 'J' and resid 294 through 298 removed outlier: 3.579A pdb=" N GLU J 297 " --> pdb=" O GLY J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 324 Processing helix chain 'J' and resid 339 through 349 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.698A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.682A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 229 removed outlier: 3.640A pdb=" N TYR A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.535A pdb=" N GLU A 297 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.661A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.773A pdb=" N GLU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.545A pdb=" N VAL B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 229 removed outlier: 3.632A pdb=" N TYR B 219 " --> pdb=" O TRP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 274 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.508A pdb=" N GLU B 297 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.747A pdb=" N ALA C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.711A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 229 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.688A pdb=" N THR C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.691A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 123 removed outlier: 3.772A pdb=" N GLU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.544A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.317A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR D 219 " --> pdb=" O TRP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.600A pdb=" N ASN D 259 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 Processing helix chain 'D' and resid 276 through 284 Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.600A pdb=" N GLU D 297 " --> pdb=" O GLY D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.565A pdb=" N GLU D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 11 through 15 removed outlier: 3.941A pdb=" N ASP E 14 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.673A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.508A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 229 removed outlier: 4.138A pdb=" N GLY E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 227 " --> pdb=" O ARG E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 removed outlier: 4.082A pdb=" N VAL E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 318 through 325 Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'F' and resid 11 through 15 removed outlier: 3.889A pdb=" N ASP F 14 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 removed outlier: 3.634A pdb=" N LEU F 50 " --> pdb=" O PRO F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 207 through 229 removed outlier: 4.177A pdb=" N GLY F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 261 through 274 removed outlier: 4.137A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 283 Processing helix chain 'F' and resid 287 through 292 removed outlier: 3.525A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'G' and resid 11 through 15 removed outlier: 3.896A pdb=" N ASP G 14 " --> pdb=" O ASN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.569A pdb=" N LEU G 50 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 207 through 229 removed outlier: 4.134A pdb=" N GLY G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 261 through 274 removed outlier: 4.127A pdb=" N VAL G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 283 Processing helix chain 'G' and resid 287 through 292 removed outlier: 3.639A pdb=" N ARG G 291 " --> pdb=" O GLY G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 325 Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'H' and resid 11 through 15 removed outlier: 3.887A pdb=" N ASP H 14 " --> pdb=" O ASN H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.688A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.532A pdb=" N VAL H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 229 removed outlier: 4.082A pdb=" N GLY H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE H 227 " --> pdb=" O ARG H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 274 removed outlier: 3.991A pdb=" N VAL H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 284 Processing helix chain 'H' and resid 318 through 325 removed outlier: 3.658A pdb=" N GLU H 322 " --> pdb=" O GLY H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.664A pdb=" N LEU I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 115 Processing helix chain 'I' and resid 116 through 123 Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.526A pdb=" N VAL I 172 " --> pdb=" O GLY I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 229 removed outlier: 4.134A pdb=" N GLY I 211 " --> pdb=" O GLY I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 259 Processing helix chain 'I' and resid 262 through 274 removed outlier: 3.888A pdb=" N ILE I 266 " --> pdb=" O GLY I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 287 through 292 removed outlier: 3.641A pdb=" N ARG I 291 " --> pdb=" O GLY I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 325 Processing helix chain 'I' and resid 339 through 352 Processing sheet with id=AA1, first strand: chain 'J' and resid 33 through 40 removed outlier: 6.445A pdb=" N ILE J 20 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL J 90 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU J 22 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS J 92 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 24 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR J 94 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE