Starting phenix.real_space_refine on Sat Jul 4 20:30:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8viz_43274/07_2026/8viz_43274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8viz_43274/07_2026/8viz_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 { model { file = "/net/cci-nas-00/data/ceres_data/8viz_43274/07_2026/8viz_43274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8viz_43274/07_2026/8viz_43274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8viz_43274/07_2026/8viz_43274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8viz_43274/07_2026/8viz_43274.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 27 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 0 Ad-hoc single atom residues: {' CA': 8} Chain breaks: 8 Time building chain proxies: 6.30, per 1000 atoms: 0.27 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: 1.80 Conformation dependent library (CDL) restraints added in 1.4 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: 0.93 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: 5.55 Time building geometry restraints manager: 2.46 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: 7.260 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.280 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 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= 0.280 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 : 1.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.018 0.001 ARG G 221 TYR 0.032 0.003 TYR G 133 PHE 0.031 0.003 PHE C 31 TRP 0.027 0.003 TRP G 736 HIS 0.011 0.002 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.28 (23782) covalent geometry : angle 1.05326 / 0.55 (32269) hydrogen bonds : bond 0.18115 / 11.72 ( 1006) hydrogen bonds : angle 7.18392 / 4.94 ( 2691) *********************** 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 : 0.963 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: 0.9005 time to fit residues: 169.9519 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 : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 49 GLN B 101 HIS B 296 ASN C 314 GLN D 111 ASN D 115 ASN D 137 GLN D 246 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 128 ASN G 86 HIS G 232 HIS G 401 HIS G 452 ASN G 461 GLN G 530 GLN G 679 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.035381 restraints weight = 83956.276| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.81 r_work: 0.2554 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 23782 Z= 0.230 Angle : 0.663 9.137 32269 Z= 0.331 Chirality : 0.047 0.189 3543 Planarity : 0.006 0.064 4163 Dihedral : 7.175 79.582 3313 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.73 % Allowed : 4.48 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 2924 helix: -0.24 (0.15), residues: 1069 sheet: 0.37 (0.21), residues: 607 loop : -0.27 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.018 0.001 TYR E 362 PHE 0.014 0.002 PHE C 31 TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS G 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (23782) covalent geometry : angle 0.66252 / 0.33 (32269) hydrogen bonds : bond 0.04064 / 2.66 ( 1006) hydrogen bonds : angle 5.04386 / 3.50 ( 2691) *********************** 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 149 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: -0.0568 (ttt) cc_final: -0.0833 (ttt) REVERT: A 372 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8838 (mtm110) REVERT: C 372 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8773 (ptp-110) REVERT: E 75 ILE cc_start: 0.9356 (pt) cc_final: 0.9083 (pp) REVERT: F 82 MET cc_start: 0.9440 (tpt) cc_final: 0.9155 (mmm) REVERT: G 342 MET cc_start: 0.9036 (mpp) cc_final: 0.8572 (mpp) REVERT: G 347 GLN cc_start: 0.8504 (pm20) cc_final: 0.8256 (pm20) REVERT: G 349 GLN cc_start: 0.8845 (mm110) cc_final: 0.8599 (mm110) REVERT: G 662 MET cc_start: 0.8360 (mtm) cc_final: 0.7217 (mpt) outliers start: 16 outliers final: 1 residues processed: 142 average time/residue: 0.8317 time to fit residues: 132.5403 Evaluate side-chains 128 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain C residue 372 ARG 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 34 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 280 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 234 optimal weight: 0.0470 chunk 188 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.036481 restraints weight = 82872.496| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.80 r_work: 0.2593 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 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 = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23782 Z= 0.109 Angle : 0.578 8.686 32269 Z= 0.283 Chirality : 0.044 0.185 3543 Planarity : 0.004 0.052 4163 Dihedral : 6.729 78.385 3313 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.85 % Allowed : 6.02 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2924 helix: 0.47 (0.16), residues: 1069 sheet: 0.57 (0.21), residues: 608 loop : -0.07 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.020 0.001 TYR G 133 PHE 0.013 0.001 PHE C 31 TRP 0.011 0.001 TRP D 79 HIS 0.004 0.001 HIS G 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (23782) covalent geometry : angle 0.57821 / 0.28 (32269) hydrogen bonds : bond 0.03170 / 2.10 ( 1006) hydrogen bonds : angle 4.63673 / 3.22 ( 2691) *********************** 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 149 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.0353 (ttt) cc_final: 0.0122 (ttt) REVERT: C 107 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: D 47 MET cc_start: 0.8736 (pmm) cc_final: 0.8477 (pmm) REVERT: D 117 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: E 75 ILE cc_start: 0.9394 (pt) cc_final: 0.9123 (pp) REVERT: F 82 MET cc_start: 0.9420 (tpt) cc_final: 0.9194 (mmm) REVERT: G 342 MET cc_start: 0.9067 (mpp) cc_final: 0.8522 (mpp) REVERT: G 347 GLN cc_start: 0.8469 (pm20) cc_final: 0.8208 (pm20) REVERT: G 349 GLN cc_start: 0.8829 (mm110) cc_final: 0.8619 (mm110) REVERT: G 438 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: G 635 MET cc_start: 0.7500 (ptt) cc_final: 0.7236 (ptt) REVERT: G 662 MET cc_start: 0.8297 (mtm) cc_final: 0.7083 (mpp) outliers start: 19 outliers final: 2 residues processed: 140 average time/residue: 0.8460 time to fit residues: 132.8678 Evaluate side-chains 131 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain D residue 117 GLU 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 135 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 261 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 101 HIS C 12 ASN D 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 473 GLN G 663 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.033676 restraints weight = 84161.124| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 2.76 r_work: 0.2487 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2354 r_free = 0.2354 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2354 r_free = 0.2354 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9231 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 23782 Z= 0.339 Angle : 0.694 8.757 32269 Z= 0.345 Chirality : 0.050 0.197 3543 Planarity : 0.005 0.056 4163 Dihedral : 7.014 83.012 3313 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.13 % Allowed : 6.95 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2924 helix: 0.64 (0.16), residues: 1047 sheet: 0.65 (0.21), residues: 616 loop : -0.02 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 372 TYR 0.018 0.002 TYR G 87 PHE 0.016 0.002 PHE F 31 TRP 0.016 0.002 TRP A 86 HIS 0.009 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.34 (23782) covalent geometry : angle 0.69388 / 0.35 (32269) hydrogen bonds : bond 0.04289 / 2.84 ( 1006) hydrogen bonds : angle 4.80019 / 3.35 ( 2691) *********************** 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 157 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.9024 (mmm) cc_final: 0.8773 (mmt) REVERT: B 325 MET cc_start: 0.9280 (mmp) cc_final: 0.9068 (mmm) REVERT: C 107 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: C 372 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8906 (ptp-110) REVERT: E 75 ILE cc_start: 0.9471 (pt) cc_final: 0.9190 (pp) REVERT: E 176 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8355 (mtt) REVERT: F 82 MET cc_start: 0.9596 (tpt) cc_final: 0.9294 (mmm) REVERT: G 342 MET cc_start: 0.9196 (mpp) cc_final: 0.8487 (mpp) REVERT: G 347 GLN cc_start: 0.8655 (pm20) cc_final: 0.8405 (pm20) REVERT: G 438 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: G 662 MET cc_start: 0.8556 (mtm) cc_final: 0.7168 (mpp) outliers start: 26 outliers final: 3 residues processed: 146 average time/residue: 0.8413 time to fit residues: 137.8125 Evaluate side-chains 134 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 17 VAL 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 18 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 168 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 chunk 239 optimal weight: 0.5980 chunk 284 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 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 = 0.3040 r_free = 0.3040 target = 0.046786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035442 restraints weight = 82466.373| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.77 r_work: 0.2556 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 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 = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23782 Z= 0.114 Angle : 0.578 9.297 32269 Z= 0.283 Chirality : 0.044 0.178 3543 Planarity : 0.004 0.051 4163 Dihedral : 6.650 