Starting phenix.real_space_refine on Sun Jun 22 13:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ztd_14958/06_2025/7ztd_14958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ztd_14958/06_2025/7ztd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ztd_14958/06_2025/7ztd_14958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ztd_14958/06_2025/7ztd_14958.map" model { file = "/net/cci-nas-00/data/ceres_data/7ztd_14958/06_2025/7ztd_14958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ztd_14958/06_2025/7ztd_14958.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.22, per 1000 atoms: 0.59 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: 6.19 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.41 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: 10.13 Time building geometry restraints manager: 7.37 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: 0.03 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: 4.470 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: 0.030 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.880 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.056 0.005 TRP H 79 HIS 0.013 0.003 HIS A 88 PHE 0.027 0.003 PHE D 90 TYR 0.069 0.006 TYR C 169 ARG 0.030 0.005 ARG H 312 Details of bonding type rmsd hydrogen bonds : bond 0.19848 ( 1551) hydrogen bonds : angle 7.38643 ( 4200) covalent geometry : bond 0.00723 (26248) covalent geometry : angle 1.04474 (35720) *********************** 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 : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7704 (ttm110) REVERT: A 115 ASN cc_start: 0.8870 (t0) cc_final: 0.8363 (t0) REVERT: A 119 MET cc_start: 0.8510 (ttm) cc_final: 0.8185 (ttm) REVERT: A 167 GLU cc_start: 0.7703 (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: 0.8343 (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: 0.8483 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1698 time to fit residues: 17.0544 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 : 0.352 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 : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0424 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 : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 137 optimal weight: 0.0770 chunk 266 optimal weight: 0.5980 chunk 103 optimal weight: 0.0020 chunk 162 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 overall best weight: 0.9148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.068820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.059490 restraints weight = 10036.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061339 restraints weight = 6145.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062685 restraints weight = 4122.758| |-----------------------------------------------------------------------------| r_work (final): 0.2877 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.053940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.049820 restraints weight = 16685.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.050143 restraints weight = 13757.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.050407 restraints weight = 11723.664| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.381 26248 Z= 0.580 Angle : 1.245 24.748 35720 Z= 0.592 Chirality : 0.053 0.543 4092 Planarity : 0.005 0.052 4616 Dihedral : 12.654 152.726 3808 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2912 helix: -0.97 (0.14), residues: 1216 sheet: 0.05 (0.23), residues: 496 loop : 0.41 (0.20), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 356 HIS 0.006 0.002 HIS C 88 PHE 0.008 0.001 PHE E 262 TYR 0.028 0.002 TYR C 169 ARG 0.004 0.001 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.16832 ( 1551) hydrogen bonds : angle 6.73963 ( 4200) covalent geometry : bond 0.01134 (26248) covalent geometry : angle 1.24460 (35720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7452 (ttm110) REVERT: A 82 MET cc_start: 0.9071 (tpp) cc_final: 0.8493 (mmm) REVERT: A 157 ASP cc_start: 0.7805 (t0) cc_final: 0.7146 (t0) REVERT: A 179 ASP cc_start: 0.7362 (p0) cc_final: 0.6999 (p0) REVERT: A 180 LEU cc_start: 0.8842 (tp) cc_final: 0.8572 (tt) REVERT: A 293 LEU cc_start: 0.9474 (mt) cc_final: 0.9154 (mt) REVERT: A 314 GLN cc_start: 0.8613 (tt0) cc_final: 0.7897 (tm-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1728 time to fit residues: 12.4905 Evaluate side-chains 41 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.377 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 : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0427 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 : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 68 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 329 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 61 optimal weight: 0.0370 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.069449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.060309 restraints weight = 9686.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.062145 restraints weight = 5814.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063498 restraints weight = 3876.557| |-----------------------------------------------------------------------------| r_work (final): 0.2904 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.059670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.055027 restraints weight = 15131.