J 26 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU J 89 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE J 77 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE J 91 " --> pdb=" O GLN J 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP J 53 " --> pdb=" O ILE J 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 186 through 191 removed outlier: 5.684A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR J 126 " --> pdb=" O PRO J 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 186 through 191 removed outlier: 5.684A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR J 126 " --> pdb=" O PRO J 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 307 " --> pdb=" O VAL J 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.543A pdb=" N ILE A 20 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 90 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU A 22 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N CYS A 92 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 24 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 94 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE A 26 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 89 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 77 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 91 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 5.919A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A 191 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 197 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 126 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 206 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 124 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 186 through 191 removed outlier: 5.919A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A 191 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 197 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 126 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 206 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 124 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 307 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 40 removed outlier: 6.458A pdb=" N ILE B 20 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 90 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS B 92 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 24 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 94 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ILE B 26 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 89 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 77 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 91 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 186 through 191 removed outlier: 5.800A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 191 removed outlier: 5.800A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 307 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 40 removed outlier: 6.456A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N CYS C 92 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 24 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR C 94 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ILE C 26 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 89 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 77 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 91 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 191 removed outlier: 5.688A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 191 removed outlier: 5.688A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 307 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.497A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS D 92 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 24 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR D 94 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ILE D 26 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 89 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D 77 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 91 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 186 through 191 removed outlier: 5.865A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 186 through 191 removed outlier: 5.865A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 40 removed outlier: 6.333A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE E 26 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 89 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE E 77 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE E 91 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 230 through 233 Processing sheet with id=AB9, first strand: chain 'E' and resid 230 through 233 removed outlier: 6.391A pdb=" N TYR E 126 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN E 197 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY E 191 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU E 199 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE E 189 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN E 201 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 187 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR G 39 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY E 191 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER G 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE G 20 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL G 90 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU G 22 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS G 92 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE G 24 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR G 94 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE G 26 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU G 89 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE G 77 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 91 " --> pdb=" O GLN G 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O GLN F 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 77 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 89 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 20 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL F 90 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE F 26 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 35 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY G 191 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY G 188 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR G 126 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O GLN F 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 77 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 89 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 20 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL F 90 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE F 26 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 35 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY G 191 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY G 188 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR G 126 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 230 through 233 Processing sheet with id=AC4, first strand: chain 'F' and resid 230 through 233 removed outlier: 6.288A pdb=" N TYR F 126 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY F 191 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER H 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE H 20 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL H 90 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ILE H 26 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU H 89 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE H 77 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE H 91 " --> pdb=" O GLN H 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 231 through 233 Processing sheet with id=AC6, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.277A pdb=" N TYR H 126 " --> pdb=" O PRO H 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLY H 191 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER I 35 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE I 20 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL I 90 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU I 22 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS I 92 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE I 24 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR I 94 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ILE I 26 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU I 89 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE I 77 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE I 91 " --> pdb=" O GLN I 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 186 through 191 removed outlier: 5.922A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR I 126 " --> pdb=" O PRO I 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 186 through 191 removed outlier: 5.922A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR I 126 " --> pdb=" O PRO I 204 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3303 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: 4.99 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9053 1.34 - 1.45: 4195 1.45 - 1.57: 14692 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 28070 Sorted by residual: bond pdb=" CB TRP J 53 " pdb=" CG TRP J 53 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.54e+00 bond pdb=" C GLY D 99 " pdb=" N GLU D 100 " ideal model delta sigma weight residual 1.331 1.295 0.036 2.07e-02 2.33e+03 2.97e+00 bond pdb=" CB TRP I 53 " pdb=" CG TRP I 53 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.58e+00 bond pdb=" CB GLU E 199 " pdb=" CG GLU E 199 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB TRP F 53 " pdb=" CG TRP F 53 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.34e+00 ... (remaining 28065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 37237 1.62 - 3.23: 769 3.23 - 4.85: 153 4.85 - 6.46: 17 6.46 - 8.08: 4 Bond angle restraints: 38180 Sorted by residual: angle pdb=" CA TRP D 53 " pdb=" CB TRP D 53 " pdb=" CG TRP D 53 " ideal model delta sigma weight residual 113.60 120.31 -6.71 1.90e+00 2.77e-01 1.25e+01 angle pdb=" CA TRP C 53 " pdb=" CB TRP C 53 " pdb=" CG TRP C 53 " ideal model delta sigma weight residual 113.60 120.30 -6.70 1.90e+00 2.77e-01 1.24e+01 angle pdb=" N GLY E 188 " pdb=" CA GLY E 188 " pdb=" C GLY E 188 " ideal model delta sigma weight residual 110.96 114.97 -4.01 1.19e+00 7.06e-01 1.13e+01 angle pdb=" N TRP H 53 " pdb=" CA TRP H 53 " pdb=" C TRP H 53 " ideal model delta sigma weight residual 109.18 113.84 -4.66 1.42e+00 4.96e-01 1.08e+01 angle pdb=" N TRP I 53 " pdb=" CA TRP I 53 " pdb=" C TRP I 53 " ideal model delta sigma weight residual 109.18 113.74 -4.56 1.42e+00 4.96e-01 1.03e+01 ... (remaining 38175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14934 17.48 - 34.97: 1213 34.97 - 52.45: 238 52.45 - 69.93: 37 69.93 - 87.42: 28 Dihedral angle restraints: 16450 sinusoidal: 6540 harmonic: 9910 Sorted by residual: dihedral pdb=" CA MET C 338 " pdb=" C MET C 338 " pdb=" N ASP C 339 " pdb=" CA ASP C 339 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET J 338 " pdb=" C MET J 338 " pdb=" N ASP J 339 " pdb=" CA ASP J 