Starting phenix.real_space_refine on Sat Jan 25 19:08:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azq_44019/01_2025/9azq_44019.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azq_44019/01_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_44019/01_2025/9azq_44019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azq_44019/01_2025/9azq_44019.map" model { file = "/net/cci-nas-00/data/ceres_data/9azq_44019/01_2025/9azq_44019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azq_44019/01_2025/9azq_44019.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 14.77, per 1000 atoms: 0.63 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: 5.78 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.14 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: 9.33 Time building geometry restraints manager: 6.68 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: 3.160 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: 0.040 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.020 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.860 ------------------------------------------------------------------------------- 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 24058 Z= 0.314 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (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 TRP 0.019 0.002 TRP G 569 HIS 0.010 0.001 HIS I 40 PHE 0.027 0.002 PHE B 124 TYR 0.023 0.002 TYR H 705 ARG 0.006 0.001 ARG H 837 *********************** 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 : 2.417 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: 0.9256 (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: 0.4146 time to fit residues: 134.2638 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 : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.3413 r_free = 0.3413 target = 0.036869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.024782 restraints weight = 266603.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.025433 restraints weight = 172122.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.025860 restraints weight = 125038.422| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24058 Z= 0.227 Angle : 0.646 11.489 32622 Z= 0.314 Chirality : 0.042 0.165 3636 Planarity : 0.005 0.068 4179 Dihedral : 11.019 174.711 3330 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.32 % Allowed : 4.00 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2941 helix: -0.13 (0.13), residues: 1335 sheet: -0.48 (0.23), residues: 455 loop : -0.04 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 569 HIS 0.009 0.001 HIS H 703 PHE 0.013 0.001 PHE I 352 TYR 0.012 0.001 TYR I 53 ARG 0.006 0.000 ARG A 116 *********************** 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 153 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 2.912 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: A 44 MET cc_start: 0.8545 (tpp) cc_final: 0.8144 (tpp) REVERT: A 82 MET cc_start: 0.9362 (tpt) cc_final: 0.8801 (tpt) REVERT: A 119 MET cc_start: 0.9671 (ttp) cc_final: 0.8939 (tmm) REVERT: A 123 MET cc_start: 0.9584 (mmp) cc_final: 0.9231 (mmm) REVERT: A 132 MET cc_start: 0.9237 (tmm) cc_final: 0.8835 (tmm) REVERT: A 257 CYS cc_start: 0.9502 (t) cc_final: 0.9227 (t) REVERT: A 269 MET cc_start: 0.8936 (mtp) cc_final: 0.8546 (mtp) REVERT: A 299 MET cc_start: 0.8568 (mtm) cc_final: 0.8037 (ptm) REVERT: B 123 MET cc_start: 0.9082 (mmm) cc_final: 0.8816 (mmm) REVERT: B 227 MET cc_start: 0.9085 (mmm) cc_final: 0.8815 (mmm) REVERT: B 299 MET cc_start: 0.8020 (ptm) cc_final: 0.7683 (ptm) REVERT: B 355 MET cc_start: 0.8949 (mtp) cc_final: 0.8417 (mmm) REVERT: C 44 MET cc_start: 0.8808 (mpp) cc_final: 0.8529 (mmp) REVERT: C 82 MET cc_start: 0.8744 (tpt) cc_final: 0.8234 (tpt) REVERT: C 355 MET cc_start: 0.9429 (mtp) cc_final: 0.9062 (mtp) REVERT: D 47 MET cc_start: 0.6336 (ptm) cc_final: 0.5709 (ppp) REVERT: D 82 MET cc_start: 0.9036 (tpt) cc_final: 0.8628 (tpt) REVERT: D 305 MET cc_start: 0.8894 (mmm) cc_final: 0.8681 (mmm) REVERT: D 325 MET cc_start: 0.9111 (mmt) cc_final: 0.8546 (mmm) REVERT: E 82 MET cc_start: 0.9427 (tpt) cc_final: 0.8836 (tpp) REVERT: E 119 MET cc_start: 0.9216 (ptm) cc_final: 0.8937 (ptt) REVERT: E 299 MET cc_start: 0.8460 (mtm) cc_final: 0.7915 (mmp) REVERT: E 325 MET cc_start: 0.8544 (mmm) cc_final: 0.8138 (mmm) REVERT: F 82 MET cc_start: 0.9532 (tpt) cc_final: 0.9000 (tpt) REVERT: F 269 MET cc_start: 0.8015 (ttt) cc_final: 0.7714 (ttt) REVERT: G 583 MET cc_start: 0.1063 (ttm) cc_final: 0.0699 (mpp) REVERT: H 694 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8843 (tp30) REVERT: H 812 HIS cc_start: 0.7286 (m90) cc_final: 0.6702 (t-170) REVERT: I 47 MET cc_start: 0.4111 (mpp) cc_final: 0.3895 (mpp) REVERT: I 82 MET cc_start: 0.9278 (mmm) cc_final: 0.8996 (mmm) REVERT: I 113 LYS cc_start: 0.8498 (mmtm) cc_final: 0.7990 (tppt) outliers start: 8 outliers final: 4 residues processed: 150 average time/residue: 0.3651 time to fit residues: 88.2183 Evaluate side-chains 141 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 4 optimal weight: 0.0070 chunk 165 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- 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** B 12 ASN D 173 HIS ** H 703 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 = 0.3371 r_free = 0.3371 target = 0.035732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.024025 restraints weight = 268573.