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.055277 restraints weight = 13720.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.055455 restraints weight = 12571.165| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.348 26248 Z= 0.401 Angle : 0.914 15.615 35720 Z= 0.438 Chirality : 0.046 0.279 4092 Planarity : 0.005 0.039 4616 Dihedral : 11.415 144.153 3808 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2912 helix: -0.24 (0.15), residues: 1224 sheet: 0.09 (0.22), residues: 496 loop : 0.51 (0.20), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 356 HIS 0.005 0.001 HIS D 40 PHE 0.004 0.001 PHE D 127 TYR 0.013 0.001 TYR G 169 ARG 0.002 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.12716 ( 1551) hydrogen bonds : angle 5.58388 ( 4200) covalent geometry : bond 0.00793 (26248) covalent geometry : angle 0.91434 (35720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.335 Fit side-chains REVERT: A 28 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7308 (ttm110) REVERT: A 82 MET cc_start: 0.9058 (tpp) cc_final: 0.8394 (mmm) REVERT: A 111 ASN cc_start: 0.8682 (t0) cc_final: 0.8417 (t0) REVERT: A 155 SER cc_start: 0.8475 (m) cc_final: 0.8237 (p) REVERT: A 157 ASP cc_start: 0.7635 (t0) cc_final: 0.7041 (t70) REVERT: A 169 TYR cc_start: 0.7816 (m-80) cc_final: 0.7484 (m-10) REVERT: A 179 ASP cc_start: 0.7432 (p0) cc_final: 0.7044 (p0) REVERT: A 180 LEU cc_start: 0.8794 (tp) cc_final: 0.8465 (tt) REVERT: A 293 LEU cc_start: 0.9437 (mt) cc_final: 0.9106 (mt) REVERT: A 314 GLN cc_start: 0.8593 (tt0) cc_final: 0.8013 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1360 time to fit residues: 10.1380 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 : 0.306 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 : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0379 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 : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 68 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 87 optimal weight: 0.0060 chunk 102 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 272 optimal weight: 0.4980 chunk 203 optimal weight: 3.9990 chunk 328 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 overall best weight: 2.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.058219 restraints weight = 10412.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.060118 restraints weight = 6260.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061483 restraints weight = 4166.698| |-----------------------------------------------------------------------------| r_work (final): 0.2840 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.063258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.057435 restraints weight = 11834.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.057804 restraints weight = 10172.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.058052 restraints weight = 8967.811| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.8753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 26248 Z= 0.304 Angle : 0.992 21.433 35720 Z= 0.488 Chirality : 0.048 0.443 4092 Planarity : 0.004 0.035 4616 Dihedral : 10.835 127.736 3808 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2912 helix: 0.03 (0.15), residues: 1272 sheet: -0.15 (0.22), residues: 496 loop : 0.26 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP H 356 HIS 0.006 0.002 HIS F 40 PHE 0.014 0.001 PHE H 124 TYR 0.017 0.002 TYR B 169 ARG 0.008 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.09213 ( 1551) hydrogen bonds : angle 5.30631 ( 4200) covalent geometry : bond 0.00616 (26248) covalent geometry : angle 0.99172 (35720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7173 (ttm110) REVERT: A 111 ASN cc_start: 0.8892 (t0) cc_final: 0.8549 (t0) REVERT: A 151 ILE cc_start: 0.9127 (tt) cc_final: 0.8753 (mp) REVERT: A 154 ASP cc_start: 0.8755 (t0) cc_final: 0.8505 (t0) REVERT: A 155 SER cc_start: 0.8751 (m) cc_final: 0.8408 (p) REVERT: A 157 ASP cc_start: 0.8033 (t0) cc_final: 0.7394 (t0) REVERT: A 179 ASP cc_start: 0.7395 (p0) cc_final: 0.7079 (p0) REVERT: A 314 GLN cc_start: 0.8552 (tt0) cc_final: 0.8072 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1399 time to fit residues: 9.6925 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 : 0.304 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 : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0366 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 : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 223 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 323 optimal weight: 0.0040 chunk 168 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 overall best weight: 2.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.059578 restraints weight = 10319.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.061456 restraints weight = 6059.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.062671 restraints weight = 3961.410| |-----------------------------------------------------------------------------| r_work (final): 0.2866 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.067185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.061588 restraints weight = 10714.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.061736 restraints weight = 9940.