Starting phenix.real_space_refine on Fri Sep 19 06:19:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azq_44019/09_2025/9azq_44019.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azq_44019/09_2025/9azq_44019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9azq_44019/09_2025/9azq_44019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azq_44019/09_2025/9azq_44019.map" model { file = "/net/cci-nas-00/data/ceres_data/9azq_44019/09_2025/9azq_44019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azq_44019/09_2025/9azq_44019.cif" } resolution = 3.82 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= 0.017 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: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 7 5.21 5 S 160 5.16 5 C 14863 2.51 5 N 3996 2.21 5 O 4523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 23563 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 483 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 7, 'TRANS': 52} Chain: "H" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 314} Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.65, per 1000 atoms: 0.24 Number of scatterers: 23563 At special positions: 0 Unit cell: (103.68, 115.56, 247.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 P 14 15.00 Mg 7 11.99 O 4523 8.00 N 3996 7.00 C 14863 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 41 sheets defined 52.1% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.892A 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 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.854A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.537A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.525A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 4.168A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.519A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.657A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.155A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.519A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.925A 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 368 through 374 removed outlier: 4.200A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.639A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.942A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.777A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.889A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.052A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.576A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 273 through 284 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 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.072A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.527A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.631A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.883A 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 368 through 374 removed outlier: 4.252A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.592A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.844A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.788A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.734A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.481A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.531A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.556A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.040A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.805A 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 368 through 374 removed outlier: 3.954A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.787A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.913A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.667A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.575A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.531A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.670A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.858A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.666A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.518A pdb=" N LEU D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.009A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.765A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.820A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.931A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.568A pdb=" N GLU E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.817A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.711A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.037A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.914A 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 368 through 374 removed outlier: 3.967A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.734A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.688A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 263 removed outlier: 3.629A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix removed outlier: 4.624A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 267 removed outlier: 3.676A pdb=" N ILE F 267 " --> pdb=" O PRO F 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 264 through 267' Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.719A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.687A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) 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 346 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.605A pdb=" N PHE F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 349 through 353' Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 3.974A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 578 Processing helix chain 'G' and resid 583 through 588 removed outlier: 4.039A pdb=" N LEU G 587 " --> pdb=" O MET G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 606 Processing helix chain 'H' and resid 634 through 647 removed outlier: 3.540A pdb=" N SER H 638 " --> pdb=" O ASP H 634 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS H 646 " --> pdb=" O ASN H 642 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 662 removed outlier: 3.514A pdb=" N VAL H 655 " --> pdb=" O SER H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 Processing helix chain 'H' and resid 681 through 690 Processing helix chain 'H' and resid 694 through 698 Processing helix chain 'H' and resid 699 through 711 removed outlier: 3.570A pdb=" N ILE H 711 " --> pdb=" O LEU H 707 " (cutoff:3.500A) Processing helix chain 'H' and resid 713 through 750 Proline residue: H 736 - end of helix Processing helix chain 'H' and resid 753 through 769 Processing helix chain 'H' and resid 781 through 785 removed outlier: 3.531A pdb=" N LEU H 785 " --> pdb=" O ILE H 782 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 811 removed outlier: 3.837A pdb=" N LYS H 810 " --> pdb=" O GLU H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 816 removed outlier: 