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.024517 restraints weight = 174660.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.024877 restraints weight = 127949.812| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24058 Z= 0.279 Angle : 0.680 8.681 32622 Z= 0.331 Chirality : 0.042 0.188 3636 Planarity : 0.004 0.066 4179 Dihedral : 10.157 178.763 3330 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.47 % Allowed : 5.18 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2941 helix: 0.55 (0.14), residues: 1336 sheet: -0.24 (0.24), residues: 455 loop : 0.21 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 79 HIS 0.006 0.001 HIS H 703 PHE 0.014 0.001 PHE E 200 TYR 0.015 0.002 TYR B 69 ARG 0.017 0.001 ARG H 820 *********************** 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 151 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 2.693 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: A 44 MET cc_start: 0.8528 (tpp) cc_final: 0.8030 (tpp) REVERT: A 82 MET cc_start: 0.9325 (tpt) cc_final: 0.8863 (tpt) REVERT: A 119 MET cc_start: 0.9649 (ttp) cc_final: 0.9039 (tmm) REVERT: A 123 MET cc_start: 0.9610 (mmp) cc_final: 0.9269 (mmm) REVERT: A 132 MET cc_start: 0.9287 (tmm) cc_final: 0.9004 (tmm) REVERT: A 257 CYS cc_start: 0.9462 (t) cc_final: 0.9237 (t) REVERT: A 305 MET cc_start: 0.8842 (mmm) cc_final: 0.8520 (mmm) REVERT: B 123 MET cc_start: 0.9123 (mmm) cc_final: 0.8833 (mmm) REVERT: B 227 MET cc_start: 0.9076 (mmm) cc_final: 0.8824 (mmm) REVERT: B 299 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7648 (ptm) REVERT: B 355 MET cc_start: 0.8881 (mtp) cc_final: 0.8322 (mmm) REVERT: C 44 MET cc_start: 0.8740 (mpp) cc_final: 0.8439 (mmp) REVERT: C 82 MET cc_start: 0.8723 (tpt) cc_final: 0.8163 (tpt) REVERT: C 305 MET cc_start: 0.8031 (mmt) cc_final: 0.7656 (mmt) REVERT: C 355 MET cc_start: 0.9348 (mtp) cc_final: 0.9140 (mtp) REVERT: D 82 MET cc_start: 0.8975 (tpt) cc_final: 0.8581 (tpt) REVERT: D 132 MET cc_start: 0.8465 (ppp) cc_final: 0.8083 (ppp) REVERT: D 227 MET cc_start: 0.9065 (mmm) cc_final: 0.8697 (mmm) REVERT: D 305 MET cc_start: 0.8794 (mmm) cc_final: 0.8538 (mmm) REVERT: D 325 MET cc_start: 0.9073 (mmt) cc_final: 0.8332 (mmm) REVERT: E 82 MET cc_start: 0.9418 (tpt) cc_final: 0.8836 (tpp) REVERT: E 299 MET cc_start: 0.8436 (mtm) cc_final: 0.7932 (mmp) REVERT: E 325 MET cc_start: 0.8542 (mmm) cc_final: 0.8112 (mmm) REVERT: F 82 MET cc_start: 0.9531 (tpt) cc_final: 0.8977 (tpt) REVERT: F 269 MET cc_start: 0.8056 (ttt) cc_final: 0.7795 (ttt) REVERT: H 694 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8883 (tp30) REVERT: H 812 HIS cc_start: 0.7031 (m90) cc_final: 0.6384 (t-170) REVERT: I 82 MET cc_start: 0.9413 (mmm) cc_final: 0.9114 (mmm) outliers start: 12 outliers final: 6 residues processed: 146 average time/residue: 0.3754 time to fit residues: 87.5400 Evaluate side-chains 141 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain B 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 44 MET 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 206 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 185 optimal weight: 30.0000 chunk 259 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.035797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.024137 restraints weight = 269808.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.024568 restraints weight = 174677.