339 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU E 199 " pdb=" C GLU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 16447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2347 0.034 - 0.067: 1109 0.067 - 0.101: 327 0.101 - 0.135: 190 0.135 - 0.169: 17 Chirality restraints: 3990 Sorted by residual: chirality pdb=" CA ILE H 139 " pdb=" N ILE H 139 " pdb=" C ILE H 139 " pdb=" CB ILE H 139 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA TRP I 53 " pdb=" N TRP I 53 " pdb=" C TRP I 53 " pdb=" CB TRP I 53 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA VAL B 230 " pdb=" N VAL B 230 " pdb=" C VAL B 230 " pdb=" CB VAL B 230 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3987 not shown) Planarity restraints: 5030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 53 " -0.043 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP D 53 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP D 53 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 53 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 53 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 53 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 53 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 53 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 53 " -0.033 2.00e-02 2.50e+03 1.84e-02 8.47e+00 pdb=" CG TRP I 53 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP I 53 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP I 53 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 53 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP I 53 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 53 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 53 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP I 53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 53 " 0.031 2.00e-02 2.50e+03 1.74e-02 7.58e+00 pdb=" CG TRP H 53 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP H 53 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 53 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 53 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 53 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 53 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 53 " 0.002 2.00e-02 2.50e+03 ... (remaining 5027 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 291 2.65 - 3.21: 24342 3.21 - 3.77: 41309 3.77 - 4.34: 60277 4.34 - 4.90: 100624 Nonbonded interactions: 226843 Sorted by model distance: nonbonded pdb=" ND2 ASN A 190 " pdb=" OE2 GLU A 199 " model vdw 2.083 3.120 nonbonded pdb=" OD2 ASP C 46 " pdb=" OG SER C 48 " model vdw 2.149 3.040 nonbonded pdb=" NH2 ARG E 84 " pdb=" O ASP G 6 " model vdw 2.168 3.120 nonbonded pdb=" O GLY H 318 " pdb=" OG1 THR H 321 " model vdw 2.169 3.040 nonbonded pdb=" O THR I 293 " pdb=" OG1 THR I 298 " model vdw 2.170 3.040 ... (remaining 226838 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.260 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.004 0.058 28070 Z= 0.161 Angle : 0.589 8.080 38180 Z= 0.316 Chirality : 0.046 0.169 3990 Planarity : 0.005 0.063 5030 Dihedral : 13.651 87.417 10210 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3500 helix: -0.42 (0.15), residues: 1110 sheet: -0.56 (0.19), residues: 790 loop : -0.92 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.024 0.002 TYR A 176 PHE 0.016 0.001 PHE G 200 TRP 0.079 0.002 TRP D 53 HIS 0.003 0.001 HIS E 280 Details of bonding type rmsd covalent geometry : bond 0.00383 (28070) covalent geometry : angle 0.58856 (38180) hydrogen bonds : bond 0.16142 ( 1098) hydrogen bonds : angle 7.32515 ( 3303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.214 Fit side-chains REVERT: D 56 ASP cc_start: 0.7882 (t70) cc_final: 0.7617 (t70) REVERT: I 199 GLU cc_start: 0.7787 (tt0) cc_final: 0.7511 (tt0) outliers start: 0 outliers final: 1 residues processed: 268 average time/residue: 0.6627 time to fit residues: 206.8566 Evaluate side-chains 193 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN H 136 GLN I 9 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.183045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124253 restraints weight = 29576.831| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.19 r_work: 0.3227 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28070 Z= 0.204 Angle : 0.624 9.020 38180 Z= 0.328 Chirality : 0.048 0.168 3990 Planarity : 0.005 0.066 5030 Dihedral : 4.902 30.066 3863 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.58 % Allowed : 7.32 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3500 helix: 0.34 (0.15), residues: 1130 sheet: -0.47 (0.19), residues: 720 loop : -1.08 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 316 TYR 0.030 0.002 TYR A 176 PHE 0.018 0.002 PHE G 200 TRP 0.060 0.002 TRP D 53 HIS 0.005 0.001 HIS E 280 Details of bonding type rmsd covalent geometry : bond 0.00509 (28070) covalent geometry : angle 0.62419 (38180) hydrogen bonds : bond 0.05178 ( 1098) hydrogen bonds : angle 5.19855 ( 3303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.106 Fit side-chains REVERT: J 53 TRP cc_start: 0.8614 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: J 136 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: B 136 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: F 49 LYS cc_start: 0.7707 (pttm) cc_final: 0.7425 (pttp) REVERT: G 49 LYS cc_start: 0.7661 (pttm) cc_final: 0.7296 (pttp) REVERT: H 140 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8426 (mm110) outliers start: 45 outliers final: 25 residues processed: 234 average time/residue: 0.6880 time to fit residues: 187.4045 Evaluate side-chains 210 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 136 