82.044 3313 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 8.08 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2924 helix: 0.84 (0.16), residues: 1073 sheet: 0.69 (0.21), residues: 613 loop : 0.13 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 714 TYR 0.018 0.001 TYR G 133 PHE 0.014 0.001 PHE C 31 TRP 0.012 0.001 TRP D 79 HIS 0.004 0.001 HIS G 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (23782) covalent geometry : angle 0.57778 / 0.28 (32269) hydrogen bonds : bond 0.03032 / 2.01 ( 1006) hydrogen bonds : angle 4.49896 / 3.13 ( 2691) *********************** 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 154 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: F 82 MET cc_start: 0.9477 (tpt) cc_final: 0.9192 (mmm) REVERT: G 243 MET cc_start: 0.9165 (mtp) cc_final: 0.8819 (ttm) REVERT: G 342 MET cc_start: 0.9174 (mpp) cc_final: 0.8796 (mpp) REVERT: G 347 GLN cc_start: 0.8421 (pm20) cc_final: 0.8176 (pm20) REVERT: G 349 GLN cc_start: 0.8637 (mm110) cc_final: 0.8362 (mm110) REVERT: G 438 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: G 662 MET cc_start: 0.8250 (mtm) cc_final: 0.7771 (mpp) REVERT: G 705 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7603 (mp0) outliers start: 24 outliers final: 3 residues processed: 142 average time/residue: 0.8651 time to fit residues: 137.4381 Evaluate side-chains 136 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain G residue 438 TYR 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 225 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034889 restraints weight = 83793.794| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.78 r_work: 0.2533 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 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 = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.2036 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= 0.172 Angle : 0.596 9.979 32269 Z= 0.292 Chirality : 0.045 0.225 3543 Planarity : 0.004 0.047 4163 Dihedral : 6.629 82.873 3313 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.05 % Allowed : 8.80 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2924 helix: 1.02 (0.17), residues: 1048 sheet: 0.74 (0.21), residues: 620 loop : 0.19 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 714 TYR 0.015 0.001 TYR G 133 PHE 0.013 0.001 PHE F 31 TRP 0.011 0.001 TRP D 79 HIS 0.004 0.001 HIS G 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (23782) covalent geometry : angle 0.59595 / 0.29 (32269) hydrogen bonds : bond 0.03254 / 2.16 ( 1006) hydrogen bonds : angle 4.46572 / 3.11 ( 2691) *********************** 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 155 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.3250 (mmt) cc_final: 0.3047 (mmt) REVERT: C 107 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: D 47 MET cc_start: 0.8641 (pmm) cc_final: 0.8373 (pmm) REVERT: E 355 MET cc_start: 0.8683 (mtm) cc_final: 0.8476 (pmm) REVERT: F 82 MET cc_start: 0.9492 (tpt) cc_final: 0.9242 (mmm) REVERT: G 243 MET cc_start: 0.9140 (mtp) cc_final: 0.8839 (ttm) REVERT: G 342 MET cc_start: 0.9191 (mpp) cc_final: 0.8505 (mpp) REVERT: G 347 GLN cc_start: 0.8444 (pm20) cc_final: 0.8158 (pm20) REVERT: G 349 GLN cc_start: 0.8629 (mm110) cc_final: 0.8331 (mm110) REVERT: G 438 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7017 (m-10) REVERT: G 660 GLU cc_start: 0.7429 (pp20) cc_final: 0.7095 (pp20) REVERT: G 662 MET cc_start: 0.8292 (mtm) cc_final: 0.7574 (mmm) REVERT: G 705 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7594 (mp0) outliers start: 24 outliers final: 7 residues processed: 143 average time/residue: 0.8490 time to fit residues: 135.7587 Evaluate side-chains 140 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 GLU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 132 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 265 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 289 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 283 optimal weight: 0.0370 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS B 173 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS G 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.036070 restraints weight = 82969.557| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.78 r_work: 0.2572 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 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 = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23782 Z= 0.098 Angle : 0.566 10.723 32269 Z= 0.275 Chirality : 0.043 0.217 3543 Planarity : 0.004 0.046 4163 Dihedral : 6.433 83.709 3313 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.81 % Allowed : 9.