3.650A pdb=" N LEU H 815 " --> pdb=" O HIS H 812 " (cutoff:3.500A) Processing helix chain 'H' and resid 817 through 822 removed outlier: 3.919A pdb=" N ASP H 821 " --> pdb=" O GLN H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 832 through 856 Processing helix chain 'H' and resid 858 through 897 removed outlier: 5.831A pdb=" N GLU H 867 " --> pdb=" O GLU H 863 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG H 868 " --> pdb=" O GLN H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 906 through 947 Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.792A pdb=" N GLU I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 97 through 101' Processing helix chain 'I' and resid 112 through 125 removed outlier: 4.059A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'I' and resid 202 through 216 removed outlier: 3.704A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.670A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 removed outlier: 3.843A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 267 removed outlier: 3.523A pdb=" N ILE I 267 " --> pdb=" O PRO I 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 264 through 267' Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 289 through 296 Processing helix chain 'I' and resid 302 through 306 removed outlier: 4.192A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 350 through 355 removed outlier: 3.880A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 Processing helix chain 'I' and resid 368 through 374 removed outlier: 4.208A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.557A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.481A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.152A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.546A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.309A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.476A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.518A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.427A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.379A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 4.151A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.536A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.319A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.665A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.717A pdb=" N SER F 155 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.404A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR I 133 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET I 132 " --> pdb=" O ILE I 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.376A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 238 through 241 1146 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6244 1.33 - 1.45: 4273 1.45 - 1.57: 13240 1.57 - 1.69: 23 1.69 - 1.81: 278 Bond restraints: 24058 Sorted by residual: bond pdb=" CA VAL G 551 " pdb=" C VAL G 551 " ideal model delta sigma weight residual 1.525 1.604 -0.079 2.10e-02 2.27e+03 1.42e+01 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" CE1 HIC I 73 " pdb=" NE2 HIC I 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 24053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 31597 2.22 - 4.45: 869 4.45 - 6.67: 114 6.67 - 8.89: 34 8.89 - 11.12: 8 Bond angle restraints: 32622 Sorted by residual: angle pdb=" C GLU H 629 " pdb=" N ILE H 630 " pdb=" CA ILE H 630 " ideal model delta sigma weight residual 121.97 132.40 -10.43 1.80e+00 3.09e-01 3.36e+01 angle pdb=" N ASN A 128 " pdb=" CA ASN A 128 " pdb=" C ASN A 128 " ideal model delta sigma weight residual 110.30 118.30 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" CA VAL G 551 " pdb=" C VAL G 551 " pdb=" N PRO G 552 " ideal model delta sigma weight residual 116.90 124.02 -7.12 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C ALA H 828 " pdb=" CA ALA H 828 " pdb=" CB ALA H 828 " ideal model delta sigma weight residual 115.79 110.15 5.64 1.19e+00 7.06e-01 2.24e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 122.08 128.74 -6.66 1.47e+00 4.63e-01 2.05e+01 ... (remaining 32617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 14328 35.99 - 71.97: 197 71.97 - 107.96: 13 107.96 - 143.94: 8 143.94 - 179.93: 8 Dihedral angle restraints: 14554 sinusoidal: 5912 harmonic: 8642 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 119.93 -179.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP I 401 " pdb=" O5' ADP I 401 " pdb=" PA ADP I 401 " pdb=" O2A ADP I 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.94 -167.94 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.68 -167.68 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 14551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3093 0.072 - 0.143: 473 0.143 - 0.215: 53 0.215 - 0.286: 14 0.286 - 0.358: 3 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CB VAL G 551 " pdb=" CA VAL G 551 " pdb=" CG1 VAL G 551 " pdb=" CG2 VAL G 551 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE H 630 " pdb=" CA ILE H 630 " pdb=" CG1 ILE H 630 " pdb=" CG2 ILE H 630 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3633 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 824 " 0.058 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO H 825 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO H 825 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 825 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.051 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO D 243 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO E 112 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " 0.041 5.00e-02 4.00e+02 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 320 2.64 - 3.20: 19409 3.20 - 3.77: 37672 3.77 - 4.33: 52864 4.33 - 4.90: 84629 Nonbonded interactions: 194894 Sorted by model distance: nonbonded pdb=" O2B ADP F 401 " pdb="MG MG F 402 " model vdw 2.075 2.170 nonbonded pdb=" O3A ADP A 401 " pdb="MG MG A 402 " model vdw 2.087 2.170 nonbonded pdb=" O2A ADP B 401 " pdb="MG MG B 402 " model vdw 2.107 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.108 2.170 nonbonded pdb=" O1B ADP I 401 " pdb="MG MG I 402 " model vdw 2.114 2.170 ... (remaining 194889 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: 0.00 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 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.720 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.240 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.005 0.095 24063 Z= 0.245 Angle : 0.880 11.117 32622 Z= 0.481 Chirality : 0.054 0.358 3636 Planarity : 0.008 0.086 4179 Dihedral : 15.038 179.931 9000 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.04 % 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: -2.89 (0.13), residues: 2941 helix: -2.64 (0.09), residues: 1382 sheet: -0.83 (0.22), residues: 462 loop : -1.04 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 837 TYR 0.023 0.002 TYR H 705 