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.025012 restraints weight = 128471.743| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24058 Z= 0.205 Angle : 0.623 8.580 32622 Z= 0.298 Chirality : 0.042 0.176 3636 Planarity : 0.004 0.062 4179 Dihedral : 9.379 178.787 3330 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.51 % Allowed : 6.53 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2941 helix: 0.94 (0.14), residues: 1335 sheet: -0.34 (0.24), residues: 490 loop : 0.44 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 79 HIS 0.005 0.001 HIS H 703 PHE 0.009 0.001 PHE B 255 TYR 0.015 0.001 TYR B 143 ARG 0.004 0.000 ARG A 116 *********************** 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 146 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 2.818 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: 0.8437 (tpp) cc_final: 0.7956 (tpp) REVERT: A 47 MET cc_start: 0.5249 (ptt) cc_final: 0.4982 (ptp) REVERT: A 82 MET cc_start: 0.9424 (tpt) cc_final: 0.8912 (tpt) REVERT: A 119 MET cc_start: 0.9677 (ttp) cc_final: 0.9088 (tmm) REVERT: A 123 MET cc_start: 0.9610 (mmp) cc_final: 0.9323 (mmm) REVERT: A 132 MET cc_start: 0.9376 (tmm) cc_final: 0.9034 (tmm) REVERT: A 257 CYS cc_start: 0.9491 (t) cc_final: 0.9243 (t) REVERT: A 269 MET cc_start: 0.8866 (mtp) cc_final: 0.8477 (mtp) REVERT: A 305 MET cc_start: 0.8807 (mmm) cc_final: 0.8486 (mmm) REVERT: B 44 MET cc_start: 0.4785 (pmm) cc_final: 0.4296 (pmm) REVERT: B 123 MET cc_start: 0.9243 (mmm) cc_final: 0.8930 (mmm) REVERT: B 227 MET cc_start: 0.9087 (mmm) cc_final: 0.8831 (mmm) REVERT: B 305 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: B 355 MET cc_start: 0.8937 (mtp) cc_final: 0.8313 (mmm) REVERT: C 44 MET cc_start: 0.8657 (mpp) cc_final: 0.8445 (mmp) REVERT: C 82 MET cc_start: 0.8749 (tpt) cc_final: 0.8158 (tpt) REVERT: C 132 MET cc_start: 0.9607 (tmm) cc_final: 0.9404 (tmm) REVERT: C 190 MET cc_start: 0.8913 (tpp) cc_final: 0.8585 (tpt) REVERT: C 227 MET cc_start: 0.8623 (tpp) cc_final: 0.8350 (mmm) REVERT: C 305 MET cc_start: 0.8261 (mmt) cc_final: 0.8038 (mmm) REVERT: C 313 MET cc_start: 0.8957 (mmm) cc_final: 0.8732 (mmm) REVERT: C 355 MET cc_start: 0.9385 (mtp) cc_final: 0.9153 (mtp) REVERT: D 44 MET cc_start: 0.9028 (mmm) cc_final: 0.8384 (mmm) REVERT: D 47 MET cc_start: 0.6816 (ptm) cc_final: 0.5399 (ppp) REVERT: D 82 MET cc_start: 0.9032 (tpt) cc_final: 0.8684 (tpt) REVERT: D 132 MET cc_start: 0.8510 (ppp) cc_final: 0.8183 (ppp) REVERT: D 227 MET cc_start: 0.9214 (mmm) cc_final: 0.8878 (mmm) REVERT: D 305 MET cc_start: 0.8803 (mmm) cc_final: 0.8498 (mmm) REVERT: D 325 MET cc_start: 0.9135 (mmt) cc_final: 0.8342 (mmm) REVERT: E 82 MET cc_start: 0.9447 (tpt) cc_final: 0.8799 (tpt) REVERT: E 115 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8550 (t0) REVERT: E 119 MET cc_start: 0.9138 (ptm) cc_final: 0.8731 (ptt) REVERT: E 190 MET cc_start: 0.8937 (tmm) cc_final: 0.8694 (tmm) REVERT: E 283 MET cc_start: 0.9179 (mmm) cc_final: 0.8824 (mmm) REVERT: E 299 MET cc_start: 0.8554 (mtm) cc_final: 0.7929 (mmp) REVERT: E 305 MET cc_start: 0.9526 (mmm) cc_final: 0.9238 (mmm) REVERT: E 325 MET cc_start: 0.8429 (mmm) cc_final: 0.8045 (mmm) REVERT: F 82 MET cc_start: 0.9551 (tpt) cc_final: 0.8983 (tpt) REVERT: F 269 MET cc_start: 0.8033 (ttt) cc_final: 0.7765 (ttt) REVERT: H 694 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8902 (tp30) REVERT: H 812 HIS cc_start: 0.6829 (m90) cc_final: 0.6157 (t-170) REVERT: H 913 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.3494 (tpt) REVERT: I 82 MET cc_start: 0.9439 (mmm) cc_final: 0.9191 (mmm) outliers start: 13 outliers final: 4 residues processed: 139 average time/residue: 0.3509 time to fit residues: 80.3159 Evaluate side-chains 139 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 41 GLN Chi-restraints excluded: chain H residue 913 MET Chi-restraints excluded: chain I residue 176 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 273 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 263 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 173 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN E 297 ASN H 640 ASN ** H 703 HIS ** 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 = 0.3333 r_free = 0.3333 target = 0.034680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.022748 restraints weight = 262383.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.023204 restraints weight = 178346.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.023530 restraints weight = 134867.653| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24058 Z= 0.298 Angle : 0.696 8.794 32622 Z= 0.340 Chirality : 0.043 0.187 3636 Planarity : 0.004 0.060 4179 Dihedral : 9.047 177.945 3330 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.59 % Allowed : 7.91 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2941 helix: 0.81 (0.14), residues: 1334 sheet: -0.22 (0.24), residues: 476 loop : 0.33 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 79 HIS 0.007 0.001 HIS D 173 PHE 0.014 0.002 PHE E 200 TYR 0.015 0.002 TYR C 337 ARG 0.005 0.000 ARG C 116 *********************** 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 146 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 2.607 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: A 44 MET cc_start: 0.8563 (tpp) cc_final: 0.8326 (tpp) REVERT: A 82 MET cc_start: 0.9486 (tpt) cc_final: 0.8969 (tpt) REVERT: A 119 MET cc_start: 0.9717 (ttp) cc_final: 0.9198 (tmm) REVERT: A 123 MET cc_start: 0.9691 (mmp) cc_final: 0.9412 (mmm) REVERT: A 132 MET cc_start: 0.9466 (tmm) cc_final: 0.9175 (tmm) REVERT: A 257 CYS cc_start: 0.9603 (t) cc_final: 0.9366 (t) REVERT: A 283 MET cc_start: 0.9262 (mmm) cc_final: 0.9049 (mmm) REVERT: B 123 MET cc_start: 0.9178 (mmm) cc_final: 0.8857 (mmm) REVERT: B 227 MET cc_start: 0.9067 (mmm) cc_final: 0.8820 (mmm) REVERT: B 269 MET cc_start: 0.9300 (mtp) cc_final: 0.8886 (ptp) REVERT: B 305 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8706 (mmm) REVERT: B 355 MET cc_start: 0.8937 (mtp) cc_final: 0.8271 (tmm) REVERT: C 82 MET cc_start: 0.8737 (tpt) cc_final: 0.8139 (tpt) REVERT: C 176 MET cc_start: 0.9179 (mmm) cc_final: 0.8825 (mmt) REVERT: C 227 MET cc_start: 0.8762 (tpp) cc_final: 0.8478 (mmm) REVERT: C 305 MET cc_start: 0.8161 (mmt) cc_final: 0.7884 (mmm) REVERT: C 313 MET cc_start: 0.9001 (mmm) cc_final: 0.8737 (mmm) REVERT: D 44 MET cc_start: 0.9019 (mmm) cc_final: 0.8382 (mmm) REVERT: D 82 MET cc_start: 0.8954 (tpt) cc_final: 0.8557 (tpt) REVERT: D 132 MET cc_start: 0.8506 (ppp) cc_final: 0.8265 (ppp) REVERT: D 227 MET cc_start: 0.9239 (mmm) cc_final: 0.8862 (mmm) REVERT: D 305 MET cc_start: 0.8745 (mmm) cc_final: 0.8466 (mmm) REVERT: D 325 MET cc_start: 0.9151 (mmt) cc_final: 0.8382 (mmm) REVERT: E 47 MET cc_start: 0.4841 (ppp) cc_final: 0.4521 (ppp) REVERT: E 82 MET cc_start: 0.9377 (tpt) cc_final: 0.8619 (tpt) REVERT: E 190 MET cc_start: 0.9105 (tmm) cc_final: 0.8824 (tmm) REVERT: E 299 MET cc_start: 0.8375 (mtm) cc_final: 0.7927 (mmp) REVERT: E 305 MET cc_start: 0.9486 (mmm) cc_final: 0.9182 (mmm) REVERT: E 325 MET cc_start: 0.8438 (mmm) cc_final: 0.8030 (mmm) REVERT: F 44 MET cc_start: 0.8131 (mtm) cc_final: 0.7735 (ptt) REVERT: F 123 MET cc_start: 0.9315 (tpp) cc_final: 0.8964 (tpp) REVERT: F 269 MET cc_start: 0.8249 (ttt) cc_final: 0.8023 (ttt) REVERT: F 355 MET cc_start: 0.8504 (mpp) cc_final: 0.8234 (pmm) REVERT: H 694 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8981 (tp30) REVERT: H 812 HIS cc_start: 0.5848 (m90) cc_final: 0.5035 (t-170) REVERT: H 913 MET cc_start: 0.3867 (OUTLIER) cc_final: 0.3389 (tpt) REVERT: I 82 MET cc_start: 0.9424 (mmm) cc_final: 0.9166 (mmm) REVERT: I 132 MET cc_start: 0.8304 (tpp) cc_final: 0.7657 (tpp) outliers start: 15 outliers final: 7 residues processed: 143 average time/residue: 0.3624 time to fit residues: 83.7699 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 : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 116 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.034260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.023008 restraints weight = 281371.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.023365 restraints weight = 181740.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.023782 restraints weight = 133166.886| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24058 Z= 0.329 Angle : 0.728 8.461 32622 Z= 0.354 Chirality : 0.043 0.205 3636 Planarity : 0.004 0.059 4179 Dihedral : 8.987 167.771 3330 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.95 % Allowed : 8.66 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2941 helix: 0.76 (0.14), residues: 1320 sheet: -0.37 (0.24), residues: 483 loop : 0.26 (0.20), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.007 0.002 HIS B 173 PHE 0.014 0.002 PHE B 200 TYR 0.015 0.002 TYR D 306 ARG 0.004 0.000 ARG H 837 *********************** 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 154 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 2.714 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: 0.8470 (tpp) cc_final: 0.8198 (tpp) REVERT: A 82 MET cc_start: 0.9428 (tpt) cc_final: 0.8915 (tpt) REVERT: A 119 MET cc_start: 0.9699 (ttp) cc_final: 0.9205 (tmm) REVERT: A 123 MET cc_start: 0.9633 (mmp) cc_final: 0.9380 (mmm) REVERT: A 132 MET cc_start: 0.9350 (tmm) cc_final: 0.9030 (tmm) REVERT: A 305 MET cc_start: 0.8767 (mmm) cc_final: 0.8327 (mmm) REVERT: B 123 MET cc_start: 0.9145 (mmm) cc_final: 0.8841 (mmm) REVERT: B 137 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: B 227 MET cc_start: 0.9064 (mmm) cc_final: 0.8815 (mmm) REVERT: B 305 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8741 (mmm) REVERT: B 355 MET cc_start: 0.8952 (mtp) cc_final: 0.8284 (tmm) REVERT: C 82 MET cc_start: 0.8722 (tpt) cc_final: 0.8322 (tpt) REVERT: C 176 MET cc_start: 0.9179 (mmm) cc_final: 0.8840 (mmt) REVERT: C 190 MET cc_start: 0.8922 (tpp) cc_final: 0.8594 (tpt) REVERT: C 227 MET cc_start: 0.8797 (tpp) cc_final: 0.8507 (mmm) REVERT: C 305 MET cc_start: 0.8154 (mmt) cc_final: 0.7874 (mmm) REVERT: C 313 MET cc_start: 0.9029 (mmm) cc_final: 0.8758 (mmm) REVERT: C 325 MET cc_start: 0.8299 (mmm) cc_final: 0.7946 (tmm) REVERT: C 355 MET cc_start: 0.9239 (mtp) cc_final: 0.9009 (mtp) REVERT: D 44 MET cc_start: 0.9024 (mmm) cc_final: 0.8783 (mmm) REVERT: D 47 MET cc_start: 0.6717 (ptm) cc_final: 0.6326 (pmm) REVERT: D 82 MET cc_start: 0.8984 (tpt) cc_final: 0.8620 (tpt) REVERT: D 132 MET cc_start: 0.8613 (ppp) cc_final: 0.8365 (ppp) REVERT: D 227 MET cc_start: 0.9291 (mmm) cc_final: 0.8931 (mmm) REVERT: D 263 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8881 (mp10) REVERT: D 283 MET cc_start: 0.9198 (mmm) cc_final: 0.8916 (mmm) REVERT: D 305 MET cc_start: 0.8659 (mmm) cc_final: 0.8356 (mmm) REVERT: D 325 MET cc_start: 0.9160 (mmt) cc_final: 0.8294 (mmm) REVERT: E 47 MET cc_start: 0.4447 (ppp) cc_final: 0.4213 (ppp) REVERT: E 82 MET cc_start: 0.9362 (tpt) cc_final: 0.8727 (tpp) REVERT: E 190 MET cc_start: 0.9107 (tmm) cc_final: 0.8850 (tmm) REVERT: E 283 MET cc_start: 0.9125 (mmm) cc_final: 0.8726 (mmm) REVERT: E 299 MET cc_start: 0.8381 (mtm) cc_final: 0.7978 (mmt) REVERT: E 305 MET cc_start: 0.9510 (mmm) cc_final: 0.9223 (mmm) REVERT: E 325 MET cc_start: 0.8374 (mmm) cc_final: 0.8052 (mmm) REVERT: F 123 MET cc_start: 0.9263 (tpp) cc_final: 0.8949 (tpp) REVERT: F 299 MET cc_start: 0.6072 (ttp) cc_final: 0.5227 (tmm) REVERT: H 694 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9021 (tp30) REVERT: H 913 MET cc_start: 0.4234 (OUTLIER) cc_final: 0.3979 (tpt) REVERT: I 82 MET cc_start: 0.9471 (mmm) cc_final: 0.9211 (mmm) outliers start: 24 outliers final: 10 residues processed: 149 average time/residue: 0.3453 time to fit residues: 84.6367 Evaluate side-chains 142 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 116 ARG 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 43 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 109 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** E 137 GLN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.034746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.023492 restraints weight = 275676.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.023900 restraints weight = 181891.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.024330 restraints weight = 134108.053| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24058 Z= 0.210 Angle : 0.653 9.609 32622 Z= 0.310 Chirality : 0.042 0.178 3636 Planarity : 0.004 0.058 4179 Dihedral : 8.641 155.582 3330 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.67 % Allowed : 9.81 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2941 helix: 1.05 (0.14), residues: 1321 sheet: -0.29 (0.24), residues: 483 loop : 0.41 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.008 0.001 HIS H 812 PHE 0.009 0.001 PHE H 920 TYR 0.011 0.001 TYR B 143 ARG 0.004 0.000 ARG F 177 *********************** 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 149 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 2.810 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: 0.8487 (tpp) cc_final: 0.8208 (tpp) REVERT: A 82 MET cc_start: 0.9474 (tpt) cc_final: 0.8964 (tpt) REVERT: A 119 MET cc_start: 0.9711 (ttp) cc_final: 0.9234 (tmm) REVERT: A 123 MET cc_start: 0.9633 (mmp) cc_final: 0.9367 (mmm) REVERT: A 132 MET cc_start: 0.9377 (tmm) cc_final: 0.9098 (tmm) REVERT: A 305 MET cc_start: 0.8799 (mmm) cc_final: 0.8415 (mmm) REVERT: B 82 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8720 (mtt) REVERT: B 123 MET cc_start: 0.9164 (mmm) cc_final: 0.8819 (mmm) REVERT: B 227 MET cc_start: 0.9072 (mmm) cc_final: 0.8763 (mmm) REVERT: B 305 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8670 (mmm) REVERT: B 355 MET cc_start: 0.8950 (mtp) cc_final: 0.8265 (tmm) REVERT: C 82 MET cc_start: 0.8779 (tpt) cc_final: 0.8384 (tpt) REVERT: C 176 MET cc_start: 0.9142 (mmm) cc_final: 0.8774 (mmt) REVERT: C 190 MET cc_start: 0.8970 (tpp) cc_final: 0.8604 (tpt) REVERT: C 227 MET cc_start: 0.8750 (tpp) cc_final: 0.8411 (mmm) REVERT: C 305 MET cc_start: 0.8248 (mmt) cc_final: 0.7941 (mmm) REVERT: C 313 MET cc_start: 0.9149 (mmm) cc_final: 0.8856 (mmm) REVERT: C 325 MET cc_start: 0.8257 (mmm) cc_final: 0.7996 (tmm) REVERT: C 355 MET cc_start: 0.9268 (mtp) cc_final: 0.9028 (mtp) REVERT: D 44 MET cc_start: 0.9057 (mmm) cc_final: 0.8600 (mmm) REVERT: D 47 MET cc_start: 0.6954 (ptm) cc_final: 0.6112 (ppp) REVERT: D 82 MET cc_start: 0.9019 (tpt) cc_final: 0.8618 (tpt) REVERT: D 227 MET cc_start: 0.9354 (mmm) cc_final: 0.9145 (mmm) REVERT: D 283 MET cc_start: 0.9287 (mmm) cc_final: 0.9058 (mmm) REVERT: D 305 MET cc_start: 0.8609 (mmm) cc_final: 0.8296 (mmm) REVERT: D 325 MET cc_start: 0.9213 (mmt) cc_final: 0.8341 (mmm) REVERT: E 47 MET cc_start: 0.4623 (ppp) cc_final: 0.4332 (ppp) REVERT: E 82 MET cc_start: 0.9362 (tpt) cc_final: 0.8706 (tpp) REVERT: E 176 MET cc_start: 0.8622 (pmm) cc_final: 0.8098 (pmm) REVERT: E 