Starting phenix.real_space_refine on Fri Sep 19 12:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ztd_14958/09_2025/7ztd_14958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ztd_14958/09_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_14958/09_2025/7ztd_14958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ztd_14958/09_2025/7ztd_14958.map" model { file = "/net/cci-nas-00/data/ceres_data/7ztd_14958/09_2025/7ztd_14958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ztd_14958/09_2025/7ztd_14958.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 16148 2.51 5 N 4428 2.21 5 O 4980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 20 Chain: "E" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "A" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "B" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "C" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "D" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "F" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "G" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "H" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2853 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain: "P" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "R" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "S" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.26 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: 2.78 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.21 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: 6.11 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8424 1.33 - 1.45: 3595 1.45 - 1.57: 13909 1.57 - 1.69: 24 1.69 - 1.81: 296 Bond restraints: 26248 Sorted by residual: bond pdb=" CB ASN H 78 " pdb=" CG ASN H 78 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CB TRP A 79 " pdb=" CG TRP A 79 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.65e+00 bond pdb=" CG1 ILE A 64 " pdb=" CD1 ILE A 64 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.64e+00 bond pdb=" CG GLU D 270 " pdb=" CD GLU D 270 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CD1 TYR F 169 " pdb=" CE1 TYR F 169 " ideal model delta sigma weight residual 1.382 1.336 0.046 3.00e-02 1.11e+03 2.34e+00 ... (remaining 26243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 33242 1.94 - 3.88: 2142 3.88 - 5.82: 272 5.82 - 7.76: 47 7.76 - 9.70: 17 Bond angle restraints: 35720 Sorted by residual: angle pdb=" CA TYR C 169 " pdb=" CB TYR C 169 " pdb=" CG TYR C 169 " ideal model delta sigma weight residual 113.90 106.63 7.27 1.80e+00 3.09e-01 1.63e+01 angle pdb=" N ALA C 181 " pdb=" CA ALA C 181 " pdb=" C ALA C 181 " ideal model delta sigma weight residual 110.35 115.24 -4.89 1.38e+00 5.25e-01 1.26e+01 angle pdb=" N MET B 16 " pdb=" CA MET B 16 " pdb=" C MET B 16 " ideal model delta sigma weight residual 108.32 114.00 -5.68 1.64e+00 3.72e-01 1.20e+01 angle pdb=" N PHE A 255 " pdb=" CA PHE A 255 " pdb=" C PHE A 255 " ideal model delta sigma weight residual 113.88 118.09 -4.21 1.23e+00 6.61e-01 1.17e+01 angle pdb=" N ALA B 181 " pdb=" CA ALA B 181 " pdb=" C ALA B 181 " ideal model delta sigma weight residual 110.35 114.95 -4.60 1.38e+00 5.25e-01 1.11e+01 ... (remaining 35715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 15348 30.21 - 60.41: 340 60.41 - 90.62: 72 90.62 - 120.82: 16 120.82 - 151.03: 16 Dihedral angle restraints: 15792 sinusoidal: 5728 harmonic: 10064 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.03 -151.03 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.06 -149.06 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP H 401 " pdb=" O5' ADP H 401 " pdb=" PA ADP H 401 " pdb=" O2A ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.97 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2244 0.042 - 0.083: 1154 0.083 - 0.125: 509 0.125 - 0.166: 145 0.166 - 0.208: 40 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CA GLU B 270 " pdb=" N GLU B 270 " pdb=" C GLU B 270 " pdb=" CB GLU B 270 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PHE B 255 " pdb=" N PHE B 255 " pdb=" C PHE B 255 " pdb=" CB PHE B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA GLU G 270 " pdb=" N GLU G 270 " pdb=" C GLU G 270 " pdb=" CB GLU G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4089 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.030 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR C 169 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 169 " 0.027 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR F 169 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR F 169 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 169 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 169 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR F 169 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR F 169 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 169 " 0.028 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR B 169 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 169 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 169 