PHE 0.027 0.002 PHE B 124 TRP 0.019 0.002 TRP G 569 HIS 0.010 0.001 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00491 (24058) covalent geometry : angle 0.88020 (32622) hydrogen bonds : bond 0.14594 ( 1128) hydrogen bonds : angle 7.10450 ( 3114) Misc. bond : bond 0.00337 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9385 (tpt) cc_final: 0.8834 (tpt) REVERT: A 123 MET cc_start: 0.9485 (mmp) cc_final: 0.9188 (mmm) REVERT: A 257 CYS cc_start: 0.9546 (t) cc_final: 0.9287 (p) REVERT: A 299 MET cc_start: 0.8675 (mtm) cc_final: 0.8353 (ptp) REVERT: A 313 MET cc_start: 0.9570 (tpp) cc_final: 0.9027 (tpp) REVERT: A 325 MET cc_start: 0.8780 (mmm) cc_final: 0.8160 (mpp) REVERT: A 355 MET cc_start: 0.8945 (mtp) cc_final: 0.8744 (tpt) REVERT: B 72 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9066 (mp0) REVERT: B 82 MET cc_start: 0.9231 (tpt) cc_final: 0.8411 (tpt) REVERT: B 227 MET cc_start: 0.9149 (mmm) cc_final: 0.8850 (mmm) REVERT: B 355 MET cc_start: 0.8976 (mtp) cc_final: 0.8405 (tpp) REVERT: C 311 ASP cc_start: 0.9291 (m-30) cc_final: 0.9061 (p0) REVERT: C 355 MET cc_start: 0.9410 (mtp) cc_final: 0.9063 (mtp) REVERT: D 82 MET cc_start: 0.8986 (tpt) cc_final: 0.8622 (tpt) REVERT: D 325 MET cc_start: 0.8974 (mmt) cc_final: 0.8745 (mmm) REVERT: E 82 MET cc_start: 0.9394 (tpt) cc_final: 0.8633 (tpt) REVERT: E 283 MET cc_start: 0.9462 (mmm) cc_final: 0.9231 (mmm) REVERT: E 299 MET cc_start: 0.8682 (mtm) cc_final: 0.7877 (mmp) REVERT: E 305 MET cc_start: 0.9532 (mmm) cc_final: 0.9322 (mmm) REVERT: E 313 MET cc_start: 0.9467 (tpp) cc_final: 0.9113 (tpp) REVERT: E 325 MET cc_start: 0.8542 (mmm) cc_final: 0.8250 (mpp) REVERT: E 355 MET cc_start: 0.9328 (mtp) cc_final: 0.9063 (mtp) REVERT: F 82 MET cc_start: 0.9482 (tpt) cc_final: 0.9073 (tpp) REVERT: F 190 MET cc_start: 0.8780 (mtp) cc_final: 0.8524 (mmm) REVERT: F 299 MET cc_start: 0.5634 (mtm) cc_final: 0.5153 (ptt) REVERT: F 313 MET cc_start: 0.9656 (tpp) cc_final: 0.9455 (tpp) REVERT: G 583 MET cc_start: 0.0790 (ttm) cc_final: 0.0240 (mpp) REVERT: H 694 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8832 (tm-30) REVERT: H 812 HIS cc_start: 0.7021 (m90) cc_final: 0.6471 (t-170) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1783 time to fit residues: 58.1683 Evaluate side-chains 145 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 173 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 111 ASN ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 864 GLN I 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.036067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.024202 restraints weight = 271341.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.024798 restraints weight = 175953.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.025215 restraints weight = 127734.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.025569 restraints weight = 101988.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.025726 restraints weight = 85983.347| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24063 Z= 0.229 Angle : 0.711 11.025 32622 Z= 0.352 Chirality : 0.043 0.169 3636 Planarity : 0.005 0.069 4179 Dihedral : 10.997 176.645 3330 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.44 % Allowed : 4.63 % Favored : 94.94 % 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: -0.33 (0.15), residues: 2941 helix: -0.10 (0.13), residues: 1335 sheet: -0.46 (0.23), residues: 455 loop : 0.01 (0.20), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.017 0.002 TYR D 91 PHE 0.019 0.002 PHE E 200 TRP 0.013 0.001 TRP F 79 HIS 0.008 0.001 HIS H 703 Details of bonding type rmsd covalent geometry : bond 0.00468 (24058) covalent geometry : angle 0.71118 (32622) hydrogen bonds : bond 0.03550 ( 1128) hydrogen bonds : angle 4.93773 ( 3114) Misc. bond : bond 0.00167 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8479 (tpp) cc_final: 0.8078 (tpp) REVERT: A 82 MET cc_start: 0.9287 (tpt) cc_final: 0.8846 (tpt) REVERT: A 119 MET cc_start: 0.9658 (ttp) cc_final: 0.9040 (tmm) REVERT: A 123 MET cc_start: 0.9566 (mmp) cc_final: 0.9226 (mmm) REVERT: A 132 MET cc_start: 0.9218 (tmm) cc_final: 0.8857 (tmm) REVERT: A 257 CYS cc_start: 0.9457 (t) cc_final: 0.9191 (t) REVERT: A 269 MET cc_start: 0.8874 (mtp) cc_final: 0.8469 (mtp) REVERT: A 325 MET cc_start: 0.8658 (mmm) cc_final: 0.8446 (mmm) REVERT: B 44 MET cc_start: 0.7946 (tpp) cc_final: 0.7699 (tpp) REVERT: B 123 MET cc_start: 0.9071 (mmm) cc_final: 0.8813 (mmm) REVERT: B 227 MET cc_start: 0.9034 (mmm) cc_final: 0.8779 (mmm) REVERT: B 299 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7601 (ptt) REVERT: B 355 MET cc_start: 0.8888 (mtp) cc_final: 0.8421 (mmm) REVERT: C 44 MET cc_start: 0.8715 (tpp) cc_final: 0.8501 (mmp) REVERT: C 82 MET cc_start: 0.8736 (tpt) cc_final: 0.8275 (tpt) REVERT: C 283 MET cc_start: 0.8508 (mmm) cc_final: 0.8305 (mmm) REVERT: C 355 MET cc_start: 0.9341 (mtp) cc_final: 0.9126 (mtp) REVERT: D 47 MET cc_start: 0.6519 (ptm) cc_final: 0.5909 (ppp) REVERT: D 82 MET cc_start: 0.8991 (tpt) cc_final: 0.8538 (tpt) REVERT: D 305 MET cc_start: 0.8885 (mmm) cc_final: 0.8615 (mmt) REVERT: D 325 MET cc_start: 0.9069 (mmt) cc_final: 0.8495 (mmm) REVERT: E 82 MET cc_start: 0.9401 (tpt) cc_final: 0.8858 (tpp) REVERT: E 119 MET cc_start: 0.9207 (ptm) cc_final: 0.8903 (ptt) REVERT: E 299 MET cc_start: 0.8327 (mtm) cc_final: 0.7912 (mmp) REVERT: E 325 MET cc_start: 0.8585 (mmm) cc_final: 0.8134 (mmm) REVERT: F 82 MET cc_start: 0.9519 (tpt) cc_final: 0.8922 (tpt) REVERT: F 269 MET cc_start: 0.7997 (ttt) cc_final: 0.7720 (ttt) REVERT: G 583 MET cc_start: 0.1146 (ttm) cc_final: 0.0856 (mpp) REVERT: H 694 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8813 (tp30) REVERT: H 812 HIS cc_start: 0.7100 (m90) cc_final: 0.6442 (t-170) REVERT: I 47 MET cc_start: 0.4365 (mpp) cc_final: 0.4120 (mpp) REVERT: I 82 MET cc_start: 0.9291 (mmm) cc_final: 0.9004 (mmm) outliers start: 11 outliers final: 5 residues processed: 152 average time/residue: 0.1607 time to fit residues: 39.9077 Evaluate side-chains 140 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 41 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.036260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.024350 restraints weight = 267527.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.024866 restraints weight = 172685.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.025421 restraints weight = 126941.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.025723 restraints weight = 100636.