Starting phenix.real_space_refine on Sun Jul 5 05:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ztd_14958/07_2026/7ztd_14958.map" } resolution = 4.6 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= 0.004 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 16148 2.51 5 N 4428 2.21 5 O 4980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "A" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "B" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "C" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "D" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "F" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "G" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "H" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "P" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "R" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "S" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.48, per 1000 atoms: 0.21 Number of scatterers: 25740 At special positions: 0 Unit cell: (100.88, 101.85, 281.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 16 15.00 O 4980 8.00 N 4428 7.00 C 16148 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: 1.95 Conformation dependent library (CDL) restraints added in 819.0 milliseconds 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 48 sheets defined 66.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.547A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.518A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 182 through 194 removed outlier: 4.229A pdb=" N TYR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.567A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 232 removed outlier: 3.504A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 260 removed outlier: 3.901A pdb=" N ALA E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.578A pdb=" N PHE E 266 " --> pdb=" O GLN E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.578A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.546A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.800A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.132A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 182 through 194 removed outlier: 4.253A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.665A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 255 through 260 removed outlier: 4.038A pdb=" N ALA A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.592A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.653A pdb=" N ARG A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.704A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.561A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.204A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.555A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.079A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 4.089A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.978A pdb=" N ALA B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.605A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.503A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 285 No H-bonds generated for 'chain 'B' and resid 284 through 285' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.906A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.120A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.507A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 194 removed outlier: 4.157A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.592A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 255 through 260 removed outlier: 4.190A pdb=" N ALA C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.604A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.692A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.651A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.847A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 54 through 59 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.150A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.554A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.236A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.715A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 255 through 260 removed outlier: 4.092A pdb=" N ALA D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.618A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.504A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 349 removed outlier: 4.557A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.846A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 113 through 126 Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.504A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.963A pdb=" N TYR F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 216 removed outlier: 3.538A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 255 through 260 removed outlier: 4.037A pdb=" N ALA F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 262 No H-bonds generated for 'chain 'F' and resid 261 through 262' Processing helix chain 'F' and resid 263 through 268 removed outlier: 3.624A pdb=" N PHE F 266 " --> pdb=" O GLN F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 283 removed outlier: 3.671A pdb=" N ILE F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.953A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.543A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 126 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.559A pdb=" N SER G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 182 through 194 removed outlier: 4.237A