Starting phenix.real_space_refine on Fri Jun 20 04:40:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8viz_43274/06_2025/8viz_43274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8viz_43274/06_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_43274/06_2025/8viz_43274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8viz_43274/06_2025/8viz_43274.map" model { file = "/net/cci-nas-00/data/ceres_data/8viz_43274/06_2025/8viz_43274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8viz_43274/06_2025/8viz_43274.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 14 9.91 5 P 13 5.49 5 S 142 5.16 5 C 14667 2.51 5 N 3955 2.21 5 O 4483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23274 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2934 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 5615 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 720, 5613 Classifications: {'peptide': 720} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} Conformer: "B" Number of residues, atoms: 720, 5613 Classifications: {'peptide': 720} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} bond proxies already assigned to first conformer: 5739 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' CA': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 17.22, per 1000 atoms: 0.74 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: 5.56 Conformation dependent library (CDL) restraints added in 3.5 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 43 sheets defined 42.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.520A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.593A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.824A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.923A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.683A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.746A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.536A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.564A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.125A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.722A pdb=" N ILE A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.458A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.755A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.553A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.553A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.362A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.561A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.931A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.554A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.712A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.953A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.340A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.876A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.026A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.568A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.194A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.570A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.988A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.726A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.608A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.640A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.539A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.819A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.755A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.140A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.511A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.775A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.077A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.702A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.604A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.193A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.691A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.663A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.615A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.802A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.950A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 4.060A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 removed outlier: 3.658A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.594A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.625A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.515A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.793A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.718A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.922A pdb=" N THR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 removed outlier: 3.502A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.842A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.576A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.302A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 35 removed outlier: 3.655A pdb=" N LYS G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 94 through 112 Processing helix chain 'G' and resid 127 through 134 removed outlier: 4.318A pdb=" N PHE G 134 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 183 Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 240 through 248 Processing helix chain 'G' and resid 261 through 269 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 324 through 342 removed outlier: 3.889A pdb=" N ILE G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR G 340 " --> pdb=" O SER G 336 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 366 removed outlier: 3.790A pdb=" N PHE G 365 " --> pdb=" O PHE G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 400 removed outlier: 3.731A pdb=" N THR G 399 