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 169 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 169 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 169 " -0.010 2.00e-02 2.50e+03 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 381 2.66 - 3.22: 26644 3.22 - 3.78: 38554 3.78 - 4.34: 50723 4.34 - 4.90: 80837 Nonbonded interactions: 197139 Sorted by model distance: nonbonded pdb=" OG1 THR H 160 " pdb=" O LEU H 178 " model vdw 2.097 3.040 nonbonded pdb=" O GLY A 48 " pdb=" OH TYR A 53 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR E 160 " pdb=" O LEU E 178 " model vdw 2.127 3.040 nonbonded pdb=" OE1 GLN F 49 " pdb=" OH TYR F 53 " model vdw 2.140 3.040 nonbonded pdb=" OD2 ASP E 244 " pdb=" NH1 ARG B 290 " model vdw 2.160 3.120 ... (remaining 197134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.230 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.14), residues: 2912 helix: -2.74 (0.11), residues: 1168 sheet: -0.37 (0.21), residues: 488 loop : -0.53 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.005 ARG H 312 TYR 0.069 0.006 TYR C 169 PHE 0.027 0.003 PHE D 90 TRP 0.056 0.005 TRP H 79 HIS 0.013 0.003 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00723 (26248) covalent geometry : angle 1.04474 (35720) hydrogen bonds : bond 0.19848 ( 1551) hydrogen bonds : angle 7.38643 ( 4200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7705 (ttm110) REVERT: A 115 ASN cc_start: 0.8870 (t0) cc_final: 0.8365 (t0) REVERT: A 119 MET cc_start: 0.8510 (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: 0.8347 (mm) REVERT: A 356 TRP cc_start: 0.8104 (m-90) cc_final: 0.7804 (m-90) REVERT: A 357 ILE cc_start: 0.9084 (mp) cc_final: 0.8484 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0669 time to fit residues: 6.7286 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 : 0.112 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0138 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2949 r_free = 0.2949 target = 0.065937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.056793 restraints weight = 10524.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.058576 restraints weight = 6311.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.059893 restraints weight = 4196.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060825 restraints weight = 2997.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.061428 restraints weight = 2268.225| |-----------------------------------------------------------------------------| r_work (final): 0.2844 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.053811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.049742 restraints weight = 17555.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.050099 restraints weight = 14237.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.050377 restraints weight = 11917.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.050541 restraints weight = 10240.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.050747 restraints weight = 9153.570| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.367 26248 Z= 0.607 Angle : 1.291 25.928 35720 Z= 0.619 Chirality : 0.056 0.567 4092 Planarity : 0.006 0.050 4616 Dihedral : 12.891 156.749 3808 Min Nonbonded Distance : 1.363 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.16), residues: 2912 helix: -1.12 (0.13), residues: 1224 sheet: -0.23 (0.23), residues: 456 loop : 0.13 (0.20), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 183 TYR 0.030 0.002 TYR B 169 PHE 0.010 0.001 PHE B 124 TRP 0.017 0.002 TRP D 79 HIS 0.007 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.01190 (26248) covalent geometry : angle 1.29080 (35720) hydrogen bonds : bond 0.17147 ( 1551) hydrogen bonds : angle 6.91309 ( 4200) *********************** 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 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7582 (ttm110) REVERT: A 82 MET cc_start: 0.9128 (tpp) cc_final: 0.8572 (mmm) REVERT: A 157 ASP cc_start: 0.7975 (t0) cc_final: 0.7353 (t0) REVERT: A 179 ASP cc_start: 0.7397 (p0) cc_final: 0.7066 (p0) REVERT: A 246 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7924 (mm-40) REVERT: A 293 LEU cc_start: 0.9497 (mt) cc_final: 0.9187 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0748 time to fit residues: 4.9186 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 : 0.114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 111 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 51 optimal weight: 5.9990 chunk 262 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 99 optimal weight: 0.0060 chunk 281 optimal weight: 0.1980 chunk 295 optimal weight: 0.0470 overall best weight: 0.0810 ------------------------------------------------------------------------------- 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** 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 = 0.3005 r_free = 0.3005 target = 0.068404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.059364 restraints weight = 10026.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.061233 restraints weight = 5923.