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2924 helix: 1.02 (0.17), residues: 1079 sheet: 0.82 (0.21), residues: 618 loop : 0.20 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.016 0.001 TYR G 133 PHE 0.013 0.001 PHE C 31 TRP 0.011 0.001 TRP C 356 HIS 0.004 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (23782) covalent geometry : angle 0.56564 / 0.28 (32269) hydrogen bonds : bond 0.02757 / 1.83 ( 1006) hydrogen bonds : angle 4.31907 / 3.01 ( 2691) *********************** 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: 18 poor density : 131 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.9196 (mmp) cc_final: 0.8994 (mmm) REVERT: C 107 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: D 47 MET cc_start: 0.8660 (pmm) cc_final: 0.8339 (pmm) REVERT: F 82 MET cc_start: 0.9467 (tpt) cc_final: 0.9194 (mmm) REVERT: G 243 MET cc_start: 0.9051 (mtp) cc_final: 0.8818 (ttm) REVERT: G 342 MET cc_start: 0.9167 (mpp) cc_final: 0.8647 (mpp) REVERT: G 347 GLN cc_start: 0.8451 (pm20) cc_final: 0.8230 (pm20) REVERT: G 349 GLN cc_start: 0.8607 (mm110) cc_final: 0.8403 (mm110) REVERT: G 438 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: G 660 GLU cc_start: 0.7363 (pp20) cc_final: 0.6949 (pp20) REVERT: G 662 MET cc_start: 0.8256 (mtm) cc_final: 0.7512 (mmm) REVERT: G 705 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7689 (mp0) outliers start: 18 outliers final: 4 residues processed: 142 average time/residue: 0.7820 time to fit residues: 124.5658 Evaluate side-chains 138 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain G residue 438 TYR 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 28 optimal weight: 0.0030 chunk 255 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 222 optimal weight: 0.2980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035762 restraints weight = 82657.628| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.80 r_work: 0.2570 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 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 = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23782 Z= 0.113 Angle : 0.574 9.886 32269 Z= 0.278 Chirality : 0.043 0.209 3543 Planarity : 0.004 0.046 4163 Dihedral : 6.392 83.829 3313 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.97 % Allowed : 9.73 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2924 helix: 1.19 (0.17), residues: 1055 sheet: 0.85 (0.22), residues: 618 loop : 0.27 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 372 TYR 0.016 0.001 TYR G 133 PHE 0.012 0.001 PHE C 31 TRP 0.012 0.001 TRP E 356 HIS 0.005 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (23782) covalent geometry : angle 0.57413 / 0.28 (32269) hydrogen bonds : bond 0.02806 / 1.86 ( 1006) hydrogen bonds : angle 4.28109 / 2.98 ( 2691) *********************** 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 155 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: B 325 MET cc_start: 0.9200 (mmp) cc_final: 0.8995 (mmm) REVERT: B 364 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8075 (pp20) REVERT: C 107 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: D 47 MET cc_start: 0.8643 (pmm) cc_final: 0.8407 (pmm) REVERT: F 82 MET cc_start: 0.9466 (tpt) cc_final: 0.9197 (mmm) REVERT: G 342 MET cc_start: 0.9158 (mpp) cc_final: 0.8634 (mpp) REVERT: G 347 GLN cc_start: 0.8428 (pm20) cc_final: 0.8188 (pm20) REVERT: G 349 GLN cc_start: 0.8606 (mm110) cc_final: 0.8392 (mm110) REVERT: G 438 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: G 655 GLU cc_start: 0.8906 (tp30) cc_final: 0.8698 (mm-30) REVERT: G 660 GLU cc_start: 0.7418 (pp20) cc_final: 0.7002 (pp20) REVERT: G 662 MET cc_start: 0.8283 (mtm) cc_final: 0.7750 (mmm) REVERT: G 705 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7704 (mp0) outliers start: 22 outliers final: 3 residues processed: 148 average time/residue: 0.7301 time to fit residues: 121.0836 Evaluate side-chains 139 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain G residue 438 TYR 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 72 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.033738 restraints weight = 84577.007| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 2.80 r_work: 0.2495 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 23782 Z= 0.308 Angle : 0.684 11.331 32269 Z= 0.337 Chirality : 0.049 0.208 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.734 85.623 3313 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.65 % Allowed : 10.06 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2924 helix: 0.85 (0.16), residues: 1082 sheet: 0.73 (0.21), residues: 617 loop : 0.15 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 372 TYR 0.017 0.001 TYR G 87 PHE 0.014 0.002 PHE G 512 TRP 0.012 0.002 TRP G 677 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.31 (23782) covalent geometry : angle 0.68357 / 0.34 (32269) hydrogen bonds : bond 0.03901 / 2.59 ( 1006) hydrogen bonds : angle 4.58746 / 3.20 ( 2691) *********************** 