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.025977 restraints weight = 85666.695| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24063 Z= 0.135 Angle : 0.607 8.969 32622 Z= 0.289 Chirality : 0.041 0.182 3636 Planarity : 0.004 0.065 4179 Dihedral : 10.033 179.257 3330 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.32 % Allowed : 5.10 % Favored : 94.58 % 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: 0.42 (0.16), residues: 2941 helix: 0.69 (0.14), residues: 1335 sheet: -0.26 (0.24), residues: 455 loop : 0.26 (0.20), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.011 0.001 TYR B 143 PHE 0.011 0.001 PHE G 606 TRP 0.011 0.001 TRP F 79 HIS 0.007 0.001 HIS H 703 Details of bonding type rmsd covalent geometry : bond 0.00286 (24058) covalent geometry : angle 0.60670 (32622) hydrogen bonds : bond 0.02918 ( 1128) hydrogen bonds : angle 4.57538 ( 3114) Misc. bond : bond 0.00106 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8447 (tpp) cc_final: 0.8203 (tpp) REVERT: A 82 MET cc_start: 0.9332 (tpt) cc_final: 0.8866 (tpt) REVERT: A 119 MET cc_start: 0.9651 (ttp) cc_final: 0.8911 (tmm) REVERT: A 123 MET cc_start: 0.9546 (mmp) cc_final: 0.9151 (mmm) REVERT: A 132 MET cc_start: 0.9184 (tmm) cc_final: 0.8803 (tmm) REVERT: A 257 CYS cc_start: 0.9425 (t) cc_final: 0.9221 (t) REVERT: A 305 MET cc_start: 0.8868 (mmm) cc_final: 0.8559 (mmm) REVERT: A 355 MET cc_start: 0.9272 (mmm) cc_final: 0.8730 (tpp) REVERT: B 123 MET cc_start: 0.9050 (mmm) cc_final: 0.8751 (mmm) REVERT: B 227 MET cc_start: 0.9051 (mmm) cc_final: 0.8794 (mmm) REVERT: B 305 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8571 (mmm) REVERT: B 355 MET cc_start: 0.8869 (mtp) cc_final: 0.8354 (mmm) REVERT: C 47 MET cc_start: 0.7684 (ptp) cc_final: 0.7364 (pmm) REVERT: C 82 MET cc_start: 0.8800 (tpt) cc_final: 0.8204 (tpt) REVERT: C 190 MET cc_start: 0.8876 (tpp) cc_final: 0.8554 (tpt) REVERT: C 227 MET cc_start: 0.8645 (tpp) cc_final: 0.8262 (mmm) REVERT: C 283 MET cc_start: 0.8673 (mmm) cc_final: 0.8397 (mmm) REVERT: C 305 MET cc_start: 0.8035 (mmt) cc_final: 0.7651 (mmt) REVERT: C 355 MET cc_start: 0.9319 (mtp) cc_final: 0.9104 (mtp) REVERT: D 44 MET cc_start: 0.8994 (mmm) cc_final: 0.8736 (mmm) REVERT: D 47 MET cc_start: 0.6580 (ptm) cc_final: 0.5414 (ppp) REVERT: D 82 MET cc_start: 0.8892 (tpt) cc_final: 0.8574 (tpt) REVERT: D 132 MET cc_start: 0.8424 (ppp) cc_final: 0.8066 (ppp) REVERT: D 227 MET cc_start: 0.9012 (mmm) cc_final: 0.8657 (mmm) REVERT: D 305 MET cc_start: 0.8855 (mmm) cc_final: 0.8595 (mmm) REVERT: D 325 MET cc_start: 0.9076 (mmt) cc_final: 0.8414 (mmm) REVERT: E 82 MET cc_start: 0.9367 (tpt) cc_final: 0.8753 (tpp) REVERT: E 190 MET cc_start: 0.8872 (tmm) cc_final: 0.8637 (tmm) REVERT: E 299 MET cc_start: 0.8355 (mtm) cc_final: 0.7875 (mmp) REVERT: E 325 MET cc_start: 0.8454 (mmm) cc_final: 0.8078 (mmm) REVERT: F 82 MET cc_start: 0.9485 (tpt) cc_final: 0.8945 (tpt) REVERT: F 269 MET cc_start: 0.8023 (ttt) cc_final: 0.7781 (ttt) REVERT: H 694 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8843 (tp30) REVERT: H 812 HIS cc_start: 0.6985 (m90) cc_final: 0.6322 (t-170) REVERT: I 82 MET cc_start: 0.9372 (mmm) cc_final: 0.9083 (mmm) outliers start: 8 outliers final: 4 residues processed: 143 average time/residue: 0.1532 time to fit residues: 35.7767 Evaluate side-chains 139 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 41 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN E 297 ASN ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.034733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.023377 restraints weight = 279050.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.023727 restraints weight = 180931.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.024107 restraints weight = 133448.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.024401 restraints weight = 108095.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.024575 restraints weight = 92780.384| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24063 Z= 0.254 Angle : 0.739 10.466 32622 Z= 0.363 Chirality : 0.044 0.212 3636 Planarity : 0.004 0.062 4179 Dihedral : 9.487 179.615 3330 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.71 % Allowed : 6.84 % Favored : 92.44 % 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: 0.36 (0.16), residues: 2941 helix: 0.59 (0.14), residues: 1335 sheet: -0.06 (0.25), residues: 434 loop : 0.16 (0.20), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 820 TYR 0.017 0.002 TYR D 91 PHE 0.016 0.002 PHE E 200 TRP 0.017 0.002 TRP F 79 HIS 0.007 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00514 (24058) covalent geometry : angle 0.73935 (32622) hydrogen bonds : bond 0.03508 ( 1128) hydrogen bonds : angle 4.87626 ( 3114) Misc. bond : bond 0.00105 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8464 (tpp) cc_final: 0.8119 (tpp) REVERT: A 82 MET cc_start: 0.9375 (tpt) cc_final: 0.8875 (tpt) REVERT: A 119 MET cc_start: 0.9660 (ttp) cc_final: 0.9140 (tmm) REVERT: A 123 MET cc_start: 0.9603 (mmp) cc_final: 0.9340 (mmm) REVERT: A 132 MET cc_start: 0.9310 (tmm) cc_final: 0.9046 (tmm) REVERT: A 257 CYS cc_start: 0.9487 (t) cc_final: 0.9264 (t) REVERT: A 269 MET cc_start: 0.8782 (mtp) cc_final: 0.8416 (mtp) REVERT: A 305 MET cc_start: 0.8889 (mmm) cc_final: 0.8588 (mmm) REVERT: B 123 MET cc_start: 0.9147 (mmm) cc_final: 0.8856 (mmm) REVERT: B 227 MET cc_start: 0.9033 (mmm) cc_final: 0.8784 (mmm) REVERT: B 305 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: B 355 MET cc_start: 0.8877 (mtp) cc_final: 0.8338 (mmm) REVERT: C 47 MET cc_start: 0.7561 (ptp) cc_final: 0.7356 (ptp) REVERT: C 82 MET cc_start: 0.8809 (tpt) cc_final: 0.8464 (tpt) REVERT: C 176 MET cc_start: 0.9178 (mmm) cc_final: 0.8839 (mmt) REVERT: C 227 MET cc_start: 0.8784 (tpp) cc_final: 0.8539 (mmm) REVERT: C 283 MET cc_start: 0.8882 (mmm) cc_final: 0.8557 (mmm) REVERT: C 305 MET cc_start: 0.8079 (mmt) cc_final: 0.7840 (mmm) REVERT: C 313 MET cc_start: 0.9011 (mmm) cc_final: 0.8757 (mmm) REVERT: D 82 MET cc_start: 0.8939 (tpt) cc_final: 0.8616 (tpt) REVERT: D 132 MET cc_start: 0.8569 (ppp) cc_final: 0.8298 (ppp) REVERT: D 227 MET cc_start: 0.9176 (mmm) cc_final: 0.8861 (mmm) REVERT: D 305 MET cc_start: 0.8844 (mmm) cc_final: 0.8576 (mmm) REVERT: D 325 MET cc_start: 0.9068 (mmt) cc_final: 0.8297 (mmm) REVERT: E 82 MET cc_start: 0.9367 (tpt) cc_final: 0.8651 (tpt) REVERT: E 190 MET cc_start: 0.9010 (tmm) cc_final: 0.8728 (tmm) REVERT: E 283 MET cc_start: 0.9188 (mmm) cc_final: 0.8796 (mmm) REVERT: E 299 MET cc_start: 0.8304 (mtm) cc_final: 0.7837 (mmp) REVERT: E 305 MET cc_start: 0.9545 (mmt) cc_final: 0.9161 (mmm) REVERT: E 325 MET cc_start: 0.8465 (mmm) cc_final: 0.8036 (mmm) REVERT: F 82 MET cc_start: 0.9530 (tpt) cc_final: 0.9141 (tpp) REVERT: F 269 MET cc_start: 0.8052 (ttt) cc_final: 0.7806 (ttt) REVERT: F 299 MET cc_start: 0.5638 (ttp) cc_final: 0.4754 (ppp) REVERT: H 694 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8923 (tp30) REVERT: H 812 HIS cc_start: 0.6158 (m90) cc_final: 0.5395 (t70) REVERT: H 913 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3626 (tpt) REVERT: I 44 MET cc_start: 0.1481 (mpt) cc_final: 0.1220 (mpt) REVERT: I 82 MET cc_start: 0.9446 (mmm) cc_final: 0.9187 (mmm) REVERT: I 132 MET cc_start: 0.8321 (tpt) cc_final: 0.8058 (tpp) outliers start: 18 outliers final: 6 residues processed: 145 average time/residue: 0.1554 time to fit residues: 37.0277 Evaluate side-chains 138 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain H residue 913 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 229 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 258 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 161 HIS C 115 ASN I 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.035658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.024094 restraints weight = 269482.