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 489 Processing helix chain 'G' and resid 505 through 510 removed outlier: 3.529A pdb=" N MET G 509 " --> pdb=" O PRO G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 513 No H-bonds generated for 'chain 'G' and resid 511 through 513' Processing helix chain 'G' and resid 557 through 561 removed outlier: 3.773A pdb=" N LEU G 561 " --> pdb=" O ALA G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 599 Processing helix chain 'G' and resid 611 through 619 removed outlier: 3.633A pdb=" N TRP G 615 " --> pdb=" O PRO G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 632 Processing helix chain 'G' and resid 689 through 706 Processing helix chain 'G' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.876A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.314A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.551A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.101A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.567A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.605A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.761A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.825A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.564A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.208A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.601A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.719A pdb=" N ILE E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.259A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 6.357A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.141A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 53 removed outlier: 4.983A pdb=" N ALA G 67 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N VAL G 117 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR G 83 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N HIS G 119 " --> pdb=" O TYR G 83 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU G 85 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU G 121 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR G 87 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 61 through 63 removed outlier: 6.808A pdb=" N PHE G 62 " --> pdb=" O LYS G 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 172 through 175 Processing sheet with id=AE4, first strand: chain 'G' and resid 285 through 289 removed outlier: 6.731A pdb=" N LEU G 273 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE G 315 " --> pdb=" O SER G 351 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU G 353 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL G 317 " --> pdb=" O LEU G 353 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 429 through 432 removed outlier: 3.945A pdb=" N GLN G 419 " --> pdb=" O ASN G 452 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER G 446 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN G 461 " --> pdb=" O VAL G 495 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER G 497 " --> pdb=" O GLN G 461 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE G 463 " --> pdb=" O SER G 497 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL G 499 " --> pdb=" O ILE G 463 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN G 465 " --> pdb=" O VAL G 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 440 through 442 removed outlier: 7.052A pdb=" N PHE G 441 " --> pdb=" O TYR G 520 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU G 538 " --> pdb=" O VAL G 554 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA G 566 " --> pdb=" O VAL G 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 653 through 656 removed outlier: 6.748A pdb=" N VAL G 680 " --> pdb=" O THR G 718 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL G 720 " --> pdb=" O VAL G 680 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL G 682 " --> pdb=" O VAL G 720 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 6.60 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 58.120 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.520 ------------------------------------------------------------------------------- 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 : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.12 % Favored : 99.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 2924 helix: -1.95 (0.12), residues: 1034 sheet: 0.20 (0.20), residues: 603 loop : -0.90 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 736 HIS 0.011 0.002 HIS A 161 PHE 0.031 0.003 PHE C 31 TYR 0.032 0.003 TYR G 133 ARG 0.018 0.001 ARG G 221 Details of bonding type rmsd hydrogen bonds : bond 0.18115 ( 1006) hydrogen bonds : angle 7.18392 ( 2691) covalent geometry : bond 0.00663 (23782) covalent geometry : angle 1.05326 (32269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: -0.1009 (ttt) cc_final: -0.1213 (ttt) REVERT: D 44 MET cc_start: 0.9079 (mtp) cc_final: 0.8872 (mmm) REVERT: E 75 ILE cc_start: 0.9602 (pt) cc_final: 0.9371 (pp) REVERT: G 342 MET cc_start: 0.8860 (mpp) cc_final: 0.8427 (mpp) REVERT: G 347 GLN cc_start: 0.8606 (pm20) cc_final: 0.8322 (pm20) REVERT: G 349 GLN cc_start: 0.8757 (mm110) cc_final: 0.8477 (mm110) REVERT: G 635 MET cc_start: 0.7625 (ppp) cc_final: 0.7359 (ppp) REVERT: G 655 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8536 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 1.8522 time to fit residues: 351.1930 Evaluate side-chains 133 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 49 GLN B 101 HIS B 296 ASN D 111 ASN D 115 ASN D 137 GLN D 246 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN G 401 HIS G 452 ASN G 461 GLN G 530 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036804 restraints weight = 83100.740| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.80 