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.062544 restraints weight = 3894.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.063478 restraints weight = 2776.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064216 restraints weight = 2097.893| |-----------------------------------------------------------------------------| r_work (final): 0.2915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.059859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.055282 restraints weight = 15261.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.055500 restraints weight = 14111.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.055670 restraints weight = 13034.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.055836 restraints weight = 12204.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.055991 restraints weight = 11446.561| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.8454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.357 26248 Z= 0.402 Angle : 0.923 15.933 35720 Z= 0.444 Chirality : 0.046 0.304 4092 Planarity : 0.005 0.040 4616 Dihedral : 11.556 145.534 3808 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.16), residues: 2912 helix: -0.14 (0.15), residues: 1224 sheet: 0.15 (0.23), residues: 496 loop : 0.36 (0.20), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 39 TYR 0.011 0.001 TYR F 169 PHE 0.008 0.001 PHE C 124 TRP 0.017 0.002 TRP E 356 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00794 (26248) covalent geometry : angle 0.92346 (35720) hydrogen bonds : bond 0.12923 ( 1551) hydrogen bonds : angle 5.61623 ( 4200) *********************** 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 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.118 Fit side-chains REVERT: A 28 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7131 (ttm110) REVERT: A 82 MET cc_start: 0.9089 (tpp) cc_final: 0.8518 (mmm) REVERT: A 111 ASN cc_start: 0.8783 (t0) cc_final: 0.8529 (t0) REVERT: A 155 SER cc_start: 0.8600 (m) cc_final: 0.8308 (p) REVERT: A 157 ASP cc_start: 0.7836 (t0) cc_final: 0.7130 (t0) REVERT: A 179 ASP cc_start: 0.7405 (p0) cc_final: 0.7027 (p0) REVERT: A 180 LEU cc_start: 0.8712 (tp) cc_final: 0.8420 (tt) REVERT: A 246 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7879 (mp10) REVERT: A 293 LEU cc_start: 0.9453 (mt) cc_final: 0.9159 (mt) REVERT: A 314 GLN cc_start: 0.8502 (tt0) cc_final: 0.7932 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0657 time to fit residues: 4.3473 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 : 0.114 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0165 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 : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 224 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 313 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 232 optimal weight: 0.3980 chunk 243 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 = 0.2965 r_free = 0.2965 target = 0.066621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.057244 restraints weight = 10498.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.059066 restraints weight = 6361.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.060357 restraints weight = 4276.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061303 restraints weight = 3086.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.061953 restraints weight = 2351.448| |-----------------------------------------------------------------------------| r_work (final): 0.2857 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.063005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.056973 restraints weight = 12396.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.057345 restraints weight = 10797.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.057619 restraints weight = 9534.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.057799 restraints weight = 8650.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.057984 restraints weight = 8017.600| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.8666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 26248 Z= 0.309 Angle : 0.986 21.464 35720 Z= 0.485 Chirality : 0.048 0.430 4092 Planarity : 0.005 0.043 4616 Dihedral : 11.214 131.392 3808 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2912 helix: 0.19 (0.15), residues: 1272 sheet: 0.01 (0.23), residues: 496 loop : 0.01 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 39 TYR 0.018 0.002 TYR A 169 PHE 0.012 0.001 PHE E 352 TRP 0.034 0.003 TRP C 356 HIS 0.007 0.002 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00634 (26248) covalent geometry : angle 0.98646 (35720) hydrogen bonds : bond 0.09276 ( 1551) hydrogen bonds : angle 5.32174 ( 4200) *********************** 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 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9163 (tpp) cc_final: 0.8355 (tmm) REVERT: A 111 ASN cc_start: 0.8961 (t0) cc_final: 0.8635 (t0) REVERT: A 155 SER cc_start: 0.8805 (m) cc_final: 0.8163 (t) REVERT: A 157 