pdb=" N TYR G 188 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 216 removed outlier: 3.553A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 232 Processing helix chain 'G' and resid 257 through 262 Processing helix chain 'G' and resid 263 through 268 removed outlier: 3.633A pdb=" N PHE G 266 " --> pdb=" O GLN G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 283 removed outlier: 3.543A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 285 No H-bonds generated for 'chain 'G' and resid 284 through 285' Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.950A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 367 through 372 Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 113 through 126 Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.502A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 182 through 194 removed outlier: 4.143A pdb=" N TYR H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 216 removed outlier: 3.526A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 232 Processing helix chain 'H' and resid 255 through 260 removed outlier: 4.109A pdb=" N ALA H 260 " --> pdb=" O ARG H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 removed outlier: 3.601A pdb=" N PHE H 266 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 283 Processing helix chain 'H' and resid 284 through 285 No H-bonds generated for 'chain 'H' and resid 284 through 285' Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 289 through 294 Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 349 removed outlier: 4.768A pdb=" N VAL H 339 " --> pdb=" O ARG H 335 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TRP H 340 " --> pdb=" O LYS H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.913A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 367 through 372 Processing helix chain 'P' and resid 2 through 134 Processing helix chain 'Q' and resid 2 through 131 Processing helix chain 'R' and resid 2 through 134 Processing helix chain 'S' and resid 2 through 133 Processing sheet with id=AA1, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.535A pdb=" N PHE E 31 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR E 133 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.560A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.640A pdb=" N LEU E 176 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.694A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.633A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.518A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.546A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.641A pdb=" N THR A 162 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 176 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.554A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 10 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.518A pdb=" N VAL B 35 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 66 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.513A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.787A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.611A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 19 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.568A pdb=" N LEU C 176 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.811A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.626A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.556A pdb=" N VAL D 10 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 35 through 38 Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.713A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.889A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.620A pdb=" N ALA F 29 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 10 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR F 106 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.705A pdb=" N LEU F 176 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.773A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.621A pdb=" N PHE G 31 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR G 106 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.573A pdb=" N LEU G 176 " --> pdb=" O THR G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.581A pdb=" N THR G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.718A pdb=" N THR H 106 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA H 135 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET H 132 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.737A pdb=" N THR H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 238 through 241 1567 hydrogen bonds defined for protein. 4200 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: 4.31 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8424 1.33 - 1.45: 3595 1.45 - 1.57: 13909 1.57 - 1.69: 24 1.69 - 1.81: 296 Bond restraints: 26248 Sorted by residual: bond pdb=" CB ASN H 78 " pdb=" CG ASN H 78 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CB TRP A 79 " pdb=" CG TRP A 79 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.65e+00 bond pdb=" CG1 ILE A 64 " pdb=" CD1 ILE A 64 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.64e+00 bond pdb=" CG GLU D 270 " pdb=" CD GLU D 270 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CD1 TYR F 169 " pdb=" CE1 TYR F 169 " ideal model delta sigma weight residual 1.382 1.336 0.046 3.00e-02 1.11e+03 2.34e+00 ... (remaining 26243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 33242 1.94 - 3.88: 2142 3.88 - 5.82: 272 5.82 - 7.76: 47 7.76 - 9.70: 17 