r_work: 0.2602 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23782 Z= 0.135 Angle : 0.616 9.302 32269 Z= 0.305 Chirality : 0.045 0.186 3543 Planarity : 0.005 0.066 4163 Dihedral : 7.050 79.495 3313 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.65 % Allowed : 4.20 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2924 helix: -0.29 (0.15), residues: 1068 sheet: 0.39 (0.21), residues: 606 loop : -0.30 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 356 HIS 0.004 0.001 HIS E 275 PHE 0.013 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1006) hydrogen bonds : angle 5.03752 ( 2691) covalent geometry : bond 0.00324 (23782) covalent geometry : angle 0.61606 (32269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 2.523 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.8789 (pmm) cc_final: 0.8580 (pmm) REVERT: D 355 MET cc_start: 0.9225 (mtm) cc_final: 0.8956 (mtm) REVERT: E 75 ILE cc_start: 0.9345 (pt) cc_final: 0.9076 (pp) REVERT: F 82 MET cc_start: 0.9383 (tpt) cc_final: 0.9172 (mmm) REVERT: G 342 MET cc_start: 0.8996 (mpp) cc_final: 0.8593 (mpp) REVERT: G 347 GLN cc_start: 0.8471 (pm20) cc_final: 0.8209 (pm20) REVERT: G 349 GLN cc_start: 0.8822 (mm110) cc_final: 0.8575 (mm110) REVERT: G 635 MET cc_start: 0.7422 (ppp) cc_final: 0.7212 (ppp) REVERT: G 662 MET cc_start: 0.8320 (mtm) cc_final: 0.7963 (mtm) outliers start: 14 outliers final: 1 residues processed: 144 average time/residue: 1.6025 time to fit residues: 261.2101 Evaluate side-chains 126 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 156 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 211 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS C 12 ASN C 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN G 232 HIS G 455 HIS G 679 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034816 restraints weight = 83121.774| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.79 r_work: 0.2530 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23782 Z= 0.235 Angle : 0.645 9.784 32269 Z= 0.319 Chirality : 0.047 0.199 3543 Planarity : 0.005 0.052 4163 Dihedral : 6.854 79.555 3313 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.01 % Allowed : 5.94 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 2924 helix: 0.38 (0.16), residues: 1070 sheet: 0.54 (0.21), residues: 607 loop : -0.11 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.006 0.001 HIS B 161 PHE 0.014 0.002 PHE F 31 TYR 0.016 0.001 TYR E 362 ARG 0.010 0.001 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1006) hydrogen bonds : angle 4.75532 ( 2691) covalent geometry : bond 0.00567 (23782) covalent geometry : angle 0.64497 (32269) *********************** 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 : 2.645 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.8794 (pmm) cc_final: 0.8500 (pmm) REVERT: D 117 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: D 132 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8808 (ttp) REVERT: D 176 MET cc_start: 0.9352 (mmt) cc_final: 0.9121 (mmt) REVERT: E 75 ILE cc_start: 0.9382 (pt) cc_final: 0.9102 (pp) REVERT: E 176 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: F 82 MET cc_start: 0.9485 (tpt) cc_final: 0.9204 (mmm) REVERT: F 176 MET cc_start: 0.8895 (mtm) cc_final: 0.8616 (mtm) REVERT: G 342 MET cc_start: 0.9099 (mpp) cc_final: 0.8449 (mpp) REVERT: G 347 GLN cc_start: 0.8501 (pm20) cc_final: 0.8292 (pm20) REVERT: G 438 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6370 (m-10) REVERT: G 662 MET cc_start: 0.8307 (mtm) cc_final: 0.7020 (mpp) outliers start: 23 outliers final: 4 residues processed: 142 average time/residue: 1.8075 time to fit residues: 287.4439 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 : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 438 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035657 restraints weight = 83906.464| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.79 r_work: 0.2557 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 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 = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23782 Z= 0.130 Angle : 0.578 8.887 32269 Z= 0.283 Chirality : 0.044 0.205 3543 Planarity : 0.004 0.048 4163 Dihedral : 6.618 79.889 3313 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.73 % Allowed : 7.71 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2924 helix: 0.70 (0.16), residues: 1075 sheet: 0.61 (0.21), residues: 613 loop : -0.02 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.004 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.017 0.001 TYR G 133 ARG 0.015 0.001 ARG G 714 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 1006) hydrogen bonds : angle 4.53181 ( 2691) covalent geometry : bond 0.00318 (23782) covalent geometry : angle 0.57812 (32269) *********************** 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 147 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 2.743 Fit side-chains revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: B 325 MET cc_start: 0.9134 (mmp) cc_final: 0.8931 (mmm) REVERT: B 364 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8209 (pp20) REVERT: C 107 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: D 117 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: D 176 MET cc_start: 0.9332 (mmt) cc_final: 0.9052 (mmt) REVERT: E 75 ILE cc_start: 0.9417 (pt) cc_final: 0.9143 (pp) REVERT: F 82 MET cc_start: 0.9465 (tpt) cc_final: 0.9189 (mmm) REVERT: G 342 MET cc_start: 0.9126 (mpp) cc_final: 0.8796 (mpp) REVERT: G 347 GLN cc_start: 0.8370 (pm20) cc_final: 0.8170 (pm20) REVERT: G 438 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6308 (m-10) REVERT: G 662 MET cc_start: 0.8240 (mtm) cc_final: 0.6903 (mpp) outliers start: 16 outliers final: 4 residues processed: 140 average time/residue: 1.7558 time to fit residues: 276.5001 Evaluate side-chains 137 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 117 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 117 GLU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain G residue 438 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 149 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 171 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.035845 restraints weight = 83189.980| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.81 r_work: 0.2568 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 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 = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23782 Z= 0.115 Angle : 0.565 9.369 32269 Z= 0.275 Chirality : 0.043 0.199 3543 Planarity : 0.004 0.047 4163 Dihedral : 6.466 80.793 3313 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.93 % Allowed : 8.24 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2924 helix: 0.90 (0.17), residues: 1073 sheet: 0.72 (0.21), residues: 612 loop : 0.13 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.004 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.010 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 1006) hydrogen bonds : angle 4.39663 ( 2691) covalent geometry : bond 0.00282 (23782) covalent geometry : angle 0.56462 (32269) *********************** 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 151 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 2.792 Fit side-chains revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: B 364 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8168 (pp20) REVERT: C 107 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: D 117 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: D 132 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8637 (ttp) REVERT: E 75 ILE cc_start: 0.9423 (pt) cc_final: 0.9141 (pp) REVERT: E 176 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: F 82 MET cc_start: 0.9464 (tpt) cc_final: 0.9233 (mmm) REVERT: F 176 MET cc_start: 0.8756 (mtm) cc_final: 0.8494 (mtm) REVERT: G 342 MET cc_start: 0.9161 (mpp) cc_final: 0.8817 (mpp) REVERT: G 347 GLN cc_start: 0.8160 (pm20) cc_final: 0.7939 (pm20) REVERT: G 438 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6311 (m-10) REVERT: G 662 MET cc_start: 0.8238 (mtm) cc_final: 0.6889 (mpp) REVERT: G 705 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7647 (mp0) outliers start: 21 outliers final: 3 residues processed: 141 average time/residue: 1.7785 time to fit residues: 282.5022 Evaluate side-chains 139 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain G residue 438 TYR Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3033 r_free = 0.3033 target = 0.046573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035241 restraints weight = 83047.618| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.78 r_work: 0.2545 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 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 = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23782 Z= 0.159 Angle : 0.590 10.204 32269 Z= 0.287 Chirality : 0.045 0.191 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.461 81.633 3313 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.09 % Allowed : 8.44 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2924 helix: 1.05 (0.17), residues: 1055 sheet: 0.72 (0.21), residues: 616 loop : 0.20 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS B 161 PHE 0.012 0.001 PHE C 31 TYR 0.015 0.001 TYR G 133 ARG 0.013 0.001 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 1006) hydrogen bonds : angle 4.40101 ( 2691) covalent geometry : bond 0.00387 (23782) covalent geometry : angle 0.58990 (32269) *********************** 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 154 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 2.511 Fit side-chains revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: B 364 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (pp20) REVERT: C 107 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: D 47 MET cc_start: 0.8573 (pmm) cc_final: 0.8352 (pmm) REVERT: D 117 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: D 132 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8717 (ttp) REVERT: E 117 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: E 176 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: F 82 MET cc_start: 0.9487 (tpt) cc_final: 0.9242 (mmm) REVERT: F 176 MET cc_start: 0.8817 (mtm) cc_final: 0.8566 (mtm) REVERT: G 80 ASN cc_start: 0.8735 (m110) cc_final: 0.8506 (p0) REVERT: G 342 MET cc_start: 0.9151 (mpp) cc_final: 0.8643 (mpp) REVERT: G 438 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.6767 (m-10) REVERT: G 612 ASP cc_start: 0.8847 (t0) cc_final: 0.8634 (t0) REVERT: G 660 GLU cc_start: 0.7409 (pp20) cc_final: 0.7076 (pp20) REVERT: G 662 MET cc_start: 0.8262 (mtm) cc_final: 0.7533 (mmm) REVERT: G 705 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7634 (mp0) outliers start: 25 outliers final: 5 residues processed: 143 average time/residue: 1.7627 time to fit residues: 282.5001 Evaluate side-chains 141 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 305 MET 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 D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 438 TYR Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 186 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 286 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3029 r_free = 0.3029 target = 0.046472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.035168 restraints weight = 83689.248| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.78 