ASP cc_start: 0.8002 (t0) cc_final: 0.7426 (t0) REVERT: A 179 ASP cc_start: 0.7447 (p0) cc_final: 0.7125 (p0) REVERT: A 283 MET cc_start: 0.9025 (tpp) cc_final: 0.8699 (tpp) REVERT: A 293 LEU cc_start: 0.9446 (mt) cc_final: 0.9114 (mt) REVERT: A 314 GLN cc_start: 0.8586 (tt0) cc_final: 0.8081 (tm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0685 time to fit residues: 4.8328 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 : 0.115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 324 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 129 optimal weight: 0.0020 chunk 103 optimal weight: 7.9990 chunk 201 optimal weight: 0.1980 chunk 209 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 194 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 overall best weight: 1.0550 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.068668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.059204 restraints weight = 10335.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061136 restraints weight = 6124.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.062413 restraints weight = 4019.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.063428 restraints weight = 2890.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064135 restraints weight = 2209.332| |-----------------------------------------------------------------------------| r_work (final): 0.2898 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.066361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.060625 restraints weight = 10261.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.060732 restraints weight = 9665.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.060817 restraints weight = 9201.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.060817 restraints weight = 8914.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.060817 restraints weight = 8914.243| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.8975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26248 Z= 0.200 Angle : 0.779 17.291 35720 Z= 0.369 Chirality : 0.047 0.587 4092 Planarity : 0.004 0.038 4616 Dihedral : 10.418 125.805 3808 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2912 helix: 0.28 (0.15), residues: 1272 sheet: 0.17 (0.23), residues: 536 loop : 0.19 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 39 TYR 0.028 0.002 TYR G 169 PHE 0.006 0.001 PHE D 21 TRP 0.014 0.001 TRP F 356 HIS 0.003 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00410 (26248) covalent geometry : angle 0.77918 (35720) hydrogen bonds : bond 0.07529 ( 1551) hydrogen bonds : angle 4.90805 ( 4200) *********************** 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 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7826 (ptp) cc_final: 0.7611 (mtm) REVERT: A 82 MET cc_start: 0.9191 (tpp) cc_final: 0.8567 (mmm) REVERT: A 111 ASN cc_start: 0.8791 (t0) cc_final: 0.8489 (t0) REVERT: A 137 GLN cc_start: 0.8457 (mt0) cc_final: 0.8212 (mp10) REVERT: A 157 ASP cc_start: 0.7812 (t0) cc_final: 0.7283 (t0) REVERT: A 179 ASP cc_start: 0.7286 (p0) cc_final: 0.7051 (p0) REVERT: A 283 MET cc_start: 0.8949 (tpp) cc_final: 0.8630 (tpp) REVERT: A 293 LEU cc_start: 0.9428 (mt) cc_final: 0.9117 (mt) REVERT: A 314 GLN cc_start: 0.8486 (tt0) cc_final: 0.8006 (tm-30) REVERT: A 369 ILE cc_start: 0.9412 (tp) cc_final: 0.9203 (tt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0517 time to fit residues: 3.7005 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.120 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0151 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 104 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 chunk 199 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 24 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 = 0.2962 r_free = 0.2962 target = 0.066547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.056750 restraints weight = 10462.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.058662 restraints weight = 6245.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.059995 restraints weight = 4142.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061003 restraints weight = 2974.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.061738 restraints weight = 2274.826| |-----------------------------------------------------------------------------| r_work (final): 0.2848 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.068094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061988 restraints weight = 10156.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061995 restraints weight = 9680.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061995 restraints weight = 9640.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061995 restraints weight = 9640.