Bond angle restraints: 35720 Sorted by residual: angle pdb=" CA TYR C 169 " pdb=" CB TYR C 169 " pdb=" CG TYR C 169 " ideal model delta sigma weight residual 113.90 106.63 7.27 1.80e+00 3.09e-01 1.63e+01 angle pdb=" N ALA C 181 " pdb=" CA ALA C 181 " pdb=" C ALA C 181 " ideal model delta sigma weight residual 110.35 115.24 -4.89 1.38e+00 5.25e-01 1.26e+01 angle pdb=" N MET B 16 " pdb=" CA MET B 16 " pdb=" C MET B 16 " ideal model delta sigma weight residual 108.32 114.00 -5.68 1.64e+00 3.72e-01 1.20e+01 angle pdb=" N PHE A 255 " pdb=" CA PHE A 255 " pdb=" C PHE A 255 " ideal model delta sigma weight residual 113.88 118.09 -4.21 1.23e+00 6.61e-01 1.17e+01 angle pdb=" N ALA B 181 " pdb=" CA ALA B 181 " pdb=" C ALA B 181 " ideal model delta sigma weight residual 110.35 114.95 -4.60 1.38e+00 5.25e-01 1.11e+01 ... (remaining 35715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 15348 30.21 - 60.41: 340 60.41 - 90.62: 72 90.62 - 120.82: 16 120.82 - 151.03: 16 Dihedral angle restraints: 15792 sinusoidal: 5728 harmonic: 10064 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.03 -151.03 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.06 -149.06 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP H 401 " pdb=" O5' ADP H 401 " pdb=" PA ADP H 401 " pdb=" O2A ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.97 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2244 0.042 - 0.083: 1154 0.083 - 0.125: 509 0.125 - 0.166: 145 0.166 - 0.208: 40 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CA GLU B 270 " pdb=" N GLU B 270 " pdb=" C GLU B 270 " pdb=" CB GLU B 270 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PHE B 255 " pdb=" N PHE B 255 " pdb=" C PHE B 255 " pdb=" CB PHE B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA GLU G 270 " pdb=" N GLU G 270 " pdb=" C GLU G 270 " pdb=" CB GLU G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4089 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.030 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR C 169 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 169 " 0.027 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR F 169 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR F 169 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 169 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 169 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR F 169 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR F 169 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 169 " 0.028 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR B 169 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 169 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 169 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 169 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 169 " -0.010 2.00e-02 2.50e+03 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 381 2.66 - 3.22: 26644 3.22 - 3.78: 38554 3.78 - 4.34: 50723 4.34 - 4.90: 80837 Nonbonded interactions: 197139 Sorted by model distance: nonbonded pdb=" OG1 THR H 160 " pdb=" O LEU H 178 " model vdw 2.097 3.040 nonbonded pdb=" O GLY A 48 " pdb=" OH TYR A 53 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR E 160 " pdb=" O LEU E 178 " model vdw 2.127 3.040 nonbonded pdb=" OE1 GLN F 49 " pdb=" OH TYR F 53 " model vdw 2.140 3.040 nonbonded pdb=" OD2 ASP E 244 " pdb=" NH1 ARG B 290 " model vdw 2.160 3.120 ... (remaining 197134 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' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.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' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.000 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 26248 Z= 0.328 Angle : 1.045 9.702 35720 Z= 0.560 Chirality : 0.060 0.208 4092 Planarity : 0.010 0.117 4616 Dihedral : 15.694 151.030 9304 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.32 (0.14), residues: 2912 helix: -2.74 (0.11), residues: 1168 sheet: -0.37 (0.21), residues: 488 loop : -0.53 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.005 ARG H 312 TYR 0.069 0.006 TYR C 169 PHE 0.027 0.003 PHE D 90 TRP 0.056 0.005 TRP H 79 HIS 0.013 0.003 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.33 (26248) covalent geometry : angle 1.04474 / 0.56 (35720) hydrogen bonds : bond 0.19848 / 13.45 ( 1551) hydrogen bonds : angle 7.38643 / 5.20 ( 4200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7705 (ttm110) REVERT: A 115 ASN cc_start: 0.8870 (t0) cc_final: 0.8365 (t0) REVERT: A 119 MET cc_start: 0.8511 (ttm) cc_final: 0.8185 (ttm) REVERT: A 167 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7490 (tm-30) REVERT: A 238 LYS cc_start: 0.8386 (mttm) cc_final: 0.8111 (mmtt) REVERT: A 242 LEU cc_start: 0.8799 (mt) cc_final: 0.8347 (mm) REVERT: A 356 TRP cc_start: 0.8104 (m-90) cc_final: 0.7804 (m-90) REVERT: A 357 ILE cc_start: 0.9084 (mp) cc_final: 0.8484 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0525 time to fit residues: 5.3496 Evaluate side-chains 43 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.109 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0138 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 88 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.056793 restraints weight = 10524.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.058576 restraints weight = 6311.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.059893 restraints weight = 4196.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060825 restraints weight = 2997.