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.024455 restraints weight = 174546.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.024898 restraints weight = 129306.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.025167 restraints weight = 102810.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.025374 restraints weight = 88039.625| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24063 Z= 0.114 Angle : 0.611 9.426 32622 Z= 0.289 Chirality : 0.042 0.185 3636 Planarity : 0.003 0.062 4179 Dihedral : 8.954 176.233 3330 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.40 % Allowed : 7.95 % Favored : 91.65 % 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: 0.80 (0.16), residues: 2941 helix: 1.04 (0.14), residues: 1329 sheet: -0.19 (0.24), residues: 469 loop : 0.45 (0.21), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.009 0.001 TYR I 53 PHE 0.008 0.001 PHE A 255 TRP 0.011 0.001 TRP F 79 HIS 0.005 0.001 HIS H 703 Details of bonding type rmsd covalent geometry : bond 0.00248 (24058) covalent geometry : angle 0.61074 (32622) hydrogen bonds : bond 0.02866 ( 1128) hydrogen bonds : angle 4.52136 ( 3114) Misc. bond : bond 0.00097 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8514 (tpp) cc_final: 0.8040 (tpp) REVERT: A 47 MET cc_start: 0.5463 (ptt) cc_final: 0.5222 (ptt) REVERT: A 82 MET cc_start: 0.9454 (tpt) cc_final: 0.8942 (tpt) REVERT: A 119 MET cc_start: 0.9713 (ttp) cc_final: 0.9036 (tmm) REVERT: A 123 MET cc_start: 0.9595 (mmp) cc_final: 0.9224 (mmm) REVERT: A 132 MET cc_start: 0.9302 (tmm) cc_final: 0.8851 (tpt) REVERT: A 269 MET cc_start: 0.8906 (mtp) cc_final: 0.8555 (mtp) REVERT: A 305 MET cc_start: 0.8813 (mmm) cc_final: 0.8498 (mmm) REVERT: B 44 MET cc_start: 0.4801 (pmm) cc_final: 0.3886 (pmm) REVERT: B 82 MET cc_start: 0.8899 (ttm) cc_final: 0.8529 (ttm) REVERT: B 123 MET cc_start: 0.9062 (mmm) cc_final: 0.8738 (mmm) REVERT: B 227 MET cc_start: 0.9052 (mmm) cc_final: 0.8744 (mmm) REVERT: B 305 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8599 (mmm) REVERT: B 355 MET cc_start: 0.8926 (mtp) cc_final: 0.8316 (mmm) REVERT: C 47 MET cc_start: 0.7653 (ptp) cc_final: 0.7418 (ptp) REVERT: C 82 MET cc_start: 0.8834 (tpt) cc_final: 0.8456 (tpt) REVERT: C 119 MET cc_start: 0.9316 (ptp) cc_final: 0.9029 (ptp) REVERT: C 132 MET cc_start: 0.9564 (tmm) cc_final: 0.9331 (tmm) REVERT: C 190 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (tpp) REVERT: C 227 MET cc_start: 0.8598 (tpp) cc_final: 0.8293 (mmm) REVERT: C 283 MET cc_start: 0.8858 (mmm) cc_final: 0.8524 (mmm) REVERT: C 305 MET cc_start: 0.8186 (mmt) cc_final: 0.7904 (mmm) REVERT: C 313 MET cc_start: 0.9201 (mmm) cc_final: 0.8980 (mmm) REVERT: C 325 MET cc_start: 0.8437 (mmm) cc_final: 0.8039 (tmm) REVERT: C 355 MET cc_start: 0.9238 (mtp) cc_final: 0.8948 (mtp) REVERT: D 44 MET cc_start: 0.8998 (mmm) cc_final: 0.8545 (mmm) REVERT: D 47 MET cc_start: 0.6709 (ptm) cc_final: 0.5713 (ppp) REVERT: D 82 MET cc_start: 0.8911 (tpt) cc_final: 0.8560 (tpt) REVERT: D 132 MET cc_start: 0.8474 (ppp) cc_final: 0.8220 (ppp) REVERT: D 227 MET cc_start: 0.9232 (mmm) cc_final: 0.8918 (mmm) REVERT: D 305 MET cc_start: 0.8766 (mmm) cc_final: 0.8444 (mmm) REVERT: D 325 MET cc_start: 0.9095 (mmt) cc_final: 0.8305 (mmm) REVERT: E 82 MET cc_start: 0.9371 (tpt) cc_final: 0.8659 (tpp) REVERT: E 190 MET cc_start: 0.9055 (tmm) cc_final: 0.8758 (tmm) REVERT: E 283 MET cc_start: 0.9255 (mmm) cc_final: 0.8915 (mmm) REVERT: E 299 MET cc_start: 0.8415 (mtm) cc_final: 0.7936 (mmp) REVERT: E 325 MET cc_start: 0.8364 (mmm) cc_final: 0.8018 (mmm) REVERT: F 82 MET cc_start: 0.9535 (tpt) cc_final: 0.8979 (tpt) REVERT: F 269 MET cc_start: 0.8157 (ttt) cc_final: 0.7896 (ttt) REVERT: F 299 MET cc_start: 0.5802 (ttp) cc_final: 0.5524 (ppp) REVERT: H 694 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8936 (tp30) REVERT: H 812 HIS cc_start: 0.6167 (m90) cc_final: 0.5410 (t70) REVERT: H 913 MET cc_start: 0.3890 (OUTLIER) cc_final: 0.3539 (tpt) REVERT: I 44 MET cc_start: 0.1349 (mpt) cc_final: 0.0978 (mpt) REVERT: I 82 MET cc_start: 0.9421 (mmm) cc_final: 0.9170 (mmm) outliers start: 10 outliers final: 4 residues processed: 139 average time/residue: 0.1527 time to fit residues: 35.3604 Evaluate side-chains 140 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain H residue 913 MET Chi-restraints excluded: chain I residue 176 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 230 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 243 optimal weight: 50.0000 chunk 233 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 297 ASN C 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN E 137 GLN H 640 ASN ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.033726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.022071 restraints weight = 260124.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.022562 restraints weight = 177499.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.022910 restraints weight = 137477.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.023147 restraints weight = 113483.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.023292 restraints weight = 99573.492| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 24063 Z= 0.324 Angle : 0.822 10.893 32622 Z= 0.409 Chirality : 0.045 0.210 3636 Planarity : 0.005 0.064 4179 Dihedral : 9.251 170.484 3330 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.99 % Allowed : 9.18 % Favored : 89.83 % 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: 2941 helix: 0.46 (0.14), residues: 1319 sheet: -0.34 (0.24), residues: 483 loop : 0.13 (0.20), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.023 0.002 TYR D 306 PHE 0.016 0.002 PHE E 200 TRP 0.018 0.002 TRP F 79 HIS 0.014 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00652 (24058) covalent geometry : angle 0.82164 (32622) hydrogen bonds : bond 0.03908 ( 1128) hydrogen bonds : angle 5.16023 ( 3114) Misc. bond : bond 0.00150 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8555 (tpp) cc_final: 0.8281 (tpp) REVERT: A 82 MET cc_start: 0.9562 (tpt) cc_final: 0.9058 (tpt) REVERT: A 119 MET cc_start: 0.9758 (ttp) cc_final: 0.9257 (tmm) REVERT: A 123 MET cc_start: 0.9738 (mmp) cc_final: 0.9452 (mmm) REVERT: A 132 MET cc_start: 0.9471 (tmm) cc_final: 0.9174 (tmm) REVERT: A 305 MET cc_start: 0.8795 (mmm) cc_final: 0.8467 (mmm) REVERT: B 123 MET cc_start: 