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061995 restraints weight = 9640.097| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.8994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26248 Z= 0.208 Angle : 0.736 8.155 35720 Z= 0.355 Chirality : 0.044 0.222 4092 Planarity : 0.004 0.043 4616 Dihedral : 9.731 126.110 3808 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2912 helix: 0.42 (0.15), residues: 1272 sheet: 0.18 (0.22), residues: 536 loop : 0.04 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 116 TYR 0.027 0.002 TYR B 169 PHE 0.009 0.002 PHE D 21 TRP 0.036 0.003 TRP A 356 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00432 (26248) covalent geometry : angle 0.73583 (35720) hydrogen bonds : bond 0.06827 ( 1551) hydrogen bonds : angle 4.78732 ( 4200) *********************** 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 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.105 Fit side-chains REVERT: A 82 MET cc_start: 0.9228 (tpp) cc_final: 0.8443 (tmm) REVERT: A 137 GLN cc_start: 0.8370 (mt0) cc_final: 0.7982 (mp10) REVERT: A 157 ASP cc_start: 0.7712 (t0) cc_final: 0.7202 (t0) REVERT: A 179 ASP cc_start: 0.7324 (p0) cc_final: 0.7116 (p0) REVERT: A 283 MET cc_start: 0.9069 (tpp) cc_final: 0.8821 (tpp) REVERT: A 293 LEU cc_start: 0.9434 (mt) cc_final: 0.9132 (mt) REVERT: A 314 GLN cc_start: 0.8501 (tt0) cc_final: 0.8175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0545 time to fit residues: 3.5379 Evaluate side-chains 40 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.116 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 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 : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 chunk 12 optimal weight: 0.0570 chunk 331 optimal weight: 8.9990 chunk 320 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 132 optimal weight: 0.0000 overall best weight: 0.5106 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.069878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059612 restraints weight = 10356.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.061555 restraints weight = 6271.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.062938 restraints weight = 4240.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063975 restraints weight = 3095.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.064761 restraints weight = 2386.534| |-----------------------------------------------------------------------------| r_work (final): 0.2920 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.069484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.063539 restraints weight = 10112.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063645 restraints weight = 9597.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063645 restraints weight = 9126.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063645 restraints weight = 9126.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063645 restraints weight = 9126.941| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.9373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26248 Z= 0.173 Angle : 0.661 5.770 35720 Z= 0.318 Chirality : 0.042 0.120 4092 Planarity : 0.004 0.045 4616 Dihedral : 8.986 117.451 3808 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.16), residues: 2912 helix: 0.56 (0.15), residues: 1224 sheet: 0.24 (0.22), residues: 536 loop : -0.07 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 39 TYR 0.014 0.001 TYR G 169 PHE 0.009 0.001 PHE F 124 TRP 0.014 0.001 TRP F 356 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00350 (26248) covalent geometry : angle 0.66109 (35720) hydrogen bonds : bond 0.06396 ( 1551) hydrogen bonds : angle 4.44688 ( 4200) *********************** 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 61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9165 (tpp) cc_final: 0.8565 (mmm) REVERT: A 111 ASN cc_start: 0.8814 (t0) cc_final: 0.8556 (t0) REVERT: A 157 ASP cc_start: 0.7560 (t0) cc_final: 0.6957 (t0) REVERT: A 179 ASP cc_start: 0.7416 (p0) cc_final: 0.7122 (p0) REVERT: A 180 LEU cc_start: 0.8668 (tp) cc_final: 0.8291 (tt) REVERT: A 283 MET cc_start: 0.8932 (tpp) cc_final: 0.8634 (tpp) REVERT: A 293 LEU cc_start: 0.9422 (mt) cc_final: 0.9115 (mt) REVERT: A 314 GLN cc_start: 0.8412 (tt0) cc_final: 0.8051 (tm-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0455 time to fit residues: 3.6529 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 : 0.114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0145 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 217 optimal weight: 8.9990 chunk 281 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 chunk 187 optimal weight: 0.0040 chunk 277 optimal weight: 0.0070 chunk 3 optimal weight: 0.0370 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.4168 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.071179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.060904 restraints weight = 10444.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.062769 restraints weight = 6355.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.064155 restraints weight = 4310.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.065084 restraints weight = 3155.