190 MET cc_start: 0.9168 (tmm) cc_final: 0.8868 (tmm) REVERT: E 283 MET cc_start: 0.9196 (mmm) cc_final: 0.8796 (mmm) REVERT: E 299 MET cc_start: 0.8472 (mtm) cc_final: 0.8056 (mmt) REVERT: E 305 MET cc_start: 0.9504 (mmm) cc_final: 0.9194 (mmm) REVERT: E 325 MET cc_start: 0.8426 (mmm) cc_final: 0.8056 (mmm) REVERT: F 82 MET cc_start: 0.9433 (mmm) cc_final: 0.9157 (mmm) REVERT: F 269 MET cc_start: 0.8289 (ttt) cc_final: 0.8034 (ttt) REVERT: F 299 MET cc_start: 0.6444 (ttp) cc_final: 0.5894 (tmm) REVERT: F 355 MET cc_start: 0.8387 (mpp) cc_final: 0.8086 (pmm) REVERT: H 694 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9079 (tp30) REVERT: H 913 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3503 (tpt) REVERT: I 82 MET cc_start: 0.9448 (mmm) cc_final: 0.9178 (mmm) outliers start: 17 outliers final: 7 residues processed: 144 average time/residue: 0.3532 time to fit residues: 83.7682 Evaluate side-chains 140 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 82 MET 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 351 THR 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 185 optimal weight: 30.0000 chunk 126 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.034941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.023337 restraints weight = 274092.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.023824 restraints weight = 178818.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.024323 restraints weight = 132196.344| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24058 Z= 0.188 Angle : 0.651 10.688 32622 Z= 0.308 Chirality : 0.042 0.172 3636 Planarity : 0.003 0.058 4179 Dihedral : 8.351 154.616 3330 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 0.51 % Allowed : 10.32 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2941 helix: 1.14 (0.15), residues: 1328 sheet: -0.41 (0.23), residues: 511 loop : 0.64 (0.21), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 79 HIS 0.004 0.001 HIS E 88 PHE 0.009 0.001 PHE H 920 TYR 0.011 0.001 TYR B 143 ARG 0.003 0.000 ARG A 116 *********************** 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 145 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 3.101 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: 0.8524 (tpp) cc_final: 0.8210 (tpp) REVERT: A 82 MET cc_start: 0.9398 (tpt) cc_final: 0.8904 (tpt) REVERT: A 119 MET cc_start: 0.9685 (ttp) cc_final: 0.9223 (tmm) REVERT: A 123 MET cc_start: 0.9561 (mmp) cc_final: 0.9335 (mmm) REVERT: A 132 MET cc_start: 0.9299 (tmm) cc_final: 0.9027 (tmm) REVERT: A 305 MET cc_start: 0.8809 (mmm) cc_final: 0.8470 (mmm) REVERT: B 82 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8601 (mtt) REVERT: B 123 MET cc_start: 0.9068 (mmm) cc_final: 0.8708 (mmm) REVERT: B 227 MET cc_start: 0.9038 (mmm) cc_final: 0.8733 (mmm) REVERT: B 305 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8714 (mmm) REVERT: B 355 MET cc_start: 0.8915 (mtp) cc_final: 0.8253 (tmm) REVERT: C 82 MET cc_start: 0.8725 (tpt) cc_final: 0.8322 (tpt) REVERT: C 176 MET cc_start: 0.9154 (mmm) cc_final: 0.8799 (mmt) REVERT: C 190 MET cc_start: 0.8922 (tpp) cc_final: 0.8565 (tpt) REVERT: C 227 MET cc_start: 0.8722 (tpp) cc_final: 0.8404 (mmm) REVERT: C 305 MET cc_start: 0.8270 (mmt) cc_final: 0.7974 (mmm) REVERT: C 313 MET cc_start: 0.9073 (mmm) cc_final: 0.8780 (mmm) REVERT: D 44 MET cc_start: 0.8963 (mmm) cc_final: 0.8500 (mmm) REVERT: D 47 MET cc_start: 0.6961 (ptm) cc_final: 0.6074 (ppp) REVERT: D 82 MET cc_start: 0.8896 (tpt) cc_final: 0.8535 (tpt) REVERT: D 132 MET cc_start: 0.8568 (ppp) cc_final: 0.8357 (ppp) REVERT: D 227 MET cc_start: 0.9357 (mmm) cc_final: 0.9103 (mmm) REVERT: D 283 MET cc_start: 0.9360 (mmm) cc_final: 0.9125 (mmm) REVERT: D 305 MET cc_start: 0.8644 (mmm) cc_final: 0.8328 (mmm) REVERT: D 325 MET cc_start: 0.9123 (mmt) cc_final: 0.8242 (mmm) REVERT: E 47 MET cc_start: 0.4291 (ppp) cc_final: 0.4013 (ppp) REVERT: E 82 MET cc_start: 0.9278 (tpt) cc_final: 0.8667 (tpp) REVERT: E 176 MET cc_start: 0.8866 (pmm) cc_final: 0.8390 (pmm) REVERT: E 190 MET cc_start: 0.9097 (tmm) cc_final: 0.8775 (tmm) REVERT: E 283 MET cc_start: 0.9229 (mmm) cc_final: 0.8829 (mmm) REVERT: E 299 MET cc_start: 0.8269 (mtm) cc_final: 0.8061 (mmp) REVERT: E 305 MET cc_start: 0.9464 (mmm) cc_final: 0.9236 (mmm) REVERT: E 325 MET cc_start: 0.8429 (mmm) cc_final: 0.8057 (mmm) REVERT: F 82 MET cc_start: 0.9456 (mmm) cc_final: 0.9213 (mmm) REVERT: F 269 MET cc_start: 0.8318 (ttt) cc_final: 0.8064 (ttt) REVERT: F 299 MET cc_start: 0.6485 (ttp) cc_final: 0.5982 (tmm) REVERT: H 913 MET cc_start: 0.4143 (OUTLIER) cc_final: 0.3876 (tpt) REVERT: I 82 MET cc_start: 0.9440 (mmm) cc_final: 0.9023 (mmm) REVERT: I 86 TRP cc_start: 0.9125 (m-10) cc_final: 0.8778 (m-90) REVERT: I 132 MET