Starting phenix.real_space_refine on Sat Jan 25 12:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8viz_43274/01_2025/8viz_43274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8viz_43274/01_2025/8viz_43274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8viz_43274/01_2025/8viz_43274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8viz_43274/01_2025/8viz_43274.map" model { file = "/net/cci-nas-00/data/ceres_data/8viz_43274/01_2025/8viz_43274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8viz_43274/01_2025/8viz_43274.cif" } resolution = 2.63 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= 0.002 sd= 0.009 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 Ca 14 9.91 5 P 13 5.49 5 S 142 5.16 5 C 14667 2.51 5 N 3955 2.21 5 O 4483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23274 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2934 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 5615 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 720, 5613 Classifications: {'peptide': 720} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} Conformer: "B" Number of residues, atoms: 720, 5613 Classifications: {'peptide': 720} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} bond proxies already assigned to first conformer: 5739 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 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: {' CA': 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: {' CA': 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: {' CA': 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: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' CA': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 17.68, per 1000 atoms: 0.76 Number of scatterers: 23274 At special positions: 0 Unit cell: (111.24, 136.08, 239.76, 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) Ca 14 19.99 S 142 16.00 P 13 15.00 O 4483 8.00 N 3955 7.00 C 14667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 3.8 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 43 sheets defined 42.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.520A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.593A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.824A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.923A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.683A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.746A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.536A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.564A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.125A 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 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.722A pdb=" N ILE A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.458A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.755A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.553A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.553A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.362A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.561A 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 197 Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.931A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.554A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.712A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.953A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.340A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.876A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.026A 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: 3.568A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.725A 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 126 removed outlier: 4.194A 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 172 through 175 removed outlier: 3.570A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' 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: 3.988A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.847A 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 257 removed outlier: 3.726A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.608A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.640A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.539A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.819A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (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: 3.755A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.566A 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 126 removed outlier: 4.140A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.511A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.775A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.077A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.702A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.604A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.193A 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 348 removed outlier: 