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065626 restraints weight = 2461.638| |-----------------------------------------------------------------------------| r_work (final): 0.2939 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.070191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.063817 restraints weight = 10242.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.063905 restraints weight = 9751.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.063968 restraints weight = 9384.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063997 restraints weight = 9213.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063997 restraints weight = 9083.511| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.9615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26248 Z= 0.161 Angle : 0.645 5.788 35720 Z= 0.309 Chirality : 0.041 0.121 4092 Planarity : 0.004 0.046 4616 Dihedral : 8.269 112.412 3808 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2912 helix: 0.56 (0.15), residues: 1224 sheet: 0.05 (0.22), residues: 496 loop : -0.18 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 28 TYR 0.019 0.001 TYR H 169 PHE 0.009 0.001 PHE F 124 TRP 0.012 0.002 TRP F 356 HIS 0.003 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00324 (26248) covalent geometry : angle 0.64451 (35720) hydrogen bonds : bond 0.06162 ( 1551) hydrogen bonds : angle 4.37892 ( 4200) *********************** 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 : 0.070 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8987 (tpp) cc_final: 0.8449 (mmm) REVERT: A 111 ASN cc_start: 0.8745 (t0) cc_final: 0.8496 (t0) REVERT: A 157 ASP cc_start: 0.7362 (t0) cc_final: 0.6875 (t0) REVERT: A 179 ASP cc_start: 0.7293 (p0) cc_final: 0.7055 (p0) REVERT: A 180 LEU cc_start: 0.8615 (tp) cc_final: 0.8284 (tt) REVERT: A 283 MET cc_start: 0.8821 (tpp) cc_final: 0.8340 (tpp) REVERT: A 293 LEU cc_start: 0.9407 (mt) cc_final: 0.9120 (mt) REVERT: A 314 GLN cc_start: 0.8498 (tt0) cc_final: 0.8101 (tm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0324 time to fit residues: 2.4564 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 : 0.113 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0137 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 291 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 335 optimal weight: 20.0000 chunk 153 optimal weight: 0.0050 chunk 299 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 266 optimal weight: 0.4980 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.069871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.059880 restraints weight = 10221.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.061675 restraints weight = 6387.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.062978 restraints weight = 4409.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.063962 restraints weight = 3287.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.064695 restraints weight = 2580.207| |-----------------------------------------------------------------------------| r_work (final): 0.2922 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.067563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.058502 restraints weight = 9935.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.058673 restraints weight = 9424.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.058769 restraints weight = 8941.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.058869 restraints weight = 8652.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.058956 restraints weight = 8403.288| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.9596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26248 Z= 0.166 Angle : 0.646 5.751 35720 Z= 0.317 Chirality : 0.042 0.118 4092 Planarity : 0.004 0.047 4616 Dihedral : 8.331 116.154 3808 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2912 helix: 0.61 (0.15), residues: 1224 sheet: 0.02 (0.22), residues: 496 loop : -0.22 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 177 TYR 0.018 0.001 TYR B 169 PHE 0.007 0.001 PHE B 21 TRP 0.009 0.001 TRP F 356 HIS 0.003 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00345 (26248) covalent geometry : angle 0.64576 (35720) hydrogen bonds : bond 0.06069 ( 1551) hydrogen bonds : angle 4.30909 ( 4200) *********************** 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 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9116 (tpp) cc_final: 0.8382 (tmm) REVERT: A 111 ASN cc_start: 0.8746 (t0) cc_final: 0.8517 (t0) REVERT: A 157 ASP cc_start: 0.7449 (t0) cc_final: 0.6911 (t0) REVERT: A 179 ASP cc_start: 0.7429 (p0) cc_final: 0.7226 (p0) REVERT: A 180 LEU cc_start: 0.8643 (tp) cc_final: 0.8291 (tt) REVERT: A 283 MET cc_start: 0.8942 (tpp) cc_final: 0.8453 (tpp) REVERT: A 293 LEU cc_start: 0.9431 (mt) cc_final: 0.9130 (mt) REVERT: A 314 GLN cc_start: 0.8474 (tt0) cc_final: 0.8065 (tm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0381 time to fit residues: 2.6317 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 : 0.115 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0139 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 27 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 197 optimal weight: 0.0770 chunk 142 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3074 r_free = 0.3074 target = 0.071672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.061551 restraints weight = 10254.