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.061428 restraints weight = 2268.225| |-----------------------------------------------------------------------------| r_work (final): 0.2844 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.053811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.049742 restraints weight = 17555.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.050099 restraints weight = 14237.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.050377 restraints weight = 11917.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.050541 restraints weight = 10240.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.050747 restraints weight = 9153.570| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.367 26248 Z= 0.607 Angle : 1.291 25.928 35720 Z= 0.619 Chirality : 0.056 0.567 4092 Planarity : 0.006 0.050 4616 Dihedral : 12.891 156.749 3808 Min Nonbonded Distance : 1.363 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.49 % 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: -0.89 (0.16), residues: 2912 helix: -1.12 (0.13), residues: 1224 sheet: -0.23 (0.23), residues: 456 loop : 0.13 (0.20), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 183 TYR 0.030 0.002 TYR B 169 PHE 0.010 0.001 PHE B 124 TRP 0.017 0.002 TRP D 79 HIS 0.007 0.002 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01190 / 0.61 (26248) covalent geometry : angle 1.29080 / 0.62 (35720) hydrogen bonds : bond 0.17147 / 11.24 ( 1551) hydrogen bonds : angle 6.91309 / 4.88 ( 4200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7582 (ttm110) REVERT: A 82 MET cc_start: 0.9129 (tpp) cc_final: 0.8573 (mmm) REVERT: A 157 ASP cc_start: 0.7975 (t0) cc_final: 0.7354 (t0) REVERT: A 179 ASP cc_start: 0.7396 (p0) cc_final: 0.7066 (p0) REVERT: A 246 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7924 (mm-40) REVERT: A 293 LEU cc_start: 0.9497 (mt) cc_final: 0.9187 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0656 time to fit residues: 4.3455 Evaluate side-chains 38 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.111 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0145 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 111 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 98 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 chunk 262 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 309 optimal weight: 20.0000 chunk 99 optimal weight: 0.0060 chunk 281 optimal weight: 0.1980 chunk 295 optimal weight: 20.0000 overall best weight: 0.0910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.059210 restraints weight = 10040.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061042 restraints weight = 5944.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.062378 restraints weight = 3931.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.063240 restraints weight = 2795.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.063997 restraints weight = 2144.429| |-----------------------------------------------------------------------------| r_work (final): 0.2910 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.059439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.054894 restraints weight = 15197.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.055090 restraints weight = 13768.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.055286 restraints weight = 12790.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.055502 restraints weight = 11876.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.055655 restraints weight = 11054.820| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.353 26248 Z= 0.399 Angle : 0.919 15.653 35720 Z= 0.442 Chirality : 0.046 0.291 4092 Planarity : 0.005 0.038 4616 Dihedral : 11.573 145.861 3808 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.12 % 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: 0.13 (0.16), residues: 2912 helix: -0.05 (0.15), residues: 1224 sheet: 0.17 (0.23), residues: 496 loop : 0.48 (0.21), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 39 TYR 0.013 0.001 TYR F 169 PHE 0.006 0.001 PHE G 124 TRP 0.016 0.002 TRP G 356 HIS 0.005 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.40 (26248) covalent geometry : angle 0.91912 / 0.44 (35720) hydrogen bonds : bond 0.12836 / 8.91 ( 1551) hydrogen bonds : angle 5.61973 / 4.00 ( 4200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.080 Fit side-chains REVERT: A 28 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7104 (ttm110) REVERT: A 82 MET cc_start: 0.9079 (tpp) cc_final: 0.8517 (mmm) REVERT: A 111 ASN cc_start: 0.8787 (t0) cc_final: 0.8532 (t0) REVERT: A 155 SER cc_start: 0.8596 (m) cc_final: 0.8320 (p) REVERT: A 157 ASP cc_start: 0.7835 (t0) cc_final: 0.7128 (t0) REVERT: A 179 ASP cc_start: 0.7406 (p0) cc_final: 0.7031 (p0) REVERT: A 180 LEU cc_start: 0.8720 (tp) cc_final: 0.8427 (tt) REVERT: A 246 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7884 (mp10) REVERT: A 293 LEU cc_start: 0.9434 (mt) cc_final: 0.9093 (mt) REVERT: A 314 GLN cc_start: 0.8511 (tt0) cc_final: 0.7932 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0480 time to fit residues: 3.2051 Evaluate side-chains 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.108 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0139 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 224 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 281 optimal weight: 0.3980 chunk 327 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.067167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057860 restraints weight = 10269.