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 309 optimal weight: 0.1980 chunk 338 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 346 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN E 280 HIS F 9 ASN F 140 GLN G 9 ASN G 105 ASN G 140 GLN H 9 ASN H 105 ASN I 9 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.183877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125034 restraints weight = 29591.575| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.19 r_work: 0.3249 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28070 Z= 0.162 Angle : 0.566 8.686 38180 Z= 0.296 Chirality : 0.046 0.158 3990 Planarity : 0.005 0.065 5030 Dihedral : 4.664 23.412 3860 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.76 % Allowed : 10.18 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3500 helix: 0.57 (0.15), residues: 1130 sheet: -0.37 (0.19), residues: 730 loop : -1.13 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 316 TYR 0.024 0.002 TYR A 176 PHE 0.018 0.001 PHE G 200 TRP 0.032 0.001 TRP D 53 HIS 0.003 0.001 HIS E 280 Details of bonding type rmsd covalent geometry : bond 0.00399 (28070) covalent geometry : angle 0.56631 (38180) hydrogen bonds : bond 0.04658 ( 1098) hydrogen bonds : angle 4.92681 ( 3303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: J 136 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: B 136 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: D 22 GLU cc_start: 0.8324 (tp30) cc_final: 0.8104 (tp30) REVERT: F 49 LYS cc_start: 0.7738 (pttm) cc_final: 0.7449 (pttp) REVERT: G 49 LYS cc_start: 0.7692 (pttm) cc_final: 0.7317 (pttp) REVERT: H 140 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8424 (mm110) outliers start: 50 outliers final: 33 residues processed: 242 average time/residue: 0.6483 time to fit residues: 183.7736 Evaluate side-chains 225 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 332 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 171 optimal weight: 30.0000 chunk 120 optimal weight: 0.9980 chunk 339 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 108 HIS G 140 GLN H 9 ASN H 108 HIS I 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.181648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122694 restraints weight = 29546.337| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.18 r_work: 0.3202 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28070 Z= 0.223 Angle : 0.623 9.517 38180 Z= 0.324 Chirality : 0.048 0.159 3990 Planarity : 0.005 0.068 5030 Dihedral : 4.925 25.077 3860 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.61 % Allowed : 11.69 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3500 helix: 0.46 (0.15), residues: 1130 sheet: -0.43 (0.19), residues: 730 loop : -1.25 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 332 TYR 0.033 0.002 TYR A 176 PHE 0.019 0.002 PHE B 200 TRP 0.031 0.002 TRP J 53 HIS 0.004 0.001 HIS H 280 Details of bonding type rmsd covalent geometry : bond 0.00562 (28070) covalent geometry : angle 0.62273 (38180) hydrogen bonds : bond 0.05233 ( 1098) hydrogen bonds : angle 4.99829 ( 3303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: B 136 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: C 136 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: D 22 GLU cc_start: 0.8273 (tp30) cc_final: 0.8037 (tp30) REVERT: E 271 GLU cc_start: 0.3911 (OUTLIER) cc_final: 0.3463 (mp0) REVERT: F 49 LYS cc_start: 0.7803 (pttm) cc_final: 0.7487 (pttp) REVERT: G 49 LYS cc_start: 0.7745 (pttm) cc_final: 0.7375 (pttp) REVERT: I 49 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6878 (pttp) outliers start: 74 outliers final: 42 residues processed: 251 average time/residue: 0.6578 time to fit residues: 193.6601 Evaluate side-chains 239 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 244 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 323 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN G 302 ASN H 9 ASN I 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.182151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123196 restraints weight = 29454.431| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.19 r_work: 0.3238 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28070 Z= 0.200 Angle : 0.596 9.328 38180 Z= 0.311 Chirality : 0.047 0.159 3990 Planarity : 0.005 0.067 5030 Dihedral : 4.852 24.316 3860 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.71 % Allowed : 13.20 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3500 helix: 0.50 (0.15), residues: 1130 sheet: -0.44 (0.19), residues: 730 loop : -1.24 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 316 TYR 0.029 0.002 TYR A 176 PHE 0.018 0.002 PHE G 200 TRP 0.031 0.001 TRP J 53 HIS 0.003 0.001 HIS H 280 Details of bonding type rmsd covalent geometry : bond 0.00501 (28070) covalent geometry : angle 0.59632 (38180) hydrogen bonds : bond 0.04922 ( 1098) hydrogen bonds : angle 4.92971 ( 3303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 201 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: J 136 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: B 136 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: D 22 GLU cc_start: 0.8228 (tp30) cc_final: 0.7992 (tp30) REVERT: D 136 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: E 271 GLU cc_start: 0.4023 (OUTLIER) cc_final: 0.3531 (mp0) REVERT: F 49 LYS cc_start: 0.7824 (pttm) cc_final: 0.7511 (pttp) REVERT: G 49 LYS cc_start: 0.7763 (pttm) cc_final: 0.7393 (pttp) outliers start: 77 outliers final: 48 residues processed: 259 average time/residue: 0.6412 time to fit residues: 195.2988 Evaluate side-chains 244 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 