3.691A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.663A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.615A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.802A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.950A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 4.060A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 removed outlier: 3.658A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.594A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.344A 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 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.625A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.515A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.793A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.718A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.922A pdb=" N THR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 removed outlier: 3.502A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.842A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.576A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.302A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 35 removed outlier: 3.655A pdb=" N LYS G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 94 through 112 Processing helix chain 'G' and resid 127 through 134 removed outlier: 4.318A pdb=" N PHE G 134 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 183 Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 240 through 248 Processing helix chain 'G' and resid 261 through 269 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 324 through 342 removed outlier: 3.889A pdb=" N ILE G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR G 340 " --> pdb=" O SER G 336 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 366 removed outlier: 3.790A pdb=" N PHE G 365 " --> pdb=" O PHE G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 400 removed outlier: 3.731A pdb=" N THR G 399 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 489 Processing helix chain 'G' and resid 505 through 510 removed outlier: 3.529A pdb=" N MET G 509 " --> pdb=" O PRO G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 513 No H-bonds generated for 'chain 'G' and resid 511 through 513' Processing helix chain 'G' and resid 557 through 561 removed outlier: 3.773A pdb=" N LEU G 561 " --> pdb=" O ALA G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 599 Processing helix chain 'G' and resid 611 through 619 removed outlier: 3.633A pdb=" N TRP G 615 " --> pdb=" O PRO G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 632 Processing helix chain 'G' and resid 689 through 706 Processing helix chain 'G' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.876A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (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: 6.314A 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: 3.551A 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: 4.101A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN B 12 " --> 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 176 through 178 removed outlier: 6.567A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.605A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (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: 6.761A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (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 176 through 178 Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.825A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (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: 6.564A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (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 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.208A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (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: 6.601A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (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 71 through 72 removed outlier: 3.719A pdb=" N ILE E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.259A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 6.357A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.141A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 53 removed outlier: 4.983A pdb=" N ALA G 67 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N VAL G 117 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR G 83 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N HIS G 119 " --> pdb=" O TYR G 83 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU G 85 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU G 121 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR G 87 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 61 through 63 removed outlier: 6.808A pdb=" N PHE G 62 " --> pdb=" O LYS G 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 172 through 175 Processing sheet with id=AE4, first strand: chain 'G' and resid 285 through 289 removed outlier: 6.731A pdb=" N LEU