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.059660 restraints weight = 6179.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.060975 restraints weight = 4133.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.061905 restraints weight = 2965.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.062509 restraints weight = 2252.815| |-----------------------------------------------------------------------------| r_work (final): 0.2864 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.063264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.057335 restraints weight = 12331.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.057683 restraints weight = 10804.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.057913 restraints weight = 9601.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.058155 restraints weight = 8736.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.058322 restraints weight = 8071.824| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 26248 Z= 0.325 Angle : 1.020 22.894 35720 Z= 0.501 Chirality : 0.049 0.419 4092 Planarity : 0.005 0.037 4616 Dihedral : 11.094 130.881 3808 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.25 % 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: 0.17 (0.16), residues: 2912 helix: 0.18 (0.15), residues: 1272 sheet: 0.07 (0.23), residues: 496 loop : 0.33 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 39 TYR 0.025 0.002 TYR B 169 PHE 0.020 0.002 PHE B 352 TRP 0.038 0.003 TRP F 356 HIS 0.005 0.002 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.33 (26248) covalent geometry : angle 1.01976 / 0.50 (35720) hydrogen bonds : bond 0.09467 / 6.67 ( 1551) hydrogen bonds : angle 5.35734 / 3.81 ( 4200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9169 (tpp) cc_final: 0.8357 (tmm) REVERT: A 111 ASN cc_start: 0.8957 (t0) cc_final: 0.8628 (t0) REVERT: A 154 ASP cc_start: 0.8738 (t0) cc_final: 0.8482 (t0) REVERT: A 155 SER cc_start: 0.8789 (m) cc_final: 0.8416 (p) REVERT: A 157 ASP cc_start: 0.7931 (t0) cc_final: 0.7364 (t0) REVERT: A 179 ASP cc_start: 0.7453 (p0) cc_final: 0.7123 (p0) REVERT: A 283 MET cc_start: 0.8991 (tpp) cc_final: 0.8646 (tpp) REVERT: A 293 LEU cc_start: 0.9439 (mt) cc_final: 0.9120 (mt) REVERT: A 314 GLN cc_start: 0.8579 (tt0) cc_final: 0.8086 (tm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0538 time to fit residues: 3.7911 Evaluate side-chains 40 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.113 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0140 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 324 optimal weight: 30.0000 chunk 254 optimal weight: 8.9990 chunk 129 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.056564 restraints weight = 10568.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.058338 restraints weight = 6177.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.059632 restraints weight = 4081.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.060490 restraints weight = 2917.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.061188 restraints weight = 2254.734| |-----------------------------------------------------------------------------| r_work (final): 0.2835 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.066890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.060992 restraints weight = 10365.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.061083 restraints weight = 9873.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.061149 restraints weight = 9515.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.061149 restraints weight = 9278.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.061148 restraints weight = 9278.131| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26248 Z= 0.240 Angle : 0.801 13.364 35720 Z= 0.383 Chirality : 0.046 0.454 4092 Planarity : 0.004 0.040 4616 Dihedral : 10.482 122.650 3808 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 0.31 (0.16), residues: 2912 helix: 0.38 (0.15), residues: 1272 sheet: 0.24 (0.23), residues: 536 loop : 0.22 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 116 TYR 0.024 0.002 TYR C 169 PHE 0.011 0.001 PHE G 262 TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS F 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (26248) covalent geometry : angle 0.80134 / 0.38 (35720) hydrogen bonds : bond 0.07576 / 5.20 ( 1551) hydrogen bonds : angle 5.02526 / 3.53 ( 4200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9204 (tpp) cc_final: 0.8369 (tmm) REVERT: A 111 ASN cc_start: 0.8869 (t0) cc_final: 0.8542 (t0) REVERT: A 137 GLN cc_start: 0.8354 (mt0) cc_final: 0.7977 (mp10) REVERT: A 153 MET cc_start: 0.9256 (ttt) cc_final: 0.9004 (ttt) REVERT: A 154 ASP cc_start: 0.8743 (t0) cc_final: 0.8383 (t0) REVERT: A 155 SER cc_start: 0.8895 (m) cc_final: 0.8269 (t) REVERT: A 157 ASP cc_start: 0.7884 (t0) cc_final: 0.7340 (t0) REVERT: A 179 ASP cc_start: 0.7362 (p0) cc_final: 0.7091 (p0) REVERT: A 190 MET cc_start: 0.8498 (ttm) cc_final: 0.8226 (ttm) REVERT: A 293 LEU cc_start: 0.9431 (mt) cc_final: 0.9126 (mt) REVERT: A 314 GLN cc_start: 0.8523 (tt0) cc_final: 0.8073 (tm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0338 time to fit residues: 2.3140 Evaluate side-chains 40 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.111 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0139 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 104 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 199 optimal weight: 0.0000 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 24 optimal weight: 0.0870 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.067083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057955 restraints weight = 10159.