Starting phenix.real_space_refine on Fri Sep 19 05:01:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8viz_43274/09_2025/8viz_43274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8viz_43274/09_2025/8viz_43274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8viz_43274/09_2025/8viz_43274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8viz_43274/09_2025/8viz_43274.map" model { file = "/net/cci-nas-00/data/ceres_data/8viz_43274/09_2025/8viz_43274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8viz_43274/09_2025/8viz_43274.cif" } 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-2.0-5805/lib/python3.9/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, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' CA': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 6.89, per 1000 atoms: 0.30 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: 1.94 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.20 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: 2.57 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.260 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 23782 Z= 0.280 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 aren 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 covalent geometry : bond 0.00663 (23782) covalent geometry : angle 1.05326 (32269) hydrogen bonds : bond 0.18115 ( 1006) hydrogen bonds : angle 7.18392 ( 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 : 0.965 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: 0.9711 time to fit residues: 182.4620 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 : 0.932 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN G 86 HIS G 401 HIS G 452 ASN G 461 GLN G 530 GLN G 679 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.035370 restraints weight = 83911.019| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.81 r_work: 0.2552 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 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 = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23782 Z= 0.225 Angle : 0.661 9.333 32269 Z= 0.329 Chirality : 0.047 0.186 3543 Planarity : 0.006 0.064 4163 Dihedral : 7.116 79.851 3313 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.73 % Allowed : 4.32 % Favored : 94.95 % 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 aren not related in a simple way. whole: -0.28 (0.15), residues: 2924 helix: -0.23 (0.15), residues: 1069 sheet: 0.40 (0.21), residues: 605 loop : -0.26 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.018 0.001 TYR E 362 PHE 0.015 0.002 PHE C 31 TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS G 401 Details of bonding type rmsd covalent geometry : bond 0.00544 (23782) covalent geometry : angle 0.66058 (32269) hydrogen bonds : bond 0.04028 ( 1006) hydrogen bonds : angle 5.02123 ( 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 : 0.868 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: -0.0656 (ttt) cc_final: -0.0921 (ttt) REVERT: A 372 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8823 (mtm110) REVERT: C 372 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8779 (ptp-110) REVERT: D 47 MET cc_start: 0.8839 (pmm) cc_final: 0.8617 (pmm) REVERT: E 75 ILE cc_start: 0.9355 (pt) cc_final: 0.9077 (pp) REVERT: F 82 MET cc_start: 0.9440 (tpt) cc_final: 0.9162 (mmm) REVERT: G 342 MET cc_start: 0.9045 (mpp) cc_final: 0.8578 (mpp) REVERT: G 347 GLN cc_start: 0.8500 (pm20) cc_final: 0.8260 (pm20) REVERT: G 349 GLN cc_start: 0.8844 (mm110) cc_final: 0.8626 (mm110) REVERT: G 662 MET cc_start: 0.8348 (mtm) cc_final: 0.7977 (mtm) outliers start: 16 outliers final: 1 residues processed: 142 average time/residue: 0.8812 time to fit residues: 139.8912 Evaluate side-chains 129 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 0.7980 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 141 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 234 optimal weight: 0.0570 chunk 188 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.036612 restraints weight = 82911.718| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.81 r_work: 0.2596 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 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 = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23782 Z= 0.103 Angle : 0.572 8.928 32269 Z= 0.280 Chirality : 0.044 0.176 3543 Planarity : 0.004 0.052 4163 Dihedral : 6.648 78.215 3313 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.01 % Allowed : 6.10 % Favored : 92.89 % 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 aren not related in a simple way. whole: 0.32 (0.16), residues: 2924 helix: 0.50 (0.16), residues: 1069 sheet: 0.57 (0.21), residues: 609 loop : -0.06 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 372 TYR 