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.061871 restraints weight = 9324.088| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.8927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26248 Z= 0.211 Angle : 0.770 15.243 35720 Z= 0.366 Chirality : 0.046 0.508 4092 Planarity : 0.004 0.033 4616 Dihedral : 10.114 121.476 3808 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2912 helix: 0.15 (0.15), residues: 1272 sheet: 0.25 (0.22), residues: 536 loop : 0.07 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 356 HIS 0.003 0.001 HIS F 87 PHE 0.010 0.001 PHE G 262 TYR 0.011 0.001 TYR H 53 ARG 0.003 0.000 ARG G 116 Details of bonding type rmsd hydrogen bonds : bond 0.07512 ( 1551) hydrogen bonds : angle 5.03635 ( 4200) covalent geometry : bond 0.00432 (26248) covalent geometry : angle 0.77033 (35720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.334 Fit side-chains REVERT: A 111 ASN cc_start: 0.8836 (t0) cc_final: 0.8585 (t0) REVERT: A 151 ILE cc_start: 0.9096 (tt) cc_final: 0.8706 (mp) REVERT: A 155 SER cc_start: 0.8896 (m) cc_final: 0.8608 (p) REVERT: A 157 ASP cc_start: 0.7944 (t0) cc_final: 0.7354 (t0) REVERT: A 179 ASP cc_start: 0.7397 (p0) cc_final: 0.7094 (p0) REVERT: A 283 MET cc_start: 0.8925 (tpp) cc_final: 0.8580 (tpp) REVERT: A 314 GLN cc_start: 0.8488 (tt0) cc_final: 0.8003 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1359 time to fit residues: 9.1732 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 : 0.337 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 : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0426 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 : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 290 optimal weight: 9.9990 chunk 320 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 168 optimal weight: 0.0270 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.056624 restraints weight = 10392.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.058469 restraints weight = 6206.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059750 restraints weight = 4132.802| |-----------------------------------------------------------------------------| r_work (final): 0.2798 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.068518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.062655 restraints weight = 10195.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.062789 restraints weight = 9550.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062940 restraints weight = 9028.853| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.8904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26248 Z= 0.225 Angle : 0.742 8.140 35720 Z= 0.359 Chirality : 0.044 0.268 4092 Planarity : 0.004 0.041 4616 Dihedral : 9.389 119.334 3808 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2912 helix: 0.30 (0.15), residues: 1272 sheet: -0.01 (0.21), residues: 536 loop : -0.01 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 356 HIS 0.004 0.001 HIS C 371 PHE 0.008 0.001 PHE D 255 TYR 0.011 0.001 TYR D 53 ARG 0.001 0.000 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.06816 ( 1551) hydrogen bonds : angle 4.89380 ( 4200) covalent geometry : bond 0.00471 (26248) covalent geometry : angle 0.74225 (35720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.354 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8768 (tp40) cc_final: 0.8531 (tp-100) REVERT: A 111 ASN cc_start: 0.8992 (t0) cc_final: 0.8762 (t0) REVERT: A 151 ILE cc_start: 0.9177 (tt) cc_final: 0.8859 (mp) REVERT: A 153 MET cc_start: 0.9286 (ttt) cc_final: 0.9060 (ttt) REVERT: A 155 SER cc_start: 0.8852 (m) cc_final: 0.8369 (t) REVERT: A 157 ASP cc_start: 0.7968 (t0) cc_final: 0.7387 (t0) REVERT: A 179 ASP cc_start: 0.7233 (p0) cc_final: 0.7014 (p0) REVERT: A 314 GLN cc_start: 0.8496 (tt0) cc_final: 0.8210 (tm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1075 time to fit residues: 7.2773 Evaluate side-chains 41 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.349 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 : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0378 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 : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 326 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 133 optimal weight: 0.0050 chunk 291 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 113 optimal weight: 0.0050 overall best weight: 4.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.057275 restraints weight = 10328.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.058862 restraints weight = 6298.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.060063 restraints weight = 4309.581| |-----------------------------------------------------------------------------| r_work (final): 0.2818 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.068864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.062789 restraints weight = 9563.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.062921 restraints weight = 9060.