G 273 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE G 315 " --> pdb=" O SER G 351 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU G 353 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL G 317 " --> pdb=" O LEU G 353 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 429 through 432 removed outlier: 3.945A pdb=" N GLN G 419 " --> pdb=" O ASN G 452 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER G 446 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN G 461 " --> pdb=" O VAL G 495 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER G 497 " --> pdb=" O GLN G 461 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE G 463 " --> pdb=" O SER G 497 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL G 499 " --> pdb=" O ILE G 463 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN G 465 " --> pdb=" O VAL G 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 440 through 442 removed outlier: 7.052A pdb=" N PHE G 441 " --> pdb=" O TYR G 520 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU G 538 " --> pdb=" O VAL G 554 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA G 566 " --> pdb=" O VAL G 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 653 through 656 removed outlier: 6.748A pdb=" N VAL G 680 " --> pdb=" O THR G 718 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL G 720 " --> pdb=" O VAL G 680 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL G 682 " --> pdb=" O VAL G 720 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2691 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: 9.90 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6704 1.34 - 1.45: 4185 1.45 - 1.57: 12626 1.57 - 1.69: 18 1.69 - 1.81: 249 Bond restraints: 23782 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" CG1 ILE D 329 " pdb=" CD1 ILE D 329 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.35e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 23777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 31394 2.95 - 5.90: 772 5.90 - 8.86: 88 8.86 - 11.81: 14 11.81 - 14.76: 1 Bond angle restraints: 32269 Sorted by residual: angle pdb=" N GLU B 364 " pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " ideal model delta sigma weight residual 110.40 119.35 -8.95 1.63e+00 3.76e-01 3.02e+01 angle pdb=" C GLY G 457 " pdb=" N ARG G 458 " pdb=" CA ARG G 458 " ideal model delta sigma weight residual 122.08 130.03 -7.95 1.47e+00 4.63e-01 2.92e+01 angle pdb=" C THR G 676 " pdb=" N TRP G 677 " pdb=" CA TRP G 677 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.51e+01 angle pdb=" N GLU D 117 " pdb=" CA GLU D 117 " pdb=" CB GLU D 117 " ideal model delta sigma weight residual 110.16 117.46 -7.30 1.48e+00 4.57e-01 2.44e+01 angle pdb=" CA GLU D 117 " pdb=" CB GLU D 117 " pdb=" CG GLU D 117 " ideal model delta sigma weight residual 114.10 123.87 -9.77 2.00e+00 2.50e-01 2.39e+01 ... (remaining 32264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 12973 17.44 - 34.87: 1088 34.87 - 52.31: 172 52.31 - 69.75: 32 69.75 - 87.18: 20 Dihedral angle restraints: 14285 sinusoidal: 5777 harmonic: 8508 Sorted by residual: dihedral pdb=" CA GLU G 660 " pdb=" C GLU G 660 " pdb=" N LEU G 661 " pdb=" CA LEU G 661 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN B 353 " pdb=" C GLN B 353 " pdb=" N GLN B 354 " pdb=" CA GLN B 354 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASP E 363 " pdb=" C ASP E 363 " pdb=" N GLU E 364 " pdb=" CA GLU E 364 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 14282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2952 0.082 - 0.165: 533 0.165 - 0.247: 45 0.247 - 0.330: 9 0.330 - 0.412: 4 Chirality restraints: 3543 Sorted by residual: chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 3540 not shown) Planarity restraints: 4163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " -0.062 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO E 112 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 263 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO F 264 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO F 264 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 264 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 102 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.045 5.00e-02 4.00e+02 ... (remaining 4160 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6277 2.81 - 3.33: 19880 3.33 - 3.85: 38871 3.85 - 4.38: 45805 4.38 - 4.90: 79228 Nonbonded interactions: 190061 Sorted by model distance: nonbonded pdb=" O ILE A 122 " pdb=" OG1 THR A 126 " model vdw 2.286 3.040 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR G 472 " pdb=" OD1 ASP G 474 " model vdw 2.304 3.040 nonbonded pdb=" O GLN C 314 " pdb=" OG1 THR C 318 " model vdw 2.304 3.040 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.321 3.040 ... (remaining 190056 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' and (resid 4 through 375 or resid 402)) selection = (chain 'B' and (resid 4 through 375 or resid 402)) selection = (chain 'C' and (resid 4 through 375 or resid 402)) selection = (chain 'D' and (resid 4 through 375 or resid 402)) selection = (chain 'E' and (resid 4 through 375 or resid 402)) selection = (chain 'F' and (resid 4 through 375 or resid 402)) } 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 58.820 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 23782 Z= 0.434 Angle : 1.053 14.761 32269 Z= 0.553 Chirality : 0.064 0.412 3543 Planarity : 0.009 0.092 4163 Dihedral : 13.269 87.182 8845 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.12 % Favored : 99.