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.059780 restraints weight = 5971.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060982 restraints weight = 3919.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061938 restraints weight = 2825.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.062662 restraints weight = 2173.830| |-----------------------------------------------------------------------------| r_work (final): 0.2865 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.068148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.062141 restraints weight = 10168.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.062225 restraints weight = 9536.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.062225 restraints weight = 9119.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.062225 restraints weight = 9119.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.062225 restraints weight = 9119.450| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.9055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26248 Z= 0.189 Angle : 0.717 8.257 35720 Z= 0.343 Chirality : 0.044 0.251 4092 Planarity : 0.004 0.043 4616 Dihedral : 9.730 123.557 3808 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 0.36 (0.16), residues: 2912 helix: 0.49 (0.15), residues: 1272 sheet: 0.21 (0.22), residues: 536 loop : 0.19 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.019 0.002 TYR C 169 PHE 0.010 0.001 PHE H 124 TRP 0.048 0.003 TRP B 356 HIS 0.003 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (26248) covalent geometry : angle 0.71682 / 0.34 (35720) hydrogen bonds : bond 0.06743 / 4.67 ( 1551) hydrogen bonds : angle 4.77973 / 3.36 ( 4200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9187 (tpp) cc_final: 0.8470 (tmm) REVERT: A 111 ASN cc_start: 0.8891 (t0) cc_final: 0.8621 (t0) REVERT: A 132 MET cc_start: 0.8537 (ppp) cc_final: 0.8244 (ppp) REVERT: A 151 ILE cc_start: 0.8999 (tt) cc_final: 0.8683 (mp) REVERT: A 155 SER cc_start: 0.8867 (m) cc_final: 0.8550 (p) REVERT: A 157 ASP cc_start: 0.7666 (t0) cc_final: 0.7111 (t0) REVERT: A 179 ASP cc_start: 0.7229 (p0) cc_final: 0.7026 (p0) REVERT: A 190 MET cc_start: 0.8416 (ttm) cc_final: 0.8156 (ttm) REVERT: A 283 MET cc_start: 0.9000 (tpp) cc_final: 0.8766 (tpp) REVERT: A 314 GLN cc_start: 0.8472 (tt0) cc_final: 0.8195 (tm-30) REVERT: A 356 TRP cc_start: 0.7592 (m-90) cc_final: 0.6505 (m-90) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0438 time to fit residues: 3.2043 Evaluate side-chains 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.113 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0148 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 331 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 209 optimal weight: 0.0270 chunk 132 optimal weight: 0.8980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.070971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.060738 restraints weight = 10217.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.062617 restraints weight = 6157.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.063954 restraints weight = 4152.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064939 restraints weight = 3038.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.065513 restraints weight = 2368.444| |-----------------------------------------------------------------------------| r_work (final): 0.2942 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.070090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.064046 restraints weight = 10066.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.064186 restraints weight = 9535.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.064287 restraints weight = 9029.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.064410 restraints weight = 8662.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.064410 restraints weight = 8216.461| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.9444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26248 Z= 0.163 Angle : 0.651 6.504 35720 Z= 0.311 Chirality : 0.042 0.132 4092 Planarity : 0.004 0.045 4616 Dihedral : 8.147 100.297 3808 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.46 (0.16), residues: 2912 helix: 0.53 (0.15), residues: 1272 sheet: 0.46 (0.22), residues: 536 loop : 0.19 (0.21), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 196 TYR 0.030 0.002 TYR H 169 PHE 0.008 0.001 PHE B 21 TRP 0.032 0.002 TRP B 356 HIS 0.004 0.001 HIS H 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (26248) covalent geometry : angle 0.65077 / 0.31 (35720) hydrogen bonds : bond 0.06228 / 4.31 ( 1551) hydrogen bonds : angle 4.47339 / 3.15 ( 4200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7669 (ppp) cc_final: 0.7404 (ppp) REVERT: A 82 MET cc_start: 0.9055 (tpp) cc_final: 0.8494 (mmm) REVERT: A 111 ASN cc_start: 0.8844 (t0) cc_final: 0.8622 (t0) REVERT: A 132 MET cc_start: 0.8603 (ppp) cc_final: 0.8120 (ppp) REVERT: A 151 ILE cc_start: 0.9037 (tt) cc_final: 0.8697 (mp) REVERT: A 155 SER cc_start: 0.9091 (m) cc_final: 0.8603 (p) REVERT: A 157 ASP cc_start: 0.7442 (t0) cc_final: 0.6839 (t0) REVERT: A 179 ASP cc_start: 0.7221 (p0) cc_final: 0.6985 (p0) REVERT: A 180 LEU cc_start: 0.8699 (tp) cc_final: 0.8391 (tt) REVERT: A 190 MET cc_start: 0.8434 (ttm) cc_final: 0.8183 (ttp) REVERT: A 283 MET cc_start: 0.8895 (tpp) cc_final: 0.8551 (tpp) REVERT: A 314 GLN cc_start: 0.8461 (tt0) cc_final: 0.8097 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0407 time to fit residues: 3.3180 Evaluate side-chains 42 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.107 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0135 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 217 optimal weight: 5.9990 chunk 281 optimal weight: 0.0070 chunk 102 optimal weight: 0.5980 chunk 61 optimal weight: 0.0070 chunk 23 optimal weight: 0.0980 chunk 187 optimal weight: 6.9990 chunk 277 optimal weight: 0.0970 chunk 3 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.071540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.061335 restraints weight = 10268.