r_work: 0.2541 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 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 = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23782 Z= 0.164 Angle : 0.595 10.673 32269 Z= 0.289 Chirality : 0.045 0.218 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.432 82.827 3313 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.33 % Allowed : 8.44 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2924 helix: 1.07 (0.17), residues: 1055 sheet: 0.85 (0.21), residues: 613 loop : 0.22 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.005 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.015 0.001 TYR G 87 ARG 0.013 0.001 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 1006) hydrogen bonds : angle 4.38413 ( 2691) covalent geometry : bond 0.00401 (23782) covalent geometry : angle 0.59499 (32269) *********************** 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 160 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.8858 (mmm) cc_final: 0.8645 (mmt) REVERT: B 117 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: B 364 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: C 107 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: D 117 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: D 132 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8708 (ttp) REVERT: E 176 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: E 291 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8931 (mppt) REVERT: F 82 MET cc_start: 0.9494 (tpt) cc_final: 0.9245 (mmm) REVERT: G 80 ASN cc_start: 0.8671 (m110) cc_final: 0.8467 (p0) REVERT: G 342 MET cc_start: 0.9151 (mpp) cc_final: 0.8464 (mpp) REVERT: G 660 GLU cc_start: 0.7400 (pp20) cc_final: 0.6967 (pp20) REVERT: G 662 MET cc_start: 0.8248 (mtm) cc_final: 0.7560 (mmm) REVERT: G 705 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7673 (mp0) outliers start: 31 outliers final: 7 residues processed: 148 average time/residue: 1.7887 time to fit residues: 297.8053 Evaluate side-chains 144 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 2.681 ------------------------------------------------------------------------------- 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 117 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 355 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 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 291 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 217 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035130 restraints weight = 83310.739| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.77 r_work: 0.2540 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 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 = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2103 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= 0.161 Angle : 0.598 10.515 32269 Z= 0.291 Chirality : 0.045 0.221 3543 Planarity : 0.004 0.044 4163 Dihedral : 6.421 83.668 3313 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.05 % Allowed : 9.05 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2924 helix: 1.09 (0.17), residues: 1055 sheet: 0.83 (0.21), residues: 618 loop : 0.28 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 677 HIS 0.004 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.015 0.001 TYR G 87 ARG 0.014 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 1006) hydrogen bonds : angle 4.36811 ( 2691) covalent geometry : bond 0.00394 (23782) covalent geometry : angle 0.59809 (32269) *********************** 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 153 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 2.554 Fit side-chains revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 364 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8118 (pp20) REVERT: C 107 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: D 47 MET cc_start: 0.8576 (pmm) cc_final: 0.8319 (pmm) REVERT: D 117 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: D 132 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8708 (ttp) REVERT: E 176 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: E 291 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8929 (mppt) REVERT: F 82 MET cc_start: 0.9494 (tpt) cc_final: 0.9241 (mmm) REVERT: F 205 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: G 80 ASN cc_start: 0.8638 (m110) cc_final: 0.8424 (p0) REVERT: G 342 MET cc_start: 0.9139 (mpp) cc_final: 0.8437 (mpp) REVERT: G 655 GLU cc_start: 0.8941 (tp30) cc_final: 0.8538 (mm-30) REVERT: G 660 GLU cc_start: 0.7393 (pp20) cc_final: 0.6942 (pp20) REVERT: G 662 MET cc_start: 0.8280 (mtm) cc_final: 0.7738 (mmm) REVERT: G 705 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7666 (mp0) outliers start: 24 outliers final: 6 residues processed: 143 average time/residue: 1.7500 time to fit residues: 280.9336 Evaluate side-chains 144 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 117 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 D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 687 ASP Chi-restraints excluded: chain G residue 705 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 121 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 150 optimal weight: 0.0070 chunk 39 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS E 371 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.036092 restraints weight = 83090.483| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.76 r_work: 0.2573 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 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 = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23782 Z= 0.105 Angle : 0.576 11.748 32269 Z= 0.279 Chirality : 0.043 0.218 3543 Planarity : 