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.68 % 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: -1.70 (0.14), residues: 2924 helix: -1.95 (0.12), residues: 1034 sheet: 0.20 (0.20), residues: 603 loop : -0.90 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 736 HIS 0.011 0.002 HIS A 161 PHE 0.031 0.003 PHE C 31 TYR 0.032 0.003 TYR G 133 ARG 0.018 0.001 ARG G 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.764 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: -0.1009 (ttt) cc_final: -0.1213 (ttt) REVERT: D 44 MET cc_start: 0.9079 (mtp) cc_final: 0.8872 (mmm) REVERT: E 75 ILE cc_start: 0.9602 (pt) cc_final: 0.9371 (pp) REVERT: G 342 MET cc_start: 0.8860 (mpp) cc_final: 0.8427 (mpp) REVERT: G 347 GLN cc_start: 0.8606 (pm20) cc_final: 0.8322 (pm20) REVERT: G 349 GLN cc_start: 0.8757 (mm110) cc_final: 0.8477 (mm110) REVERT: G 635 MET cc_start: 0.7625 (ppp) cc_final: 0.7359 (ppp) REVERT: G 655 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8536 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 1.9395 time to fit residues: 367.6571 Evaluate side-chains 133 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 49 GLN B 101 HIS B 296 ASN D 111 ASN D 115 ASN D 137 GLN D 246 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN G 401 HIS G 452 ASN G 461 GLN G 530 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.036793 restraints weight = 83100.734| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.81 r_work: 0.2602 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23782 Z= 0.213 Angle : 0.616 9.302 32269 Z= 0.305 Chirality : 0.045 0.186 3543 Planarity : 0.005 0.066 4163 Dihedral : 7.050 79.495 3313 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.65 % Allowed : 4.20 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.35 (0.15), residues: 2924 helix: -0.29 (0.15), residues: 1068 sheet: 0.39 (0.21), residues: 606 loop : -0.30 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 356 HIS 0.004 0.001 HIS E 275 PHE 0.013 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.008 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 2.888 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.8789 (pmm) cc_final: 0.8581 (pmm) REVERT: D 355 MET cc_start: 0.9226 (mtm) cc_final: 0.8957 (mtm) REVERT: E 75 ILE cc_start: 0.9344 (pt) cc_final: 0.9075 (pp) REVERT: F 82 MET cc_start: 0.9383 (tpt) cc_final: 0.9173 (mmm) REVERT: G 342 MET cc_start: 0.8997 (mpp) cc_final: 0.8597 (mpp) REVERT: G 347 GLN cc_start: 0.8469 (pm20) cc_final: 0.8209 (pm20) REVERT: G 349 GLN cc_start: 0.8821 (mm110) cc_final: 0.8575 (mm110) REVERT: G 635 MET cc_start: 0.7425 (ppp) cc_final: 0.7215 (ppp) REVERT: G 662 MET cc_start: 0.8326 (mtm) cc_final: 0.7972 (mtm) outliers start: 14 outliers final: 1 residues processed: 144 average time/residue: 1.7152 time to fit residues: 278.6482 Evaluate side-chains 126 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 156 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 211 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 187 optimal weight: 0.2980 chunk 224 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS C 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 232 HIS G 455 HIS G 679 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.035941 restraints weight = 82569.669| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.79 r_work: 0.2572 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23782 Z= 0.242 Angle : 0.599 9.410 32269 Z= 0.294 Chirality : 0.045 0.173 3543 Planarity : 0.005 0.052 4163 Dihedral : 6.711 78.175 3313 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.85 % Allowed : 6.14 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.29 (0.16), residues: 2924 helix: 0.46 (0.16), residues: 1069 sheet: 0.56 (0.21), residues: 609 loop : -0.07 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.005 0.001 HIS G 309 PHE 0.015 0.001 PHE E 124 TYR 0.017 0.001 TYR G 133 ARG 0.008 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: D 117 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: D 176 MET cc_start: 0.9316 (mmt) cc_final: 0.9079 (mmt) REVERT: E 75 ILE cc_start: 0.9377 (pt) cc_final: 0.9102 (pp) REVERT: F 82 MET cc_start: 0.9444 (tpt) cc_final: 0.9195 (mmm) REVERT: F 176 MET cc_start: 0.8746 (mtm) cc_final: 0.8462 (mtm) REVERT: G 342 MET cc_start: 0.9072 (mpp) cc_final: 0.8501 (mpp) REVERT: G 347 GLN cc_start: 0.8444 (pm20) cc_final: 0.8191 (pm20) REVERT: G 349 