0.020 0.001 TYR G 133 PHE 0.014 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 covalent geometry : bond 0.00245 (23782) covalent geometry : angle 0.57247 (32269) hydrogen bonds : bond 0.03108 ( 1006) hydrogen bonds : angle 4.60336 ( 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 154 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.0347 (ttt) cc_final: 0.0118 (ttt) REVERT: C 44 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9027 (mtp) REVERT: C 47 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8056 (pmm) REVERT: C 107 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: D 47 MET cc_start: 0.8750 (pmm) cc_final: 0.8447 (pmm) REVERT: D 117 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: E 75 ILE cc_start: 0.9400 (pt) cc_final: 0.9130 (pp) REVERT: F 82 MET cc_start: 0.9411 (tpt) cc_final: 0.9190 (mmm) REVERT: G 342 MET cc_start: 0.9063 (mpp) cc_final: 0.8531 (mpp) REVERT: G 347 GLN cc_start: 0.8473 (pm20) cc_final: 0.8223 (pm20) REVERT: G 349 GLN cc_start: 0.8842 (mm110) cc_final: 0.8638 (mm110) REVERT: G 438 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: G 662 MET cc_start: 0.8248 (mtm) cc_final: 0.7043 (mpp) outliers start: 23 outliers final: 3 residues processed: 142 average time/residue: 0.8666 time to fit residues: 137.4861 Evaluate side-chains 135 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 MET Chi-restraints excluded: chain C residue 47 MET 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: 2.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS C 12 ASN D 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 455 HIS G 473 GLN G 663 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.033436 restraints weight = 84162.134| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 2.75 r_work: 0.2476 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2342 r_free = 0.2342 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 = 0.2342 r_free = 0.2342 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 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 : 0.009 0.074 23782 Z= 0.359 Angle : 0.714 8.878 32269 Z= 0.356 Chirality : 0.051 0.197 3543 Planarity : 0.005 0.058 4163 Dihedral : 6.988 83.697 3313 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.17 % Allowed : 6.99 % Favored : 91.84 % 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 aren not related in a simple way. whole: 0.45 (0.16), residues: 2924 helix: 0.61 (0.16), residues: 1050 sheet: 0.64 (0.21), residues: 616 loop : 0.01 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 372 TYR 0.018 0.002 TYR E 362 PHE 0.017 0.002 PHE F 31 TRP 0.014 0.002 TRP A 86 HIS 0.009 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00860 (23782) covalent geometry : angle 0.71352 (32269) hydrogen bonds : bond 0.04484 ( 1006) hydrogen bonds : angle 4.84158 ( 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 158 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.9273 (mmp) cc_final: 0.9056 (mmm) REVERT: C 82 MET cc_start: 0.9388 (tpt) cc_final: 0.9164 (tpt) REVERT: C 107 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: C 372 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8913 (ptp-110) REVERT: E 75 ILE cc_start: 0.9474 (pt) cc_final: 0.9191 (pp) REVERT: E 176 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8328 (mtt) REVERT: F 82 MET cc_start: 0.9602 (tpt) cc_final: 0.9305 (mmm) REVERT: G 342 MET cc_start: 0.9196 (mpp) cc_final: 0.8478 (mpp) REVERT: G 347 GLN cc_start: 0.8664 (pm20) cc_final: 0.8415 (pm20) REVERT: G 612 ASP cc_start: 0.8968 (t0) cc_final: 0.8704 (t0) REVERT: G 662 MET cc_start: 0.8572 (mtm) cc_final: 0.8155 (mpp) outliers start: 27 outliers final: 4 residues processed: 146 average time/residue: 0.8226 time to fit residues: 134.7316 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 : 0.939 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 17 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 18 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 168 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.046686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035286 restraints weight = 82531.384| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.77 r_work: 0.2548 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 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 = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23782 Z= 0.116 Angle : 0.574 9.331 32269 Z= 0.283 Chirality : 0.044 0.212 3543 Planarity : 0.004 0.051 4163 Dihedral : 6.570 82.701 3313 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.85 % Allowed : 8.36 % Favored : 90.79 % 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 aren not related in a simple way. whole: 0.68 (0.16), residues: 2924 helix: 0.84 (0.16), residues: 1073 sheet: 0.67 (0.21), residues: 613 loop : 0.15 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.016 0.001 TYR G 133 PHE 0.014 0.001 PHE C 31 TRP 0.012 0.001 TRP G 677 HIS 0.004 0.001 HIS G 309 Details of bonding type rmsd covalent geometry : bond 0.00278 (23782) covalent geometry : angle 0.57436 (32269) hydrogen bonds : bond 0.03056 ( 1006) hydrogen bonds : angle 4.50543 ( 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 149 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (pp20) REVERT: C 107 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: F 82 MET cc_start: 0.9480 (tpt) cc_final: 0.9198 (mmm) REVERT: G 243 MET cc_start: 0.9135 (mtp) cc_final: 0.8802 (ttm) REVERT: G 342 MET cc_start: 0.9176 (mpp) cc_final: 0.8794 (mpp) REVERT: G 347 GLN cc_start: 0.8437 (pm20) cc_final: 0.8195 (pm20) REVERT: G 349 GLN cc_start: 0.8621 (mm110) cc_final: 0.8356 (mm110) REVERT: G 438 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.6857 (m-10) REVERT: G 595 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8874 (mm) REVERT: G 662 MET cc_start: 0.8247 (mtm) cc_final: 0.7768 (mpp) REVERT: G 705 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7653 (mp0) outliers start: 19 outliers final: 3 residues processed: 141 average time/residue: 0.8764 time to fit residues: 138.7806 Evaluate side-chains 138 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 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 595 LEU 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: 0.0770 chunk 183 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 157 optimal weight: 0.0470 chunk 7 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034597 restraints weight = 83876.200| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.78 r_work: 0.2522 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 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 = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23782 Z= 0.189 Angle : 0.603 10.003 32269 Z= 0.296 Chirality : 0.045 0.208 3543 Planarity : 0.004 0.047 4163 Dihedral : 6.558 83.530 3313 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 8.64 % Favored : 90.06 % 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 aren not related in a simple way. whole: 0.82 (0.16), residues: 2924 helix: 1.01 (0.17), residues: 1048 sheet: 0.75 (0.21), residues: 615 loop : 0.18 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 714 TYR 0.016 0.001 TYR G 87 PHE 0.014 0.001 PHE F 31 TRP 0.011 0.002 TRP D 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00461 (23782) covalent geometry : angle 0.60323 (32269) hydrogen bonds : bond 0.03371 ( 1006) hydrogen bonds : angle 4.48970 ( 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 161 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8151 (pp20) REVERT: C 107 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: E 355 MET cc_start: 0.8723 (mtm) cc_final: 0.8480 (pmm) REVERT: F 82 MET cc_start: 0.9499 (tpt) cc_final: 0.9238 (mmm) REVERT: G 243 MET cc_start: 0.9129 (mtp) cc_final: 0.8834 (ttm) REVERT: G 342 MET cc_start: 0.9194 (mpp) cc_final: 0.8466 (mpp) REVERT: G 347 GLN cc_start: 0.8464 (pm20) cc_final: 0.8176 (pm20) REVERT: G 349 GLN cc_start: 0.8647 (mm110) cc_final: 0.8355 (mm110) REVERT: G 660 GLU cc_start: 0.7401 (pp20) cc_final: 0.7024 (pp20) REVERT: G 662 MET cc_start: 0.8320 (mtm) cc_final: 0.7655 (mmm) REVERT: G 705 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7592 (mp0) outliers start: 30 outliers final: 7 residues processed: 149 average time/residue: 0.9058 time to fit residues: 150.2740 Evaluate side-chains 142 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 705 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 265 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034955 restraints weight = 83398.180| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.80 r_work: 0.2535 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23782 Z= 0.151 Angle : 0.590 10.533 32269 Z= 0.289 Chirality : 0.044 0.208 3543 Planarity : 0.004 0.046 4163 Dihedral : 6.462 84.647 3313 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.05 % Allowed : 9.21 % Favored : 89.74 % 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 aren not related in a simple way. whole: 0.85 (0.16), residues: 2924 helix: 1.03 (0.17), residues: 1055 sheet: 0.80 (0.21), residues: 613 loop : 0.18 (0.18), residues: 1256 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 0.013 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 covalent geometry : bond 0.00369 (23782) covalent geometry : angle 0.59035 (32269) hydrogen bonds : bond 0.03113 ( 1006) hydrogen bonds : angle 4.42324 ( 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 155 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: B 364 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8111 (pp20) REVERT: C 107 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: D 47 MET cc_start: 0.8652 (pmm) cc_final: 0.8325 (pmm) REVERT: E 176 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8223 (mtt) REVERT: F 82 MET cc_start: 0.9490 (tpt) cc_final: 0.9235 (mmm) REVERT: G 243 MET cc_start: 0.9121 (mtp) cc_final: 0.8885 (ttm) REVERT: G 342 MET cc_start: 0.9204 (mpp) cc_final: 0.8477 (mpp) REVERT: G 347 GLN cc_start: 0.8467 (pm20) cc_final: 0.8237 (pm20) REVERT: G 660 GLU cc_start: 0.7390 (pp20) cc_final: 0.6938 (pp20) REVERT: G 662 MET cc_start: 0.8289 (mtm) cc_final: 0.7614 (mmm) REVERT: G 705 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7655 (mp0) outliers start: 24 outliers final: 7 residues processed: 143 average time/residue: 0.8616 time to fit residues: 138.3168 Evaluate side-chains 142 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 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 E residue 176 MET Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 28 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 281 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034966 restraints weight = 82728.777| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.78 r_work: 0.2536 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 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 = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23782 Z= 0.150 Angle : 0.591 10.987 32269 Z= 0.289 Chirality : 0.044 0.198 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.415 85.551 3313 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.17 % Allowed : 9.41 % Favored : 89.42 % 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 aren not related in a simple way. whole: 0.91 (0.16), residues: 2924 helix: 1.09 (0.17), residues: 1054 sheet: 0.81 (0.21), residues: 613 loop : 0.22 (0.18), residues: 1257 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 0.011 0.001 TRP E 356 HIS 0.006 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00367 (23782) covalent geometry : angle 0.59142 (32269) hydrogen bonds : bond 0.03087 ( 1006) hydrogen bonds : angle 4.39013 ( 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 159 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 325 MET cc_start: 0.9220 (mmp) cc_final: 0.8986 (mmm) REVERT: B 364 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8099 (pp20) REVERT: C 107 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: D 44 MET cc_start: 0.9167 (mtp) cc_final: 0.8888 (mmm) REVERT: E 176 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: E 361 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: F 82 MET cc_start: 0.9498 (tpt) cc_final: 0.9240 (mmm) REVERT: G 243 MET cc_start: 0.9098 (mtp) cc_final: 0.8829 (ttm) REVERT: G 342 MET cc_start: 0.9175 (mpp) cc_final: 0.8439 (mpp) REVERT: G 660 GLU cc_start: 0.7402 (pp20) cc_final: 0.6901 (pp20) REVERT: G 662 MET cc_start: 0.8321 (mtm) cc_final: 0.7861 (mmm) REVERT: G 705 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7716 (mp0) outliers start: 27 outliers final: 7 residues processed: 148 average time/residue: 0.8071 time to fit residues: 133.4796 Evaluate side-chains 143 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 236 LEU 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: 1.9990 chunk 7 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 235 optimal weight: 4.9990 chunk 288 optimal weight: 0.0050 chunk 275 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.034641 restraints weight = 83971.486| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.78 r_work: 0.2522 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 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 = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23782 Z= 0.185 Angle : 0.615 12.490 32269 Z= 0.300 Chirality : 0.045 0.195 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.441 86.403 3313 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.85 % Allowed : 10.06 % Favored : 89.10 % 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 aren not related in a simple way. whole: 0.89 (0.16), residues: 2924 helix: 1.06 (0.17), residues: 1055 sheet: 0.79 (0.21), residues: 613 loop : 0.23 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 372 TYR 0.016 0.001 TYR G 133 PHE 0.013 0.001 PHE F 31 TRP 0.011 0.001 TRP G 677 HIS 0.008 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00452 (23782) covalent geometry : angle 0.61508 (32269) hydrogen bonds : bond 0.03273 ( 1006) hydrogen bonds : angle 4.43168 ( 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 151 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: B 325 MET cc_start: 0.9201 (mmp) cc_final: 0.8952 (mmm) REVERT: B 364 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8111 (pp20) REVERT: C 107 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: D 47 MET cc_start: 0.8714 (pmm) cc_final: 0.8427 (pmm) REVERT: E 176 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8245 (mtt) REVERT: E 361 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: F 82 MET cc_start: 0.9502 (tpt) cc_final: 0.9241 (mmm) REVERT: G 243 MET cc_start: 0.9095 (mtp) cc_final: 0.8853 (ttm) REVERT: G 438 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: G 660 GLU cc_start: 0.7388 (pp20) cc_final: 0.6891 (pp20) REVERT: G 662 MET cc_start: 0.8323 (mtm) cc_final: 0.7865 (mmm) REVERT: G 705 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7702 (mp0) outliers start: 19 outliers final: 8 residues processed: 142 average time/residue: 0.8710 time to fit residues: 138.4474 Evaluate side-chains 144 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 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 E residue 176 MET Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 438 TYR Chi-restraints excluded: chain G residue 687 ASP 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: 3.9990 chunk 291 optimal weight: 4.9990 chunk 216 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 276 optimal weight: 0.0170 chunk 274 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 HIS ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.035543 restraints weight = 83649.251| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.81 r_work: 0.2555 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23782 Z= 0.111 Angle : 0.589 13.578 32269 Z= 0.286 Chirality : 0.043 0.194 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.317 87.499 3313 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.73 % Allowed : 10.26 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.16), residues: 2924 helix: 1.16 (0.17), residues: 1054 sheet: 0.79 (0.21), residues: 611 loop : 0.34 (0.18), residues: 1259 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 0.013 0.001 PHE C 31 TRP 0.016 0.001 TRP E 356 HIS 0.007 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00274 (23782) covalent geometry : angle 0.58945 (32269) hydrogen bonds : bond 0.02810 ( 1006) hydrogen bonds : angle 4.30367 ( 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 146 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: B 325 MET cc_start: 0.9203 (mmp) cc_final: 0.8965 (mmm) REVERT: B 364 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: C 107 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: D 47 MET cc_start: 0.8605 (pmm) cc_final: 0.8399 (pmm) REVERT: E 361 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: F 82 MET cc_start: 0.9489 (tpt) cc_final: 0.9196 (mmm) REVERT: G 342 MET cc_start: 0.9243 (mpp) cc_final: 0.8345 (mpp) REVERT: G 438 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: G 660 GLU cc_start: 0.7350 (pp20) cc_final: 0.6849 (pp20) REVERT: G 662 MET cc_start: 0.8299 (mtm) cc_final: 0.7860 (mmm) REVERT: G 705 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7871 (mp0) outliers start: 16 outliers final: 7 residues processed: 141 average time/residue: 0.8150 time to fit residues: 128.5699 Evaluate side-chains 140 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 438 TYR Chi-restraints excluded: chain G residue 687 ASP 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: 0.8980 chunk 26 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 202 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 154 optimal weight: 0.0980 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 0.0020 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.036187 restraints weight = 82716.429| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.77 r_work: 0.2578 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 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 = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23782 Z= 0.096 Angle : 0.584 13.437 32269 Z= 0.281 Chirality : 0.043 0.205 3543 Planarity : 0.004 0.046 4163 Dihedral : 6.224 88.061 3313 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.77 % Allowed : 10.18 % Favored : 89.05 % 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 aren not related in a simple way. whole: 1.11 (0.16), residues: 2924 helix: 1.25 (0.17), residues: 1054 sheet: 0.87 (0.21), residues: 618 loop : 0.38 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 372 TYR 0.018 0.001 TYR G 133 PHE 0.013 0.001 PHE C 31 TRP 0.018 0.001 TRP E 356 HIS 0.006 0.001 HIS G 410 Details of bonding type rmsd covalent geometry : bond 0.00233 (23782) covalent geometry : angle 0.58372 (32269) hydrogen bonds : bond 0.02624 ( 1006) hydrogen bonds : angle 4.21625 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7948.39 seconds wall clock time: 136 minutes 15.39 seconds (8175.39 seconds total)