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 147 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.9220 (mmp) cc_final: 0.9008 (mmm) REVERT: C 107 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: D 47 MET cc_start: 0.8543 (pmm) cc_final: 0.8192 (pmm) REVERT: F 82 MET cc_start: 0.9516 (tpt) cc_final: 0.9248 (mmm) REVERT: F 372 ARG cc_start: 0.8509 (ptp-110) cc_final: 0.7921 (ptt-90) REVERT: G 342 MET cc_start: 0.9172 (mpp) cc_final: 0.8418 (mpp) REVERT: G 347 GLN cc_start: 0.8524 (pm20) cc_final: 0.8291 (pm20) REVERT: G 349 GLN cc_start: 0.8620 (mm110) cc_final: 0.8414 (mm110) REVERT: G 438 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: G 655 GLU cc_start: 0.8929 (tp30) cc_final: 0.8720 (mm-30) REVERT: G 660 GLU cc_start: 0.7397 (pp20) cc_final: 0.6943 (pp20) REVERT: G 662 MET cc_start: 0.8357 (mtm) cc_final: 0.7871 (mmm) REVERT: G 705 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7659 (mp0) outliers start: 14 outliers final: 7 residues processed: 140 average time/residue: 0.7896 time to fit residues: 123.8387 Evaluate side-chains 141 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain G residue 438 TYR 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 28 optimal weight: 0.0050 chunk 291 optimal weight: 7.9990 chunk 216 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 274 optimal weight: 0.5980 chunk 196 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 0.0170 chunk 269 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.036065 restraints weight = 83434.696| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.81 r_work: 0.2574 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 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 = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23782 Z= 0.098 Angle : 0.587 13.536 32269 Z= 0.285 Chirality : 0.043 0.208 3543 Planarity : 0.004 0.047 4163 Dihedral : 6.410 86.337 3313 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.48 % Allowed : 10.34 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2924 helix: 1.15 (0.17), residues: 1055 sheet: 0.81 (0.21), residues: 618 loop : 0.31 (0.19), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 714 TYR 0.018 0.001 TYR G 133 PHE 0.013 0.001 PHE C 31 TRP 0.019 0.002 TRP E 356 HIS 0.006 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (23782) covalent geometry : angle 0.58692 / 0.29 (32269) hydrogen bonds : bond 0.02701 / 1.79 ( 1006) hydrogen bonds : angle 4.30151 / 3.00 ( 2691) ********************** 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 141 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.9197 (mmp) cc_final: 0.8956 (mmm) REVERT: C 107 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: D 47 MET cc_start: 0.8568 (pmm) cc_final: 0.8270 (pmm) REVERT: F 82 MET cc_start: 0.9471 (tpt) cc_final: 0.9199 (mmm) REVERT: G 342 MET cc_start: 0.9173 (mpp) cc_final: 0.8693 (mpp) REVERT: G 349 GLN cc_start: 0.8590 (mm110) cc_final: 0.8384 (mm110) REVERT: G 438 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: G 655 GLU cc_start: 0.8913 (tp30) cc_final: 0.8645 (mm-30) REVERT: G 660 GLU cc_start: 0.7305 (pp20) cc_final: 0.6866 (pp20) REVERT: G 662 MET cc_start: 0.8240 (mtm) cc_final: 0.7696 (mmm) REVERT: G 705 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7853 (mp0) outliers start: 10 outliers final: 2 residues processed: 139 average time/residue: 0.7643 time to fit residues: 119.2580 Evaluate side-chains 133 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain G residue 438 TYR 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 39 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 224 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.047203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035821 restraints weight = 83058.641| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.80 r_work: 0.2568 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 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 = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23782 Z= 0.111 Angle : 0.590 13.632 32269 Z= 0.284 Chirality : 0.043 0.205 3543 Planarity : 0.004 0.047 4163 Dihedral : 6.365 86.496 3313 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.36 % Allowed : 10.46 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 2924 helix: 1.21 (0.17), residues: 1056 sheet: 0.85 (0.21), residues: 618 loop : 0.36 (0.19), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 372 TYR 0.017 0.001 TYR G 133 PHE 0.012 0.001 PHE C 31 TRP 0.015 0.001 TRP E 356 HIS 0.006 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (23782) covalent geometry : angle 0.59017 / 0.28 (32269) hydrogen bonds : bond 0.02777 / 1.84 ( 1006) hydrogen bonds : angle 4.24907 / 2.96 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7516.58 seconds wall clock time: 129 minutes 4.22 seconds (7744.22 seconds total)