GLN cc_start: 0.8829 (mm110) cc_final: 0.8613 (mm110) REVERT: G 438 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: G 662 MET cc_start: 0.8285 (mtm) cc_final: 0.7062 (mpp) outliers start: 19 outliers final: 4 residues processed: 141 average time/residue: 1.8302 time to fit residues: 289.1961 Evaluate side-chains 135 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 438 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 160 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 213 optimal weight: 0.4980 chunk 266 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036444 restraints weight = 83683.434| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.82 r_work: 0.2589 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23782 Z= 0.176 Angle : 0.564 9.104 32269 Z= 0.274 Chirality : 0.043 0.181 3543 Planarity : 0.004 0.057 4163 Dihedral : 6.505 79.782 3313 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.85 % Allowed : 7.11 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.57 (0.16), residues: 2924 helix: 0.78 (0.16), residues: 1073 sheet: 0.66 (0.21), residues: 612 loop : 0.03 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.003 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.018 0.001 TYR G 133 ARG 0.012 0.000 ARG G 714 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 3.155 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8197 (pp20) REVERT: D 117 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: D 132 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8672 (ttp) REVERT: D 176 MET cc_start: 0.9312 (mmt) cc_final: 0.9082 (mmm) REVERT: E 75 ILE cc_start: 0.9385 (pt) cc_final: 0.9112 (pp) REVERT: E 176 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: E 355 MET cc_start: 0.8643 (mtm) cc_final: 0.8437 (pmm) REVERT: F 82 MET cc_start: 0.9439 (tpt) cc_final: 0.9180 (mmm) REVERT: G 342 MET cc_start: 0.9096 (mpp) cc_final: 0.8795 (mpp) REVERT: G 347 GLN cc_start: 0.8427 (pm20) cc_final: 0.8181 (pm20) REVERT: G 438 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6377 (m-10) REVERT: G 662 MET cc_start: 0.8227 (mtm) cc_final: 0.6872 (mpp) outliers start: 19 outliers final: 0 residues processed: 141 average time/residue: 1.8442 time to fit residues: 293.6382 Evaluate side-chains 135 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain G residue 438 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 237 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.0040 chunk 194 optimal weight: 0.2980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.036661 restraints weight = 82884.348| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.80 r_work: 0.2596 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23782 Z= 0.159 Angle : 0.550 9.533 32269 Z= 0.267 Chirality : 0.043 0.215 3543 Planarity : 0.004 0.049 4163 Dihedral : 6.350 80.521 3313 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.01 % Allowed : 7.88 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.81 (0.16), residues: 2924 helix: 1.02 (0.17), residues: 1068 sheet: 0.72 (0.22), residues: 606 loop : 0.16 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.003 0.001 HIS G 309 PHE 0.012 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.009 0.000 ARG G 714 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 2.635 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8213 (pp20) REVERT: D 47 MET cc_start: 0.8712 (pmm) cc_final: 0.8460 (pmm) REVERT: D 117 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: D 132 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8644 (ttp) REVERT: D 176 MET cc_start: 0.9326 (mmt) cc_final: 0.9102 (mmm) REVERT: E 75 ILE cc_start: 0.9385 (pt) cc_final: 0.9112 (pp) REVERT: E 176 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: F 82 MET cc_start: 0.9440 (tpt) cc_final: 0.9179 (mmm) REVERT: G 342 MET cc_start: 0.9130 (mpp) cc_final: 0.8813 (mpp) REVERT: G 662 MET cc_start: 0.8203 (mtm) cc_final: 0.7793 (mtm) REVERT: G 705 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7661 (mp0) outliers start: 23 outliers final: 3 residues processed: 144 average time/residue: 1.7208 time to fit residues: 278.5764 Evaluate side-chains 141 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034940 restraints weight = 83162.883| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.81 r_work: 0.2537 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23782 Z= 0.324 Angle : 0.613 10.329 32269 Z= 0.300 Chirality : 0.046 0.206 3543 Planarity : 0.004 0.059 4163 Dihedral : 6.488 81.631 3313 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.01 % Allowed : 8.24 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.89 (0.16), residues: 2924 helix: 1.04 (0.17), residues: 1048 sheet: 0.76 (0.21), residues: 622 loop : 0.26 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.005 0.001 HIS B 161 PHE 0.014 0.001 PHE F 31 TYR 0.016 0.001 TYR G 438 ARG 0.013 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 2.842 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: D 117 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: D 132 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8775 (ttp) REVERT: D 176 MET cc_start: 0.9344 (mmt) cc_final: 0.9133 (mmt) REVERT: E 75 ILE cc_start: 0.9441 (pt) cc_final: 0.9157 (pp) REVERT: E 176 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8152 (mtt) REVERT: F 82 MET cc_start: 0.9490 (tpt) cc_final: 0.9240 (mmm) REVERT: G 342 MET cc_start: 0.9124 (mpp) cc_final: 0.8640 (mpp) REVERT: G 438 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6850 (m-10) REVERT: G 612 ASP cc_start: 0.8852 (t0) cc_final: 0.8538 (t0) REVERT: G 662 MET cc_start: 0.8256 (mtm) cc_final: 0.7818 (mtm) REVERT: G 705 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7602 (mp0) outliers start: 23 outliers final: 2 residues processed: 140 average time/residue: 1.9171 time to fit residues: 301.1477 Evaluate side-chains 137 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain G residue 438 TYR Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 186 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 213 optimal weight: 0.4980 chunk 191 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 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 = 0.3033 r_free = 0.3033 target = 0.046602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035118 restraints weight = 83631.153| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.82 r_work: 0.2541 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23782 Z= 0.270 Angle : 0.593 10.861 32269 Z= 0.289 Chirality : 0.045 0.204 3543 Planarity : 0.004 0.056 4163 Dihedral : 6.435 82.702 3313 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.89 % Allowed : 8.72 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.83 (0.16), residues: 2924 helix: 0.93 (0.17), residues: 1079 sheet: 0.84 (0.21), residues: 618 loop : 0.21 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.005 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.015 0.001 TYR G 87 ARG 0.008 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8117 (pp20) REVERT: D 117 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: D 132 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8724 (ttp) REVERT: D 283 MET cc_start: 0.9239 (mmp) cc_final: 0.9002 (mmt) REVERT: E 176 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8171 (mtt) REVERT: F 82 MET cc_start: 0.9488 (tpt) cc_final: 0.9236 (mmm) REVERT: G 342 MET cc_start: 0.9149 (mpp) cc_final: 0.8656 (mpp) REVERT: G 612 ASP cc_start: 0.8875 (t0) cc_final: 0.8554 (t0) REVERT: G 660 GLU cc_start: 0.7398 (pp20) cc_final: 0.6993 (pp20) REVERT: G 662 MET cc_start: 0.8238 (mtm) cc_final: 0.7545 (mmm) REVERT: G 705 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7658 (mp0) outliers start: 20 outliers final: 5 residues processed: 139 average time/residue: 1.8375 time to fit residues: 286.0296 Evaluate side-chains 138 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 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 = 0.3039 r_free = 0.3039 target = 0.046814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.035507 restraints weight = 82909.709| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.78 r_work: 0.2554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23782 Z= 0.219 Angle : 0.582 10.556 32269 Z= 0.283 Chirality : 0.044 0.195 3543 Planarity : 0.004 0.051 4163 Dihedral : 6.372 83.058 3313 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.77 % Allowed : 9.05 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.90 (0.16), residues: 2924 helix: 0.98 (0.17), residues: 1079 sheet: 0.87 (0.21), residues: 618 loop : 0.26 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 615 HIS 0.004 0.001 HIS E 275 PHE 0.013 0.001 PHE C 31 TYR 0.015 0.001 TYR G 133 ARG 0.007 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8117 (pp20) REVERT: D 47 MET cc_start: 0.8591 (pmm) cc_final: 0.8356 (pmm) REVERT: D 117 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: D 132 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8693 (ttp) REVERT: D 283 MET cc_start: 0.9225 (mmp) cc_final: 0.9010 (mmt) REVERT: E 176 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8127 (mtt) REVERT: F 82 MET cc_start: 0.9486 (tpt) cc_final: 0.9229 (mmm) REVERT: G 342 MET cc_start: 0.9150 (mpp) cc_final: 0.8644 (mpp) REVERT: G 612 ASP cc_start: 0.8869 (t0) cc_final: 0.8563 (t0) REVERT: G 660 GLU cc_start: 0.7373 (pp20) cc_final: 0.6839 (pp20) REVERT: G 662 MET cc_start: 0.8301 (mtm) cc_final: 0.7774 (mmm) REVERT: G 705 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7721 (mp0) outliers start: 17 outliers final: 5 residues processed: 137 average time/residue: 1.8269 time to fit residues: 280.7102 Evaluate side-chains 138 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 121 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 chunk 32 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 150 optimal weight: 0.0470 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 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 = 0.3058 r_free = 0.3058 target = 0.047480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.036212 restraints weight = 83043.609| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.78 r_work: 0.2579 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23782 Z= 0.168 Angle : 0.567 10.066 32269 Z= 0.275 Chirality : 0.043 0.192 3543 Planarity : 0.004 0.050 4163 Dihedral : 6.253 83.603 3313 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.69 % Allowed : 9.49 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.06 (0.16), residues: 2924 helix: 1.18 (0.17), residues: 1055 sheet: 0.88 (0.22), residues: 618 loop : 0.35 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 356 HIS 0.004 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.014 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 2.683 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8139 (pp20) REVERT: D 47 MET cc_start: 0.8603 (pmm) cc_final: 0.8376 (pmm) REVERT: D 117 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: D 132 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8679 (ttp) REVERT: D 283 MET cc_start: 0.9209 (mmp) cc_final: 0.8996 (mmt) REVERT: E 176 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: F 82 MET cc_start: 0.9466 (tpt) cc_final: 0.9196 (mmm) REVERT: G 243 MET cc_start: 0.9040 (ttm) cc_final: 0.8816 (ttm) REVERT: G 342 MET cc_start: 0.9153 (mpp) cc_final: 0.8653 (mpp) REVERT: G 595 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (mm) REVERT: G 655 GLU cc_start: 0.8913 (tp30) cc_final: 0.8669 (mm-30) REVERT: G 660 GLU cc_start: 0.7348 (pp20) cc_final: 0.6918 (pp20) REVERT: G 662 MET cc_start: 0.8275 (mtm) cc_final: 0.7866 (mmm) REVERT: G 705 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (mp0) outliers start: 15 outliers final: 3 residues processed: 137 average time/residue: 1.8856 time to fit residues: 290.3181 Evaluate side-chains 137 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 0.6980 chunk 270 optimal weight: 0.0000 chunk 51 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 4 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.036437 restraints weight = 82791.533| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.80 r_work: 0.2587 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23782 Z= 0.158 Angle : 0.565 10.349 32269 Z= 0.273 Chirality : 0.043 0.188 3543 Planarity : 0.004 0.050 4163 Dihedral : 6.179 83.582 3313 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.77 % Allowed : 9.45 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.14 (0.16), residues: 2924 helix: 1.25 (0.17), residues: 1055 sheet: 0.91 (0.22), residues: 618 loop : 0.41 (0.19), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 356 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.017 0.001 TYR G 133 ARG 0.015 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 2.970 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: D 47 MET cc_start: 0.8592 (pmm) cc_final: 0.8268 (pmm) REVERT: D 117 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: D 132 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8665 (ttp) REVERT: D 283 MET cc_start: 0.9210 (mmp) cc_final: 0.9003 (mmt) REVERT: E 176 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: F 82 MET cc_start: 0.9456 (tpt) cc_final: 0.9229 (mmm) REVERT: G 342 MET cc_start: 0.9146 (mpp) cc_final: 0.8652 (mpp) REVERT: G 595 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8853 (mm) REVERT: G 655 GLU cc_start: 0.8909 (tp30) cc_final: 0.8490 (mm-30) REVERT: G 660 GLU cc_start: 0.7348 (pp20) cc_final: 0.6852 (pp20) REVERT: G 662 MET cc_start: 0.8265 (mtm) cc_final: 0.7859 (mmm) REVERT: G 705 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7882 (mp0) outliers start: 17 outliers final: 4 residues processed: 140 average time/residue: 1.8553 time to fit residues: 291.4348 Evaluate side-chains 139 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 86 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 chunk 177 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 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 = 0.3050 r_free = 0.3050 target = 0.047165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.035748 restraints weight = 83104.475| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.82 r_work: 0.2563 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23782 Z= 0.218 Angle : 0.587 13.546 32269 Z= 0.283 Chirality : 0.044 0.188 3543 Planarity : 0.004 0.050 4163 Dihedral : 6.215 83.459 3313 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.69 % Allowed : 9.65 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.03 (0.16), residues: 2924 helix: 1.11 (0.17), residues: 1079 sheet: 0.88 (0.21), residues: 624 loop : 0.34 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.006 0.001 HIS E 275 PHE 0.012 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.014 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15769.72 seconds wall clock time: 280 minutes 49.34 seconds (16849.34 seconds total)