0.9219 (mmm) cc_final: 0.8927 (mmm) REVERT: B 305 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8707 (mmm) REVERT: B 355 MET cc_start: 0.8917 (mtp) cc_final: 0.8211 (tmm) REVERT: C 82 MET cc_start: 0.8916 (tpt) cc_final: 0.8519 (tpt) REVERT: C 119 MET cc_start: 0.9400 (ptp) cc_final: 0.9063 (ptp) REVERT: C 176 MET cc_start: 0.9135 (mmm) cc_final: 0.8823 (mmt) REVERT: C 190 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8624 (tpt) REVERT: C 227 MET cc_start: 0.8847 (tpp) cc_final: 0.8559 (mmm) REVERT: C 283 MET cc_start: 0.8954 (mmm) cc_final: 0.8611 (mmm) REVERT: C 305 MET cc_start: 0.8124 (mmt) cc_final: 0.7836 (mmm) REVERT: C 325 MET cc_start: 0.8395 (mmm) cc_final: 0.7955 (tmm) REVERT: C 355 MET cc_start: 0.9220 (mtp) cc_final: 0.8940 (mtp) REVERT: D 44 MET cc_start: 0.8965 (mmm) cc_final: 0.8641 (mmm) REVERT: D 82 MET cc_start: 0.8983 (tpt) cc_final: 0.8624 (tpt) REVERT: D 132 MET cc_start: 0.8569 (ppp) cc_final: 0.8340 (ppp) REVERT: D 137 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: D 227 MET cc_start: 0.9226 (mmm) cc_final: 0.8852 (mmm) REVERT: D 263 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8837 (mp10) REVERT: D 305 MET cc_start: 0.8713 (mmm) cc_final: 0.8418 (mmm) REVERT: D 325 MET cc_start: 0.9119 (mmt) cc_final: 0.8222 (mmm) REVERT: E 82 MET cc_start: 0.9367 (tpt) cc_final: 0.8784 (tpp) REVERT: E 190 MET cc_start: 0.9197 (tmm) cc_final: 0.8994 (tmm) REVERT: E 283 MET cc_start: 0.9162 (mmm) cc_final: 0.8804 (mmm) REVERT: E 299 MET cc_start: 0.8375 (mtm) cc_final: 0.7910 (mmp) REVERT: E 305 MET cc_start: 0.9439 (mmt) cc_final: 0.9016 (mmm) REVERT: E 325 MET cc_start: 0.8393 (mmm) cc_final: 0.8019 (mmm) REVERT: F 123 MET cc_start: 0.9289 (tpp) cc_final: 0.8941 (tpp) REVERT: F 299 MET cc_start: 0.6255 (ttp) cc_final: 0.5381 (ppp) REVERT: H 694 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9008 (tp30) REVERT: H 913 MET cc_start: 0.3799 (OUTLIER) cc_final: 0.3264 (tpt) REVERT: I 44 MET cc_start: 0.3399 (mpt) cc_final: 0.2833 (mpt) REVERT: I 82 MET cc_start: 0.9441 (mmm) cc_final: 0.9185 (mmm) REVERT: I 132 MET cc_start: 0.8146 (tpp) cc_final: 0.7871 (tpp) outliers start: 25 outliers final: 9 residues processed: 153 average time/residue: 0.1544 time to fit residues: 38.6961 Evaluate side-chains 144 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain H residue 913 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 24 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.034898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.022977 restraints weight = 261287.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.023467 restraints weight = 175782.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.023776 restraints weight = 132177.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.024061 restraints weight = 109535.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.024294 restraints weight = 96283.808| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24063 Z= 0.128 Angle : 0.654 9.865 32622 Z= 0.310 Chirality : 0.042 0.177 3636 Planarity : 0.004 0.066 4179 Dihedral : 8.699 157.720 3330 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.59 % Allowed : 10.13 % Favored : 89.28 % 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: 0.67 (0.16), residues: 2941 helix: 0.95 (0.14), residues: 1321 sheet: -0.26 (0.24), residues: 483 loop : 0.40 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 116 TYR 0.010 0.001 TYR B 69 PHE 0.011 0.001 PHE B 255 TRP 0.012 0.001 TRP B 79 HIS 0.007 0.001 HIS H 812 Details of bonding type rmsd covalent geometry : bond 0.00280 (24058) covalent geometry : angle 0.65361 (32622) hydrogen bonds : bond 0.03016 ( 1128) hydrogen bonds : angle 4.67485 ( 3114) Misc. bond : bond 0.00105 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8566 (tpp) cc_final: 0.8288 (tpp) REVERT: A 82 MET cc_start: 0.9487 (tpt) cc_final: 0.8985 (tpt) REVERT: A 119 MET cc_start: 0.9717 (ttp) cc_final: 0.9222 (tmm) REVERT: A 123 MET cc_start: 0.9630 (mmp) cc_final: 0.9365 (mmm) REVERT: A 132 MET cc_start: 0.9341 (tmm) cc_final: 0.8992 (tmm) REVERT: A 283 MET cc_start: 0.9310 (mmm) cc_final: 0.9078 (mmm) REVERT: A 305 MET cc_start: 0.8758 (mmm) cc_final: 0.8458 (mmm) REVERT: B 123 MET cc_start: 0.9043 (mmm) cc_final: 0.8712 (mmm) REVERT: B 137 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: B 227 MET cc_start: 0.9208 (tpp) cc_final: 0.8986 (mmm) REVERT: B 269 MET cc_start: 0.9031 (mtp) cc_final: 0.8502 (ptp) REVERT: B 305 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8660 (mmm) REVERT: B 355 MET cc_start: 0.8917 (mtp) cc_final: 0.8248 (tmm) REVERT: C 44 MET cc_start: 0.8576 (mmm) cc_final: 0.8271 (mmp) REVERT: C 47 MET cc_start: 0.7182 (ptp) cc_final: 0.6890 (pmm) REVERT: C 82 MET cc_start: 0.8859 (tpt) cc_final: 0.8464 (tpt) REVERT: C 176 MET cc_start: 0.9146 (mmm) cc_final: 0.8623 (mmt) REVERT: C 227 MET cc_start: 0.8722 (tpp) cc_final: 0.8395 (mmm) REVERT: C 283 MET cc_start: 0.8880 (mmm) cc_final: 0.8646 (mmm) REVERT: C 305 MET cc_start: 0.8155 (mmt) cc_final: 0.7856 (mmm) REVERT: C 325 MET cc_start: 0.8190 (mmm) cc_final: 0.7965 (tmm) REVERT: C 355 MET cc_start: 0.9218 (mtp) cc_final: 0.9005 (mtp) REVERT: D 82 MET cc_start: 0.8863 (tpt) cc_final: 0.8565 (tpt) REVERT: D 137 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: D 227 MET cc_start: 0.9286 (mmm) cc_final: 0.8935 (mmm) REVERT: D 305 MET cc_start: 0.8643 (mmm) cc_final: 0.8310 (mmm) REVERT: D 325 MET cc_start: 0.9175 (mmt) cc_final: 0.8327 (mmm) REVERT: E 82 MET cc_start: 0.9289 (tpt) cc_final: 0.8641 (tpp) REVERT: E 176 MET cc_start: 0.8670 (pmm) cc_final: 0.8040 (pmm) REVERT: E 190 MET cc_start: 0.9190 (tmm) cc_final: 0.8906 (tmm) REVERT: E 283 MET cc_start: 0.9217 (mmm) cc_final: 0.8891 (mmm) REVERT: E 299 MET cc_start: 0.8307 (mtm) cc_final: 0.7943 (mmp) REVERT: E 305 MET cc_start: 0.9434 (mmt) cc_final: 0.9020 (mmm) REVERT: E 325 MET cc_start: 0.8420 (mmm) cc_final: 0.8084 (mmm) REVERT: F 47 MET cc_start: 0.7213 (pmm) cc_final: 0.6584 (pmm) REVERT: F 269 MET cc_start: 0.8224 (ttt) cc_final: 0.7963 (ttt) REVERT: F 299 MET cc_start: 0.6223 (ttp) cc_final: 0.5973 (ppp) REVERT: H 694 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8993 (tp30) REVERT: H 913 MET cc_start: 0.3920 (OUTLIER) cc_final: 0.3551 (tpt) REVERT: I 44 MET cc_start: 0.3299 (mpt) cc_final: 0.3097 (mpp) REVERT: I 82 MET cc_start: 0.9410 (mmm) cc_final: 0.9164 (mmm) REVERT: I 132 MET cc_start: 0.8159 (tpp) cc_final: 0.7788 (tpp) outliers start: 15 outliers final: 4 residues processed: 143 average time/residue: 0.1498 time to fit residues: 35.7000 Evaluate side-chains 140 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain H residue 913 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 130 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 238 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 295 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.034974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.023455 restraints weight = 271274.