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.062997 restraints weight = 8658.858| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.9062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26248 Z= 0.217 Angle : 0.719 8.866 35720 Z= 0.342 Chirality : 0.043 0.145 4092 Planarity : 0.004 0.046 4616 Dihedral : 8.281 105.174 3808 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2912 helix: 0.41 (0.15), residues: 1272 sheet: 0.08 (0.22), residues: 536 loop : -0.31 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 356 HIS 0.004 0.002 HIS H 40 PHE 0.006 0.001 PHE H 262 TYR 0.011 0.001 TYR D 53 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.06418 ( 1551) hydrogen bonds : angle 4.70264 ( 4200) covalent geometry : bond 0.00456 (26248) covalent geometry : angle 0.71877 (35720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7846 (ppp) cc_final: 0.7535 (ppp) REVERT: A 59 GLN cc_start: 0.8791 (tp40) cc_final: 0.8476 (tp-100) REVERT: A 151 ILE cc_start: 0.9168 (tt) cc_final: 0.8873 (mp) REVERT: A 155 SER cc_start: 0.8841 (m) cc_final: 0.8501 (p) REVERT: A 157 ASP cc_start: 0.7886 (t0) cc_final: 0.7417 (t0) REVERT: A 283 MET cc_start: 0.9070 (tpp) cc_final: 0.8562 (tpp) REVERT: A 314 GLN cc_start: 0.8556 (tt0) cc_final: 0.8248 (tm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1225 time to fit residues: 9.3295 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 : 0.301 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 : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0396 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 : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 208 optimal weight: 7.9990 chunk 118 optimal weight: 0.0270 chunk 309 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 256 optimal weight: 0.0870 chunk 188 optimal weight: 10.0000 overall best weight: 2.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.066811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.057314 restraints weight = 10720.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.059108 restraints weight = 6565.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.060441 restraints weight = 4448.016| |-----------------------------------------------------------------------------| r_work (final): 0.2821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.069638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.063122 restraints weight = 9939.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.063306 restraints weight = 9264.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.063465 restraints weight = 8708.803| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.9323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26248 Z= 0.186 Angle : 0.673 9.109 35720 Z= 0.321 Chirality : 0.042 0.123 4092 Planarity : 0.004 0.046 4616 Dihedral : 7.451 95.555 3808 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2912 helix: 0.54 (0.15), residues: 1272 sheet: 0.04 (0.21), residues: 536 loop : -0.22 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 79 HIS 0.005 0.001 HIS D 161 PHE 0.005 0.001 PHE C 262 TYR 0.008 0.001 TYR C 53 ARG 0.003 0.000 ARG F 196 Details of bonding type rmsd hydrogen bonds : bond 0.06079 ( 1551) hydrogen bonds : angle 4.59754 ( 4200) covalent geometry : bond 0.00393 (26248) covalent geometry : angle 0.67335 (35720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.432 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7845 (ppp) cc_final: 0.7389 (ppp) REVERT: A 59 GLN cc_start: 0.8720 (tp40) cc_final: 0.8466 (tp-100) REVERT: A 111 ASN cc_start: 0.8773 (t0) cc_final: 0.8563 (t0) REVERT: A 151 ILE cc_start: 0.9168 (tt) cc_final: 0.8880 (mp) REVERT: A 155 SER cc_start: 0.8840 (m) cc_final: 0.8553 (p) REVERT: A 157 ASP cc_start: 0.7850 (t0) cc_final: 0.7311 (t0) REVERT: A 283 MET cc_start: 0.9046 (tpp) cc_final: 0.8565 (tpp) REVERT: A 314 GLN cc_start: 0.8672 (tt0) cc_final: 0.8268 (tm-30) REVERT: A 325 MET cc_start: 0.8647 (mmm) cc_final: 0.8435 (mmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1482 time to fit residues: 10.4664 Evaluate side-chains 41 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.324 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 : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0423 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 : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.0870 chunk 267 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 323 optimal weight: 0.0370 chunk 248 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.067214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057719 restraints weight = 10301.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059476 restraints weight = 6257.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.060747 restraints weight = 4269.436| |-----------------------------------------------------------------------------| r_work (final): 0.2824 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.067129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.059354 restraints weight = 11282.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.059533 restraints weight = 10467.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.059666 restraints weight = 9903.144| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.9421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26248 Z= 0.168 Angle : 0.629 6.578 35720 Z= 0.301 Chirality : 0.042 0.117 4092 Planarity : 0.004 0.044 4616 Dihedral : 6.555 79.463 3808 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2912 helix: 0.60 (0.15), residues: 1272 sheet: 0.13 (0.21), residues: 536 loop : -0.24 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 79 HIS 0.005 0.001 HIS E 161 PHE 0.007 0.001 PHE C 200 TYR 0.009 0.001 TYR D 218 ARG 0.002 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.05774 ( 1551) hydrogen bonds : angle 4.52942 ( 4200) covalent geometry : bond 0.00350 (26248) covalent geometry : angle 0.62940 (35720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.305 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7958 (ppp) cc_final: 0.7389 (ppp) REVERT: A 111 ASN cc_start: 0.8777 (t0) cc_final: 0.8505 (t0) REVERT: A 151 ILE cc_start: 0.9135 (tt) cc_final: 0.8849 (mp) REVERT: A 155 SER cc_start: 0.8779 (m) cc_final: 0.8430 (p) REVERT: A 157 ASP cc_start: 0.7817 (t0) cc_final: 0.7260 (t0) REVERT: A 179 ASP cc_start: 0.7295 (p0) cc_final: 0.7079 (p0) REVERT: A 283 MET cc_start: 0.9018 (tpp) cc_final: 0.8474 (tpp) REVERT: A 314 GLN cc_start: 0.8621 (tt0) cc_final: 0.8263 (tm-30) REVERT: A 325 MET cc_start: 0.8686 (mmm) cc_final: 0.8472 (mmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1297 time to fit residues: 9.3746 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 : 0.401 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 : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0946 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 : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 135 optimal weight: 0.0570 chunk 259 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 294 optimal weight: 0.0370 chunk 246 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.058526 restraints weight = 10251.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.060340 restraints weight = 6199.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.061671 restraints weight = 4201.124| |-----------------------------------------------------------------------------| r_work (final): 0.2849 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.071195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.062739 restraints weight = 9445.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.062999 restraints weight = 8798.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.063186 restraints weight = 8272.255| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.9550 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= 0.152 Angle : 0.629 6.774 35720 Z= 0.295 Chirality : 0.042 0.117 4092 Planarity : 0.004 0.047 4616 Dihedral : 5.996 63.319 3808 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2912 helix: 0.61 (0.15), residues: 1224 sheet: 0.08 (0.21), residues: 536 loop : -0.19 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 86 HIS 0.006 0.001 HIS E 161 PHE 0.005 0.001 PHE A 262 TYR 0.009 0.001 TYR G 218 ARG 0.002 0.000 ARG H 196 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 1551) hydrogen bonds : angle 4.43396 ( 4200) covalent geometry : bond 0.00315 (26248) covalent geometry : angle 0.62866 (35720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 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 : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7964 (ppp) cc_final: 0.7323 (ppp) REVERT: A 111 ASN cc_start: 0.8802 (t0) cc_final: 0.8549 (t0) REVERT: A 151 ILE cc_start: 0.9125 (tt) cc_final: 0.8814 (mp) REVERT: A 155 SER cc_start: 0.8804 (m) cc_final: 0.8519 (p) REVERT: A 157 ASP cc_start: 0.7772 (t0) cc_final: 0.7223 (t0) REVERT: A 179 ASP cc_start: 0.7240 (p0) cc_final: 0.7022 (p0) REVERT: A 283 MET cc_start: 0.8960 (tpp) cc_final: 0.8438 (tpp) REVERT: A 314 GLN cc_start: 0.8610 (tt0) cc_final: 0.8106 (tm-30) REVERT: A 325 MET cc_start: 0.8667 (mmm) cc_final: 0.8450 (mmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0905 time to fit residues: 7.3582 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 : 0.323 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 : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0372 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 : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 22 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 294 optimal weight: 0.0010 chunk 319 optimal weight: 0.0670 chunk 176 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 0.0060 chunk 123 optimal weight: 0.1980 overall best weight: 0.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060428 restraints weight = 10185.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.062299 restraints weight = 6204.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.063666 restraints weight = 4197.052| |-----------------------------------------------------------------------------| r_work (final): 0.2898 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.068828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.060462 restraints weight = 9513.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.060566 restraints weight = 9124.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.060686 restraints weight = 8750.092| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.9729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26248 Z= 0.147 Angle : 0.632 7.010 35720 Z= 0.296 Chirality : 0.041 0.121 4092 Planarity : 0.004 0.047 4616 Dihedral : 5.630 55.764 3808 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2912 helix: 0.60 (0.15), residues: 1224 sheet: 0.14 (0.22), residues: 536 loop : -0.11 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 356 HIS 0.006 0.001 HIS E 161 PHE 0.010 0.001 PHE C 31 TYR 0.012 0.001 TYR C 169 ARG 0.003 0.000 ARG H 177 Details of bonding type rmsd hydrogen bonds : bond 0.05374 ( 1551) hydrogen bonds : angle 4.35915 ( 4200) covalent geometry : bond 0.00297 (26248) covalent geometry : angle 0.63223 (35720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.61 seconds wall clock time: 76 minutes 14.39 seconds (4574.39 seconds total)