cc_start: 0.8295 (tpp) cc_final: 0.7736 (tpp) REVERT: I 299 MET cc_start: 0.1356 (ttp) cc_final: 0.0529 (mmm) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 0.3580 time to fit residues: 82.9597 Evaluate side-chains 140 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 82 MET 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 351 THR 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 7 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 177 optimal weight: 9.9990 chunk 223 optimal weight: 0.0000 chunk 196 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 187 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.035650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.023576 restraints weight = 264424.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.024038 restraints weight = 175827.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.024557 restraints weight = 132462.674| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24058 Z= 0.150 Angle : 0.647 12.180 32622 Z= 0.302 Chirality : 0.043 0.180 3636 Planarity : 0.003 0.058 4179 Dihedral : 8.041 153.314 3330 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.47 % Allowed : 10.36 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2941 helix: 1.28 (0.15), residues: 1328 sheet: -0.24 (0.24), residues: 483 loop : 0.71 (0.21), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 79 HIS 0.003 0.001 HIS E 88 PHE 0.020 0.001 PHE I 124 TYR 0.015 0.001 TYR C 240 ARG 0.003 0.000 ARG I 177 *********************** 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 145 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 2.924 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 82 MET cc_start: 0.9456 (tpt) cc_final: 0.8953 (tpt) REVERT: A 119 MET cc_start: 0.9730 (ttp) cc_final: 0.9251 (tmm) REVERT: A 123 MET cc_start: 0.9634 (mmp) cc_final: 0.9347 (mmm) REVERT: A 132 MET cc_start: 0.9360 (tmm) cc_final: 0.9003 (tmm) REVERT: A 227 MET cc_start: 0.9353 (ppp) cc_final: 0.9072 (ppp) REVERT: A 305 MET cc_start: 0.8765 (mmm) cc_final: 0.8422 (mmm) REVERT: B 82 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8551 (mtt) REVERT: B 123 MET cc_start: 0.9065 (mmm) cc_final: 0.8666 (mmm) REVERT: B 227 MET cc_start: 0.9033 (mmm) cc_final: 0.8726 (mmm) REVERT: B 305 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8642 (mmp) REVERT: B 355 MET cc_start: 0.8906 (mtp) cc_final: 0.8259 (mmm) REVERT: C 82 MET cc_start: 0.8787 (tpt) cc_final: 0.8375 (tpt) REVERT: C 176 MET cc_start: 0.9131 (mmm) cc_final: 0.8753 (mmt) REVERT: C 190 MET cc_start: 0.8931 (tpp) cc_final: 0.8586 (tpt) REVERT: C 227 MET cc_start: 0.8697 (tpp) cc_final: 0.8340 (mmm) REVERT: C 305 MET cc_start: 0.8342 (mmt) cc_final: 0.8071 (mmm) REVERT: C 313 MET cc_start: 0.9147 (mmm) cc_final: 0.8813 (mmm) REVERT: D 44 MET cc_start: 0.9022 (mmm) cc_final: 0.8497 (mmm) REVERT: D 47 MET cc_start: 0.7065 (ptm) cc_final: 0.6117 (ppp) REVERT: D 82 MET cc_start: 0.8902 (tpt) cc_final: 0.8598 (tpt) REVERT: D 227 MET cc_start: 0.9378 (mmm) cc_final: 0.9119 (mmm) REVERT: D 305 MET cc_start: 0.8626 (mmm) cc_final: 0.8285 (mmm) REVERT: D 325 MET cc_start: 0.9092 (mmt) cc_final: 0.8343 (mmm) REVERT: E 47 MET cc_start: 0.4333 (ppp) cc_final: 0.3995 (ppp) REVERT: E 82 MET cc_start: 0.9305 (tpt) cc_final: 0.8676 (tpp) REVERT: E 176 MET cc_start: 0.8857 (pmm) cc_final: 0.8414 (pmm) REVERT: E 190 MET cc_start: 0.9170 (tmm) cc_final: 0.8823 (tmm) REVERT: E 283 MET cc_start: 0.9320 (mmm) cc_final: 0.8947 (mmm) REVERT: E 299 MET cc_start: 0.8364 (mtm) cc_final: 0.8099 (mmp) REVERT: E 305 MET cc_start: 0.9482 (mmm) cc_final: 0.9265 (mmm) REVERT: E 325 MET cc_start: 0.8445 (mmm) cc_final: 0.8074 (mmm) REVERT: F 82 MET cc_start: 0.9482 (mmm) cc_final: 0.9228 (mmm) REVERT: F 269 MET cc_start: 0.8389 (ttt) cc_final: 0.8138 (ttt) REVERT: F 299 MET cc_start: 0.6449 (ttp) cc_final: 0.5946 (tmm) REVERT: F 355 MET cc_start: 0.8205 (mpp) cc_final: 0.7947 (pmm) REVERT: H 913 MET cc_start: 0.4059 (OUTLIER) cc_final: 0.3771 (tpt) REVERT: I 82 MET cc_start: 0.9420 (mmm) cc_final: 0.9172 (mmm) REVERT: I 86 TRP cc_start: 0.9092 (m-10) cc_final: 0.8716 (m-10) outliers start: 12 outliers final: 5 residues processed: 141 average time/residue: 0.3778 time to fit residues: 86.5673 Evaluate side-chains 141 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain B residue 82 MET 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 H residue 913 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 201 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.035334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.023917 restraints weight = 272441.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.024307 restraints weight = 178217.