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.023959 restraints weight = 177432.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.024364 restraints weight = 130143.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.024535 restraints weight = 104140.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.024830 restraints weight = 90711.071| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24063 Z= 0.130 Angle : 0.657 10.978 32622 Z= 0.310 Chirality : 0.042 0.181 3636 Planarity : 0.004 0.069 4179 Dihedral : 8.436 154.926 3330 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.51 % Allowed : 10.44 % Favored : 89.04 % 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: 0.82 (0.16), residues: 2941 helix: 1.06 (0.14), residues: 1328 sheet: -0.24 (0.24), residues: 490 loop : 0.53 (0.21), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.010 0.001 TYR B 143 PHE 0.008 0.001 PHE H 920 TRP 0.012 0.001 TRP C 79 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00283 (24058) covalent geometry : angle 0.65685 (32622) hydrogen bonds : bond 0.02935 ( 1128) hydrogen bonds : angle 4.57668 ( 3114) Misc. bond : bond 0.00099 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8457 (tpp) cc_final: 0.7834 (tpp) REVERT: A 47 MET cc_start: 0.5131 (ptt) cc_final: 0.4714 (ptp) REVERT: A 82 MET cc_start: 0.9363 (tpt) cc_final: 0.8850 (tpt) REVERT: A 119 MET cc_start: 0.9694 (ttp) cc_final: 0.9171 (tmm) REVERT: A 123 MET cc_start: 0.9560 (mmp) cc_final: 0.9335 (mmm) REVERT: A 132 MET cc_start: 0.9222 (tmm) cc_final: 0.8890 (tmm) REVERT: A 305 MET cc_start: 0.8820 (mmm) cc_final: 0.8514 (mmm) REVERT: B 123 MET cc_start: 0.9079 (mmm) cc_final: 0.8736 (mmm) REVERT: B 269 MET cc_start: 0.9025 (mtp) cc_final: 0.8503 (ptp) REVERT: B 305 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8672 (mmm) REVERT: B 355 MET cc_start: 0.8913 (mtp) cc_final: 0.8258 (tmm) REVERT: C 47 MET cc_start: 0.6974 (ptp) cc_final: 0.6516 (pmm) REVERT: C 82 MET cc_start: 0.8771 (tpt) cc_final: 0.8353 (tpt) REVERT: C 176 MET cc_start: 0.9144 (mmm) cc_final: 0.8788 (mmt) REVERT: C 190 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8566 (tpt) REVERT: C 227 MET cc_start: 0.8704 (tpp) cc_final: 0.8392 (mmm) REVERT: C 283 MET cc_start: 0.8893 (mmm) cc_final: 0.8671 (mmm) REVERT: C 305 MET cc_start: 0.8230 (mmt) cc_final: 0.7937 (mmm) REVERT: D 44 MET cc_start: 0.9097 (mmm) cc_final: 0.8705 (mmm) REVERT: D 82 MET cc_start: 0.8809 (tpt) cc_final: 0.8489 (tpt) REVERT: D 305 MET cc_start: 0.8679 (mmm) cc_final: 0.8354 (mmm) REVERT: D 325 MET cc_start: 0.9124 (mmt) cc_final: 0.8284 (mmm) REVERT: E 82 MET cc_start: 0.9244 (tpt) cc_final: 0.8526 (tpt) REVERT: E 176 MET cc_start: 0.8830 (pmm) cc_final: 0.8350 (pmm) REVERT: E 190 MET cc_start: 0.9176 (tmm) cc_final: 0.8824 (tmm) REVERT: E 283 MET cc_start: 0.9233 (mmm) cc_final: 0.8885 (mmm) REVERT: E 299 MET cc_start: 0.8230 (mtm) cc_final: 0.7966 (mmp) REVERT: E 305 MET cc_start: 0.9510 (mmt) cc_final: 0.9165 (mmm) REVERT: E 325 MET cc_start: 0.8459 (mmm) cc_final: 0.8054 (mmm) REVERT: F 47 MET cc_start: 0.7087 (pmm) cc_final: 0.6575 (pmm) REVERT: F 269 MET cc_start: 0.8242 (ttt) cc_final: 0.7995 (ttt) REVERT: F 299 MET cc_start: 0.6276 (ttp) cc_final: 0.5856 (tmm) REVERT: H 913 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.3580 (tpt) REVERT: I 82 MET cc_start: 0.9442 (mmm) cc_final: 0.9178 (mmm) REVERT: I 132 MET cc_start: 0.8261 (tpp) cc_final: 0.8046 (tpp) REVERT: I 299 MET cc_start: 0.1056 (ttp) cc_final: 0.0268 (mmm) outliers start: 13 outliers final: 6 residues processed: 140 average time/residue: 0.1452 time to fit residues: 33.8461 Evaluate side-chains 140 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain H residue 913 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 97 optimal weight: 5.9990 chunk 226 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 275 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 137 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.033224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.021677 restraints weight = 265307.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.022129 restraints weight = 181525.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.022503 restraints weight = 141373.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.022729 restraints weight = 115379.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.022887 restraints weight = 101242.228| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 24063 Z= 0.336 Angle : 0.874 12.493 32622 Z= 0.429 Chirality : 0.046 0.242 3636 Planarity : 0.005 0.088 4179 Dihedral : 8.804 149.512 3330 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.83 % Allowed : 10.96 % Favored : 88.21 % 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: 0.03 (0.16), residues: 2941 helix: 0.38 (0.14), residues: 1319 sheet: -0.56 (0.23), residues: 504 loop : 0.13 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.019 0.002 TYR B 69 PHE 0.022 0.002 PHE E 200 TRP 0.017 0.002 TRP F 79 HIS 0.014 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00678 (24058) covalent geometry : angle 0.87357 (32622) hydrogen bonds : bond 0.03977 ( 1128) hydrogen bonds : angle 5.30561 ( 3114) Misc. bond : bond 0.00156 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8586 (tpp) cc_final: 0.8327 (tpp) REVERT: A 82 MET cc_start: 0.9507 (tpt) cc_final: 0.9028 (tpt) REVERT: A 119 MET cc_start: 0.9732 (ttp) cc_final: 0.9196 (tmm) REVERT: A 123 MET cc_start: 0.9691 (mmp) cc_final: 0.9380 (mmm) REVERT: A 132 MET cc_start: 0.9365 (tmm) cc_final: 0.9129 (tmm) REVERT: A 227 MET cc_start: 0.9437 (ppp) cc_final: 0.9191 (ppp) REVERT: A 305 MET cc_start: 0.8764 (mmm) cc_final: 0.8470 (mmm) REVERT: B 123 MET cc_start: 0.9232 (mmm) cc_final: 0.8921 (mmm) REVERT: B 227 MET cc_start: 0.9289 (tpp) cc_final: 0.9048 (mmm) REVERT: B 305 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: B 355 MET cc_start: 0.8927 (mtp) cc_final: 0.8391 (mmm) REVERT: C 47 MET cc_start: 0.7069 (ptp) cc_final: 0.6835 (pmm) REVERT: C 82 MET cc_start: 0.8923 (tpt) cc_final: 0.8305 (tpt) REVERT: C 137 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8585 (mm-40) REVERT: C 176 MET cc_start: 0.9207 (mmm) cc_final: 0.8845 (mmt) REVERT: C 190 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8622 (tpt) REVERT: C 227 MET cc_start: 0.8861 (tpp) cc_final: 0.8561 (mmm) REVERT: C 283 MET cc_start: 0.8937 (mmm) cc_final: 0.8662 (mmm) REVERT: C 305 MET cc_start: 0.8180 (mmt) cc_final: 0.7906 (mmm) REVERT: C 325 MET cc_start: 0.8509 (mmm) cc_final: 0.8260 (tpp) REVERT: D 44 MET cc_start: 0.9035 (mmm) cc_final: 0.8707 (mmm) REVERT: D 82 MET cc_start: 0.8900 (tpt) cc_final: 0.8540 (tpt) REVERT: D 305 MET cc_start: 0.8623 (mmm) cc_final: 0.8309 (mmm) REVERT: D 325 MET cc_start: 0.9117 (mmt) cc_final: 0.8259 (mmm) REVERT: E 