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.063267 restraints weight = 6149.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.064418 restraints weight = 4129.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065563 restraints weight = 3087.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066341 restraints weight = 2382.226| |-----------------------------------------------------------------------------| r_work (final): 0.2957 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.070524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.064103 restraints weight = 9876.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.064213 restraints weight = 9449.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.064213 restraints weight = 9010.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.064213 restraints weight = 9010.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.064213 restraints weight = 9010.517| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.9700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26248 Z= 0.161 Angle : 0.637 5.764 35720 Z= 0.305 Chirality : 0.041 0.123 4092 Planarity : 0.004 0.046 4616 Dihedral : 7.728 103.646 3808 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.46 (0.16), residues: 2912 helix: 0.65 (0.15), residues: 1224 sheet: 0.44 (0.22), residues: 536 loop : 0.06 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 28 TYR 0.013 0.001 TYR E 337 PHE 0.008 0.001 PHE D 124 TRP 0.013 0.002 TRP F 356 HIS 0.003 0.001 HIS H 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (26248) covalent geometry : angle 0.63726 / 0.31 (35720) hydrogen bonds : bond 0.06028 / 4.17 ( 1551) hydrogen bonds : angle 4.48055 / 3.15 ( 4200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7700 (ppp) cc_final: 0.7343 (ppp) REVERT: A 82 MET cc_start: 0.8978 (tpp) cc_final: 0.8484 (mmm) REVERT: A 132 MET cc_start: 0.8397 (ppp) cc_final: 0.8118 (ppp) REVERT: A 151 ILE cc_start: 0.8994 (tt) cc_final: 0.8642 (mp) REVERT: A 155 SER cc_start: 0.8886 (m) cc_final: 0.8674 (p) REVERT: A 157 ASP cc_start: 0.7436 (t0) cc_final: 0.6828 (t0) REVERT: A 179 ASP cc_start: 0.7232 (p0) cc_final: 0.6985 (p0) REVERT: A 180 LEU cc_start: 0.8644 (tp) cc_final: 0.8347 (tt) REVERT: A 290 ARG cc_start: 0.8630 (mtt180) cc_final: 0.7470 (ptt90) REVERT: A 314 GLN cc_start: 0.8465 (tt0) cc_final: 0.8109 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0415 time to fit residues: 3.3083 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0147 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 291 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 335 optimal weight: 20.0000 chunk 153 optimal weight: 0.0070 chunk 299 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 305 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 overall best weight: 4.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.066569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.057366 restraints weight = 10198.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.059170 restraints weight = 6156.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.060467 restraints weight = 4127.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061431 restraints weight = 2971.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.062171 restraints weight = 2261.911| |-----------------------------------------------------------------------------| r_work (final): 0.2844 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.066738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.058330 restraints weight = 10359.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.058527 restraints weight = 9638.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.058696 restraints weight = 9031.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.058824 restraints weight = 8559.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.058962 restraints weight = 8166.302| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.9382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26248 Z= 0.233 Angle : 0.699 6.030 35720 Z= 0.349 Chirality : 0.043 0.133 4092 Planarity : 0.004 0.046 4616 Dihedral : 7.287 99.061 3808 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.34 (0.16), residues: 2912 helix: 0.49 (0.15), residues: 1272 sheet: 0.14 (0.22), residues: 536 loop : 0.20 (0.21), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 39 TYR 0.028 0.002 TYR H 169 PHE 0.009 0.001 PHE E 223 TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (26248) covalent geometry : angle 0.69910 / 0.35 (35720) hydrogen bonds : bond 0.06205 / 4.28 ( 1551) hydrogen bonds : angle 4.58455 / 3.21 ( 4200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.117 Fit side-chains REVERT: A 44 MET cc_start: 0.7797 (ppp) cc_final: 