288 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122623 restraints weight = 29661.870| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.19 r_work: 0.3199 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 28070 Z= 0.221 Angle : 0.620 9.559 38180 Z= 0.323 Chirality : 0.048 0.166 3990 Planarity : 0.005 0.068 5030 Dihedral : 4.958 24.998 3860 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.06 % Allowed : 13.42 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3500 helix: 0.46 (0.15), residues: 1130 sheet: -0.46 (0.19), residues: 730 loop : -1.28 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 316 TYR 0.033 0.002 TYR A 176 PHE 0.018 0.002 PHE B 200 TRP 0.032 0.002 TRP J 53 HIS 0.004 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00557 (28070) covalent geometry : angle 0.61992 (38180) hydrogen bonds : bond 0.05144 ( 1098) hydrogen bonds : angle 4.95424 ( 3303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 199 time to evaluate : 1.138 Fit side-chains REVERT: J 136 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: B 136 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: C 136 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: D 136 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: E 271 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.3515 (mp0) REVERT: F 49 LYS cc_start: 0.7813 (pttm) cc_final: 0.7502 (pttp) REVERT: G 49 LYS cc_start: 0.7755 (pttm) cc_final: 0.7390 (pttp) REVERT: G 128 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6783 (mm) outliers start: 87 outliers final: 54 residues processed: 263 average time/residue: 0.6466 time to fit residues: 200.2330 Evaluate side-chains 250 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 141 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 280 HIS Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 120 optimal weight: 0.0770 chunk 177 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 chunk 285 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.186611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127538 restraints weight = 29254.956| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.23 r_work: 0.3287 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28070 Z= 0.096 Angle : 0.507 8.045 38180 Z= 0.264 Chirality : 0.044 0.154 3990 Planarity : 0.005 0.061 5030 Dihedral : 4.360 19.348 3860 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.61 % Allowed : 14.51 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3500 helix: 0.85 (0.16), residues: 1130 sheet: -0.21 (0.18), residues: 740 loop : -1.21 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 316 TYR 0.011 0.001 TYR D 176 PHE 0.015 0.001 PHE G 200 TRP 0.025 0.001 TRP J 53 HIS 0.002 0.000 HIS H 280 Details of bonding type rmsd covalent geometry : bond 0.00214 (28070) covalent geometry : angle 0.50659 (38180) hydrogen bonds : bond 0.03553 ( 1098) hydrogen bonds : angle 4.64581 ( 3303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 1.066 Fit side-chains REVERT: J 136 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8637 (mp10) REVERT: E 271 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3477 (mp0) REVERT: F 49 LYS cc_start: 0.7735 (pttm) cc_final: 0.7447 (pttp) REVERT: G 22 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: G 31 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6651 (mtm) REVERT: G 49 LYS cc_start: 0.7694 (pttm) cc_final: 0.7339 (pttp) REVERT: G 199 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: H 140 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8340 (mm110) outliers start: 74 outliers final: 42 residues processed: 287 average time/residue: 0.5769 time to fit residues: 197.9988 Evaluate side-chains 251 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 239 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 77 optimal weight: 0.0270 chunk 274 optimal weight: 0.5980 chunk 188 optimal weight: 0.2980 chunk 115 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 105 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.187510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130189 restraints weight = 29617.181| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.38 r_work: 0.3312 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28070 Z= 0.092 Angle : 0.493 7.820 38180 Z= 0.256 Chirality : 0.044 0.145 3990 Planarity : 0.005 0.061 5030 Dihedral : 4.121 18.878 3860 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 15.49 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3500 helix: 1.00 (0.16), residues: 1130 sheet: -0.26 (0.19), residues: 670 loop : -0.97 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 316 TYR 0.011 0.001 TYR E 95 PHE 0.015 0.001 PHE G 200 TRP 0.024 0.001 TRP J 53 HIS 0.002 0.000 HIS H 280 Details of bonding type rmsd covalent geometry : bond 0.00210 (28070) covalent geometry : angle 0.49312 (38180) hydrogen bonds : bond 0.03294 ( 1098) hydrogen bonds : angle 4.43865 ( 3303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 1.113 Fit side-chains REVERT: J 206 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7481 (t) REVERT: C 35 SER cc_start: 0.8685 (t) cc_final: 0.8287 (t) REVERT: D 35 SER cc_start: 0.8620 (t) cc_final: 0.8291 (t) REVERT: E 31 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6557 (mtt) REVERT: E 54 ASN cc_start: 0.7930 (p0) cc_final: 0.7334 (p0) REVERT: E 271 GLU cc_start: 0.4041 (OUTLIER) cc_final: 0.3471 (mp0) REVERT: F 49 LYS cc_start: 0.7757 (pttm) cc_final: 0.7460 (pttp) REVERT: G 31 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6555 (mtm) REVERT: G 49 LYS cc_start: 0.7692 (pttm) cc_final: 0.7344 (pttp) REVERT: G 199 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: H 140 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8317 (mm110) outliers start: 66 outliers final: 46 residues processed: 269 average time/residue: 0.6253 time to fit residues: 198.8845 Evaluate side-chains 258 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 298 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123325 restraints weight = 29660.270| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.49 r_work: 0.3242 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28070 Z= 0.196 Angle : 0.596 9.122 38180 Z= 0.309 Chirality : 0.047 0.160 3990 Planarity : 0.005 0.064 5030 Dihedral : 4.647 23.384 3860 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.50 % Allowed : 15.81 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3500 helix: 0.79 (0.15), residues: 1130 sheet: -0.34 (0.19), residues: 730 loop : -1.01 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.026 0.002 TYR A 176 PHE 0.018 0.002 PHE B 200 TRP 0.034 0.001 TRP E 53 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00492 (28070) covalent geometry : angle 0.59563 (38180) hydrogen bonds : bond 0.04657 ( 1098) hydrogen bonds : angle 4.69285 ( 3303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.886 Fit side-chains REVERT: J 136 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: A 136 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: B 35 SER cc_start: 0.8688 (t) cc_final: 0.8349 (t) REVERT: C 22 GLU cc_start: 0.8306 (tp30) cc_final: 0.7977 (tm-30) REVERT: C 136 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: E 271 GLU cc_start: 0.4093 (OUTLIER) cc_final: 0.3471 (mp0) REVERT: F 49 LYS cc_start: 0.7859 (pttm) cc_final: 0.7567 (pttp) REVERT: G 31 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6664 (mtm) REVERT: G 49 LYS cc_start: 0.7841 (pttm) cc_final: 0.7462 (pttp) REVERT: G 199 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: H 140 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8381 (mm110) outliers start: 71 outliers final: 46 residues processed: 263 average time/residue: 0.5514 time to fit residues: 172.7994 Evaluate side-chains 251 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 105 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 205 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 328 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 140 GLN G 197 GLN G 244 ASN H 9 ASN I 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125479 restraints weight = 29604.718| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.19 r_work: 0.3243 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28070 Z= 0.130 Angle : 0.542 8.523 38180 Z= 0.281 Chirality : 0.045 0.152 3990 Planarity : 0.005 0.063 5030 Dihedral : 4.478 21.975 3860 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 16.06 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3500 helix: 0.88 (0.15), residues: 1130 sheet: -0.17 (0.19), residues: 680 loop : -1.10 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 316 TYR 0.016 0.001 TYR A 176 PHE 0.016 0.001 PHE G 200 TRP 0.036 0.001 TRP E 53 HIS 0.002 0.001 HIS H 280 Details of bonding type rmsd covalent geometry : bond 0.00316 (28070) covalent geometry : angle 0.54175 (38180) hydrogen bonds : bond 0.03952 ( 1098) hydrogen bonds : angle 4.60312 ( 3303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.958 Fit side-chains REVERT: A 136 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: C 22 GLU cc_start: 0.8230 (tp30) cc_final: 0.8028 (tm-30) REVERT: C 136 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: D 136 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: E 271 GLU cc_start: 0.4053 (OUTLIER) cc_final: 0.3464 (mp0) REVERT: F 49 LYS cc_start: 0.7744 (pttm) cc_final: 0.7452 (pttp) REVERT: G 31 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6572 (mtm) REVERT: G 49 LYS cc_start: 0.7728 (pttm) cc_final: 0.7372 (pttp) REVERT: G 199 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: H 140 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8372 (mm110) outliers start: 62 outliers final: 50 residues processed: 252 average time/residue: 0.5533 time to fit residues: 165.9261 Evaluate side-chains 255 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 179 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 309 optimal weight: 40.0000 chunk 299 optimal weight: 6.9990 chunk 330 optimal weight: 0.0170 chunk 338 optimal weight: 0.0970 chunk 212 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 overall best weight: 1.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 130 GLN ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.185836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126840 restraints weight = 29348.056| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.19 r_work: 0.3265 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28070 Z= 0.112 Angle : 0.515 8.057 38180 Z= 0.267 Chirality : 0.045 0.148 3990 Planarity : 0.005 0.062 5030 Dihedral : 4.301 22.232 3860 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.18 % Allowed : 16.13 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3500 helix: 0.98 (0.15), residues: 1130 sheet: -0.16 (0.19), residues: 680 loop : -1.03 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 316 TYR 0.014 0.001 TYR A 176 PHE 0.015 0.001 PHE G 200 TRP 0.026 0.001 TRP J 53 HIS 0.002 0.000 HIS G 175 Details of bonding type rmsd covalent geometry : bond 0.00265 (28070) covalent geometry : angle 0.51493 (38180) hydrogen bonds : bond 0.03569 ( 1098) hydrogen bonds : angle 4.49686 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8762.03 seconds wall clock time: 150 minutes 18.53 seconds (9018.53 seconds total)