82 MET cc_start: 0.9351 (tpt) cc_final: 0.8768 (tpp) REVERT: E 176 MET cc_start: 0.8962 (pmm) cc_final: 0.8421 (pmm) REVERT: E 283 MET cc_start: 0.9208 (mmm) cc_final: 0.8830 (mmm) REVERT: E 299 MET cc_start: 0.8252 (mtm) cc_final: 0.7959 (mmp) REVERT: E 305 MET cc_start: 0.9438 (mmt) cc_final: 0.8829 (mmm) REVERT: E 325 MET cc_start: 0.8431 (mmm) cc_final: 0.8093 (mmm) REVERT: F 82 MET cc_start: 0.9392 (tpp) cc_final: 0.8951 (tpp) REVERT: F 299 MET cc_start: 0.6663 (ttp) cc_final: 0.5803 (ppp) REVERT: H 913 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.3418 (tpt) REVERT: I 82 MET cc_start: 0.9443 (mmm) cc_final: 0.9135 (mmm) REVERT: I 132 MET cc_start: 0.8344 (tpp) cc_final: 0.8085 (tpp) outliers start: 21 outliers final: 12 residues processed: 147 average time/residue: 0.1518 time to fit residues: 37.2500 Evaluate side-chains 148 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain H residue 913 MET Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 81 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 271 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS E 137 GLN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.034357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.022516 restraints weight = 266335.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.022936 restraints weight = 177605.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.023407 restraints weight = 133141.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.023671 restraints weight = 109228.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.023836 restraints weight = 94719.887| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24063 Z= 0.152 Angle : 0.715 11.771 32622 Z= 0.339 Chirality : 0.044 0.219 3636 Planarity : 0.004 0.069 4179 Dihedral : 8.401 150.202 3330 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.59 % Allowed : 11.27 % Favored : 88.13 % 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: 0.44 (0.16), residues: 2941 helix: 0.76 (0.14), residues: 1321 sheet: -0.46 (0.23), residues: 504 loop : 0.34 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 177 TYR 0.015 0.001 TYR I 337 PHE 0.032 0.001 PHE I 124 TRP 0.016 0.002 TRP F 79 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00325 (24058) covalent geometry : angle 0.71509 (32622) hydrogen bonds : bond 0.03175 ( 1128) hydrogen bonds : angle 4.87784 ( 3114) Misc. bond : bond 0.00122 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8515 (tpp) cc_final: 0.7948 (tpp) REVERT: A 47 MET cc_start: 0.4596 (ptt) cc_final: 0.4232 (ptp) REVERT: A 82 MET cc_start: 0.9482 (tpt) cc_final: 0.8977 (tpt) REVERT: A 119 MET cc_start: 0.9729 (ttp) cc_final: 0.9219 (tmm) REVERT: A 123 MET cc_start: 0.9665 (mmp) cc_final: 0.9409 (mmm) REVERT: A 132 MET cc_start: 0.9341 (tmm) cc_final: 0.9004 (tmm) REVERT: A 227 MET cc_start: 0.9388 (ppp) cc_final: 0.9120 (ppp) REVERT: A 283 MET cc_start: 0.9203 (mmm) cc_final: 0.8958 (mmm) REVERT: A 305 MET cc_start: 0.8775 (mmm) cc_final: 0.8474 (mmm) REVERT: B 123 MET cc_start: 0.9131 (mmm) cc_final: 0.8779 (mmm) REVERT: B 227 MET cc_start: 0.9274 (tpp) cc_final: 0.9011 (mmm) REVERT: B 269 MET cc_start: 0.8969 (mtp) cc_final: 0.8439 (ptp) REVERT: B 305 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8699 (mmm) REVERT: B 355 MET cc_start: 0.8929 (mtp) cc_final: 0.8413 (mmm) REVERT: C 47 MET cc_start: 0.7114 (ptp) cc_final: 0.6747 (pmm) REVERT: C 82 MET cc_start: 0.8867 (tpt) cc_final: 0.8457 (tpt) REVERT: C 176 MET cc_start: 0.9194 (mmm) cc_final: 0.8821 (mmt) REVERT: C 227 MET cc_start: 0.8806 (tpp) cc_final: 0.8445 (mmm) REVERT: C 283 MET cc_start: 0.8858 (mmm) cc_final: 0.8510 (mmm) REVERT: C 305 MET cc_start: 0.8152 (mmt) cc_final: 0.7857 (mmm) REVERT: C 325 MET cc_start: 0.8473 (mmm) cc_final: 0.8179 (tpp) REVERT: D 44 MET cc_start: 0.9045 (mmm) cc_final: 0.8741 (mmm) REVERT: D 82 MET cc_start: 0.8849 (tpt) cc_final: 0.8529 (tpt) REVERT: D 305 MET cc_start: 0.8634 (mmm) cc_final: 0.8307 (mmm) REVERT: D 325 MET cc_start: 0.9150 (mmt) cc_final: 0.8221 (mmm) REVERT: E 47 MET cc_start: 0.5313 (ppp) cc_final: 0.5086 (ppp) REVERT: E 82 MET cc_start: 0.9315 (tpt) cc_final: 0.8667 (tpp) REVERT: E 123 MET cc_start: 0.9369 (mmp) cc_final: 0.9164 (mmp) REVERT: E 176 MET cc_start: 0.8933 (pmm) cc_final: 0.8396 (pmm) REVERT: E 283 MET cc_start: 0.9238 (mmm) cc_final: 0.8903 (mmm) REVERT: E 299 MET cc_start: 0.8210 (mtm) cc_final: 0.7981 (mmp) REVERT: E 305 MET cc_start: 0.9487 (mmt) cc_final: 0.9130 (mmm) REVERT: E 325 MET cc_start: 0.8501 (mmm) cc_final: 0.8154 (mmm) REVERT: E 355 MET cc_start: 0.9310 (ptp) cc_final: 0.9103 (mpp) REVERT: F 161 HIS cc_start: 0.4908 (OUTLIER) cc_final: 0.4553 (p-80) REVERT: F 269 MET cc_start: 0.8281 (ttt) cc_final: 0.7537 (ppp) REVERT: F 299 MET cc_start: 0.6585 (ttp) cc_final: 0.5745 (ppp) REVERT: F 355 MET cc_start: 0.8472 (mpp) cc_final: 0.8123 (pmm) REVERT: H 913 MET cc_start: 0.3932 (OUTLIER) cc_final: 0.3595 (tpt) REVERT: I 82 MET cc_start: 0.9433 (mmm) cc_final: 0.9083 (mmm) REVERT: I 86 TRP cc_start: 0.9118 (m-10) cc_final: 0.8774 (m-90) REVERT: I 132 MET cc_start: 0.8475 (tpp) cc_final: 0.8217 (tpp) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.1485 time to fit residues: 34.7206 Evaluate side-chains 143 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain H residue 913 MET Chi-restraints excluded: chain I residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 131 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 268 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.034670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.023317 restraints weight = 274660.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.023786 restraints weight = 178821.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.024190 restraints weight = 130553.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.024366 restraints weight = 104598.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.024655 restraints weight = 90863.514| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24063 Z= 0.135 Angle : 0.688 11.697 32622 Z= 0.323 Chirality : 0.043 0.207 3636 Planarity : 0.004 0.068 4179 Dihedral : 8.051 144.978 3330 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.47 % Allowed : 11.23 % Favored : 88.29 % 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: 0.71 (0.16), residues: 2941 helix: 0.99 (0.14), residues: 1321 sheet: -0.43 (0.24), residues: 511 loop : 0.54 (0.21), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 177 TYR 0.011 0.001 TYR I 337 PHE 0.025 0.001 PHE I 124 TRP 0.016 0.002 TRP C 356 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00292 (24058) covalent geometry : angle 0.68774 (32622) hydrogen bonds : bond 0.02936 ( 1128) hydrogen bonds : angle 4.68709 ( 3114) Misc. bond : bond 0.00111 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4549.92 seconds wall clock time: 79 minutes 29.98 seconds (4769.98 seconds total)