0.004 0.045 4163 Dihedral : 6.285 84.339 3313 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.73 % Allowed : 9.65 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2924 helix: 1.08 (0.17), residues: 1079 sheet: 0.86 (0.21), residues: 618 loop : 0.31 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 356 HIS 0.003 0.001 HIS G 309 PHE 0.013 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.014 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 1006) hydrogen bonds : angle 4.26980 ( 2691) covalent geometry : bond 0.00256 (23782) covalent geometry : angle 0.57637 (32269) *********************** 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 145 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 2.809 Fit side-chains revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 364 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8145 (pp20) REVERT: C 107 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: D 47 MET cc_start: 0.8611 (pmm) cc_final: 0.8295 (pmm) REVERT: D 117 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: D 132 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8648 (ttp) REVERT: F 82 MET cc_start: 0.9467 (tpt) cc_final: 0.9193 (mmm) REVERT: F 176 MET cc_start: 0.8819 (mtm) cc_final: 0.8477 (mtm) REVERT: G 342 MET cc_start: 0.9145 (mpp) cc_final: 0.8634 (mpp) REVERT: G 655 GLU cc_start: 0.8915 (tp30) cc_final: 0.8712 (mm-30) REVERT: G 660 GLU cc_start: 0.7394 (pp20) cc_final: 0.6912 (pp20) REVERT: G 662 MET cc_start: 0.8288 (mtm) cc_final: 0.7782 (mmm) REVERT: G 705 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7749 (mp0) outliers start: 16 outliers final: 4 residues processed: 139 average time/residue: 1.7818 time to fit residues: 277.7949 Evaluate side-chains 140 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 2.827 ------------------------------------------------------------------------------- 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 117 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET 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 78 optimal weight: 7.9990 chunk 270 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 chunk 225 optimal weight: 0.0980 chunk 157 optimal weight: 0.5980 chunk 281 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 264 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.036437 restraints weight = 82834.138| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.78 r_work: 0.2588 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 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 = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2182 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= 0.097 Angle : 0.574 11.641 32269 Z= 0.277 Chirality : 0.043 0.212 3543 Planarity : 0.004 0.047 4163 Dihedral : 6.189 84.386 3313 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.69 % Allowed : 9.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2924 helix: 1.26 (0.17), residues: 1055 sheet: 0.89 (0.22), residues: 618 loop : 0.40 (0.19), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 356 HIS 0.003 0.001 HIS A 161 PHE 0.012 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.014 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 1006) hydrogen bonds : angle 4.19579 ( 2691) covalent geometry : bond 0.00236 (23782) covalent geometry : angle 0.57440 (32269) ********************** 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: 15 poor density : 131 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 361 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: B 364 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8091 (pp20) REVERT: C 107 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: D 47 MET cc_start: 0.8600 (pmm) cc_final: 0.8290 (pmm) REVERT: D 117 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: D 132 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8624 (ttp) REVERT: F 82 MET cc_start: 0.9456 (tpt) cc_final: 0.9189 (mmm) REVERT: F 176 MET cc_start: 0.8819 (mtm) cc_final: 0.8496 (mtm) REVERT: G 342 MET cc_start: 0.9154 (mpp) cc_final: 0.8649 (mpp) REVERT: G 438 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: G 655 GLU cc_start: 0.8908 (tp30) cc_final: 0.8480 (mm-30) REVERT: G 660 GLU cc_start: 0.7364 (pp20) cc_final: 0.6896 (pp20) REVERT: G 662 MET cc_start: 0.8278 (mtm) cc_final: 0.7877 (mmm) REVERT: G 705 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7870 (mp0) outliers start: 15 outliers final: 4 residues processed: 142 average time/residue: 1.8992 time to fit residues: 301.5839 Evaluate side-chains 140 residues out of total 2474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 132 MET 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 86 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036001 restraints weight = 83144.942| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.81 r_work: 0.2573 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23782 Z= 0.116 Angle : 0.581 11.760 32269 Z= 0.280 Chirality : 0.043 0.211 3543 Planarity : 0.004 0.046 4163 Dihedral : 6.195 84.287 3313 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.77 % Allowed : 9.94 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2924 helix: 1.26 (0.17), residues: 1055 sheet: 0.87 (0.21), residues: 624 loop : 0.40 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 356 HIS 0.005 0.001 HIS E 275 PHE 0.012 0.001 PHE C 31 TYR 0.016 0.001 TYR G 133 ARG 0.014 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.02753 ( 1006) hydrogen bonds : angle 4.20201 ( 2691) covalent geometry : bond 0.00287 (23782) covalent geometry : angle 0.58075 (32269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16993.65 seconds wall clock time: 293 minutes 25.02 seconds (17605.02 seconds total)