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.063397 restraints weight = 6327.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.064769 restraints weight = 4330.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.065744 restraints weight = 3175.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066473 restraints weight = 2486.308| |-----------------------------------------------------------------------------| r_work (final): 0.2959 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.072120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.064745 restraints weight = 10795.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.064951 restraints weight = 10059.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.065148 restraints weight = 9464.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.065280 restraints weight = 9020.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.065415 restraints weight = 8611.869| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.9776 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= 0.151 Angle : 0.637 6.120 35720 Z= 0.305 Chirality : 0.042 0.131 4092 Planarity : 0.004 0.047 4616 Dihedral : 8.206 114.443 3808 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2912 helix: 0.64 (0.15), residues: 1224 sheet: -0.14 (0.22), residues: 496 loop : -0.25 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 95 TYR 0.014 0.001 TYR H 169 PHE 0.011 0.001 PHE G 124 TRP 0.011 0.002 TRP F 356 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00308 (26248) covalent geometry : angle 0.63714 (35720) hydrogen bonds : bond 0.05678 ( 1551) hydrogen bonds : angle 4.27605 ( 4200) ********************** 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 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7771 (ppp) cc_final: 0.7511 (ppp) REVERT: A 117 GLU cc_start: 0.7958 (tp30) cc_final: 0.7734 (tp30) REVERT: A 157 ASP cc_start: 0.7348 (t0) cc_final: 0.6702 (t0) REVERT: A 179 ASP cc_start: 0.7420 (p0) cc_final: 0.7131 (p0) REVERT: A 180 LEU cc_start: 0.8576 (tp) cc_final: 0.8276 (tt) REVERT: A 283 MET cc_start: 0.8826 (tpp) cc_final: 0.8295 (tpp) REVERT: A 293 LEU cc_start: 0.9417 (mt) cc_final: 0.9060 (mt) REVERT: A 314 GLN cc_start: 0.8443 (tt0) cc_final: 0.8068 (tm-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0477 time to fit residues: 3.5284 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 : 0.112 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0142 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 : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 337 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 186 optimal weight: 0.0030 chunk 329 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 231 optimal weight: 0.0270 chunk 38 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 overall best weight: 3.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2998 r_free = 0.2998 target = 0.068181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.058428 restraints weight = 10316.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060257 restraints weight = 6341.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061688 restraints weight = 4312.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.062691 restraints weight = 3124.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.063372 restraints weight = 2401.980| |-----------------------------------------------------------------------------| r_work (final): 0.2884 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.068305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.060069 restraints weight = 10184.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.060193 restraints weight = 9575.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.060370 restraints weight = 9071.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.060476 restraints weight = 8629.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.060616 restraints weight = 8259.923| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.9627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26248 Z= 0.191 Angle : 0.666 5.861 35720 Z= 0.326 Chirality : 0.042 0.148 4092 Planarity : 0.004 0.046 4616 Dihedral : 8.455 119.116 3808 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2912 helix: 0.60 (0.15), residues: 1272 sheet: -0.19 (0.21), residues: 536 loop : -0.11 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 116 TYR 0.020 0.002 TYR D 169 PHE 0.008 0.001 PHE A 223 TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS G 40 Details of bonding type rmsd covalent geometry : bond 0.00402 (26248) covalent geometry : angle 0.66583 (35720) hydrogen bonds : bond 0.05749 ( 1551) hydrogen bonds : angle 4.28545 ( 4200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.56 seconds wall clock time: 32 minutes 56.64 seconds (1976.64 seconds total)