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.024703 restraints weight = 130216.684| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24058 Z= 0.178 Angle : 0.672 15.442 32622 Z= 0.314 Chirality : 0.042 0.201 3636 Planarity : 0.003 0.058 4179 Dihedral : 7.941 151.719 3330 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.40 % Allowed : 10.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2941 helix: 1.26 (0.15), residues: 1328 sheet: -0.20 (0.24), residues: 483 loop : 0.75 (0.21), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 79 HIS 0.004 0.001 HIS E 88 PHE 0.020 0.001 PHE I 124 TYR 0.010 0.001 TYR B 143 ARG 0.003 0.000 ARG I 177 ********************** 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 143 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 2.501 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 82 MET cc_start: 0.9434 (tpt) cc_final: 0.8926 (tpt) REVERT: A 119 MET cc_start: 0.9732 (ttp) cc_final: 0.9264 (tmm) REVERT: A 123 MET cc_start: 0.9635 (mmp) cc_final: 0.9378 (mmm) REVERT: A 132 MET cc_start: 0.9341 (tmm) cc_final: 0.9066 (tmm) REVERT: A 227 MET cc_start: 0.9384 (ppp) cc_final: 0.9157 (ppp) REVERT: A 305 MET cc_start: 0.8791 (mmm) cc_final: 0.8453 (mmm) REVERT: B 82 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8631 (mtt) REVERT: B 123 MET cc_start: 0.9152 (mmm) cc_final: 0.8746 (mmm) REVERT: B 190 MET cc_start: 0.9448 (ttt) cc_final: 0.9243 (tpt) REVERT: B 227 MET cc_start: 0.9029 (mmm) cc_final: 0.8728 (mmm) REVERT: B 269 MET cc_start: 0.8948 (ptp) cc_final: 0.8728 (pmm) REVERT: B 305 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8675 (mmm) REVERT: B 355 MET cc_start: 0.8927 (mtp) cc_final: 0.8227 (tmm) REVERT: C 82 MET cc_start: 0.8793 (tpt) cc_final: 0.8363 (tpt) REVERT: C 176 MET cc_start: 0.9132 (mmm) cc_final: 0.8729 (mmt) REVERT: C 190 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8611 (tpt) REVERT: C 227 MET cc_start: 0.8701 (tpp) cc_final: 0.8366 (mmm) REVERT: C 305 MET cc_start: 0.8379 (mmt) cc_final: 0.8102 (mmm) REVERT: C 313 MET cc_start: 0.9198 (mmm) cc_final: 0.8843 (mmm) REVERT: D 44 MET cc_start: 0.9100 (mmm) cc_final: 0.8535 (mmm) REVERT: D 47 MET cc_start: 0.7018 (ptm) cc_final: 0.6050 (ppp) REVERT: D 82 MET cc_start: 0.8957 (tpt) cc_final: 0.8634 (tpt) REVERT: D 227 MET cc_start: 0.9383 (mmm) cc_final: 0.9024 (mmm) REVERT: D 305 MET cc_start: 0.8643 (mmm) cc_final: 0.8310 (mmm) REVERT: D 325 MET cc_start: 0.9093 (mmt) cc_final: 0.8304 (mmm) REVERT: E 47 MET cc_start: 0.4163 (ppp) cc_final: 0.3846 (ppp) REVERT: E 82 MET cc_start: 0.9321 (tpt) cc_final: 0.8656 (tpp) REVERT: E 176 MET cc_start: 0.8845 (pmm) cc_final: 0.8408 (pmm) REVERT: E 190 MET cc_start: 0.9197 (tmm) cc_final: 0.8868 (tmm) REVERT: E 283 MET cc_start: 0.9345 (mmm) cc_final: 0.8959 (mmm) REVERT: E 299 MET cc_start: 0.8452 (mtm) cc_final: 0.8117 (mmp) REVERT: E 305 MET cc_start: 0.9480 (mmm) cc_final: 0.9257 (mmm) REVERT: E 325 MET cc_start: 0.8468 (mmm) cc_final: 0.8049 (mmm) REVERT: F 47 MET cc_start: 0.6594 (pmm) cc_final: 0.5833 (pmm) REVERT: F 82 MET cc_start: 0.9535 (mmm) cc_final: 0.9294 (mmm) REVERT: F 269 MET cc_start: 0.8420 (ttt) cc_final: 0.8171 (ttt) REVERT: F 299 MET cc_start: 0.6472 (ttp) cc_final: 0.5939 (tmm) REVERT: F 355 MET cc_start: 0.8248 (mpp) cc_final: 0.7986 (pmm) REVERT: I 82 MET cc_start: 0.9445 (mmm) cc_final: 0.9190 (mmm) REVERT: I 86 TRP cc_start: 0.9124 (m-10) cc_final: 0.8735 (m-10) outliers start: 10 outliers final: 6 residues processed: 139 average time/residue: 0.3613 time to fit residues: 81.8204 Evaluate side-chains 141 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain B residue 82 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 51 optimal weight: 8.9990 chunk 272 optimal weight: 40.0000 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.034811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.023567 restraints weight = 274381.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.023946 restraints weight = 178428.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.024353 restraints weight = 129997.889| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24058 Z= 0.221 Angle : 0.687 11.690 32622 Z= 0.326 Chirality : 0.042 0.187 3636 Planarity : 0.004 0.058 4179 Dihedral : 7.947 151.629 3330 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.51 % Allowed : 10.56 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 2941 helix: 1.18 (0.15), residues: 1328 sheet: -0.13 (0.24), residues: 490 loop : 0.72 (0.21), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 79 HIS 0.005 0.001 HIS E 88 PHE 0.017 0.001 PHE I 124 TYR 0.010 0.001 TYR I 337 ARG 0.003 0.000 ARG I 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7534.21 seconds wall clock time: 137 minutes 35.41 seconds (8255.41 seconds total)