0.7398 (ppp) REVERT: A 82 MET cc_start: 0.9237 (tpp) cc_final: 0.8605 (tmm) REVERT: A 111 ASN cc_start: 0.8819 (t0) cc_final: 0.8613 (t0) REVERT: A 151 ILE cc_start: 0.8992 (tt) cc_final: 0.8719 (mp) REVERT: A 153 MET cc_start: 0.9328 (ttt) cc_final: 0.9046 (ttt) REVERT: A 157 ASP cc_start: 0.7581 (t0) cc_final: 0.7058 (t0) REVERT: A 283 MET cc_start: 0.9047 (tpp) cc_final: 0.8486 (tpp) REVERT: A 314 GLN cc_start: 0.8587 (tt0) cc_final: 0.8247 (tm-30) REVERT: A 340 TRP cc_start: 0.8129 (t60) cc_final: 0.7691 (t60) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0328 time to fit residues: 2.3275 Evaluate side-chains 39 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.086 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0131 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 274 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.069428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.059709 restraints weight = 9962.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.061593 restraints weight = 5986.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.062939 restraints weight = 3997.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.063840 restraints weight = 2907.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064626 restraints weight = 2257.043| |-----------------------------------------------------------------------------| r_work (final): 0.2911 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.071548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063266 restraints weight = 10358.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.063548 restraints weight = 9551.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.063799 restraints weight = 8792.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.063927 restraints weight = 8253.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.064115 restraints weight = 7938.359| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.9572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26248 Z= 0.154 Angle : 0.628 5.685 35720 Z= 0.306 Chirality : 0.042 0.120 4092 Planarity : 0.004 0.049 4616 Dihedral : 6.753 88.446 3808 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.39 (0.16), residues: 2912 helix: 0.58 (0.15), residues: 1272 sheet: 0.01 (0.22), residues: 536 loop : 0.26 (0.21), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.018 0.001 TYR H 169 PHE 0.007 0.001 PHE C 31 TRP 0.011 0.001 TRP F 356 HIS 0.003 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (26248) covalent geometry : angle 0.62758 / 0.31 (35720) hydrogen bonds : bond 0.05773 / 3.97 ( 1551) hydrogen bonds : angle 4.41139 / 3.09 ( 4200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7742 (ppp) cc_final: 0.7321 (ppp) REVERT: A 111 ASN cc_start: 0.8779 (t0) cc_final: 0.8552 (t0) REVERT: A 132 MET cc_start: 0.8349 (ppp) cc_final: 0.7950 (ppp) REVERT: A 157 ASP cc_start: 0.7384 (t0) cc_final: 0.6726 (t0) REVERT: A 179 ASP cc_start: 0.7156 (p0) cc_final: 0.6905 (p0) REVERT: A 180 LEU cc_start: 0.8687 (tp) cc_final: 0.8341 (tt) REVERT: A 283 MET cc_start: 0.8850 (tpp) cc_final: 0.8325 (tpp) REVERT: A 293 LEU cc_start: 0.9386 (mt) cc_final: 0.9091 (mt) REVERT: A 314 GLN cc_start: 0.8534 (tt0) cc_final: 0.8094 (tm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0347 time to fit residues: 2.5198 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.130 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0140 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 337 optimal weight: 20.0000 chunk 178 optimal weight: 0.0970 chunk 254 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.067149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.057476 restraints weight = 10376.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.059300 restraints weight = 6360.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.060669 restraints weight = 4288.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.061589 restraints weight = 3110.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.062320 restraints weight = 2410.095| |-----------------------------------------------------------------------------| r_work (final): 0.2855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.067802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.060003 restraints weight = 10949.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.060130 restraints weight = 10272.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.060271 restraints weight = 9757.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.060402 restraints weight = 9214.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.060402 restraints weight = 8871.072| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.9505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26248 Z= 0.208 Angle : 0.682 5.697 35720 Z= 0.332 Chirality : 0.043 0.122 4092 Planarity : 0.004 0.048 4616 Dihedral : 6.348 76.460 3808 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.35 (0.16), residues: 2912 helix: 0.58 (0.15), residues: 1272 sheet: -0.08 (0.22), residues: 536 loop : 0.21 (0.21), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 39 TYR 0.024 0.002 TYR H 169 PHE 0.008 0.001 PHE B 223 TRP 0.007 0.001 TRP B 86 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (26248) covalent geometry : angle 0.68238 / 0.33 (35720) hydrogen bonds : bond 0.05805 / 3.99 ( 1551) hydrogen bonds : angle 4.49140 / 3.14 ( 4200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.43 seconds wall clock time: 30 minutes 57.47 seconds (1857.47 seconds total)