Starting phenix.real_space_refine on Fri Sep 19 00:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo7_43366/09_2025/8vo7_43366_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo7_43366/09_2025/8vo7_43366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vo7_43366/09_2025/8vo7_43366_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo7_43366/09_2025/8vo7_43366_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vo7_43366/09_2025/8vo7_43366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo7_43366/09_2025/8vo7_43366.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 140 5.16 5 C 13504 2.51 5 N 3654 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21459 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.16, per 1000 atoms: 0.24 Number of scatterers: 21459 At special positions: 0 Unit cell: (217.33, 108.15, 160.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 12 15.00 Mg 6 11.99 O 4143 8.00 N 3654 7.00 C 13504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 951.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 53 sheets defined 40.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.828A pdb=" N LYS A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.527A pdb=" N SER A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.910A pdb=" N GLY A 211 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.130A pdb=" N TYR A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.785A pdb=" N GLY A 476 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 477 " --> pdb=" O HIS A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.656A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.860A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix 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 205 through 217 removed outlier: 3.508A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.681A 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 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.172A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 removed outlier: 3.891A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.614A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.693A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.885A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.904A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.917A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.770A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.598A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.519A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.776A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.826A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.215A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.602A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 358 through 366 removed outlier: 4.325A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.618A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.591A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.957A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.658A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.675A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.542A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.591A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.967A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.553A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.963A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.793A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.087A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.910A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.560A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.722A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.524A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.215A 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 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 352 through 356 removed outlier: 3.953A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.633A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.595A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.851A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 removed outlier: 3.589A pdb=" N LEU F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.592A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.911A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 352 through 356 removed outlier: 3.837A pdb=" N TRP F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.681A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.789A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.569A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.791A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.692A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.549A pdb=" N LEU G 261 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 296 removed outlier: 4.231A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.825A pdb=" N ARG G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.751A pdb=" N TYR A 23 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.667A pdb=" N ALA A 123 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 113 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N CYS A 121 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 152 through 155 removed outlier: 6.019A pdb=" N TYR A 152 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 166 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 217 Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 234 removed outlier: 3.840A pdb=" N LYS A 241 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.441A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.515A pdb=" N ASN A 272 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 284 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.041A pdb=" N TYR A 314 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 326 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 357 removed outlier: 6.673A pdb=" N PHE A 354 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AB6, first strand: chain 'A' and resid 394 through 397 removed outlier: 5.380A pdb=" N PHE A 394 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 407 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.602A pdb=" N PHE A 452 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS A 456 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 470 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR A 469 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 479 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.699A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.128A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.128A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.941A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.668A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.170A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.801A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.666A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.696A pdb=" N VAL E 163 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 165 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AE6, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.814A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AE8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AE9, first strand: chain 'F' and resid 176 through 178 removed outlier: 6.814A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AF2, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AF3, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.922A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AF5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AF6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AF7, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.640A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 165 " --> pdb=" O GLY G 150 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 238 through 241 881 hydrogen bonds defined for protein. 2262 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: 4.22 Time building geometry restraints manager: 2.40 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: 7028 1.34 - 1.46: 3745 1.46 - 1.57: 10894 1.57 - 1.69: 18 1.69 - 1.81: 239 Bond restraints: 21924 Sorted by residual: bond pdb=" N THR C 303 " pdb=" CA THR C 303 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.31e-02 5.83e+03 8.54e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.91e+00 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 7.75e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.45e+00 ... (remaining 21919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 29210 1.98 - 3.96: 441 3.96 - 5.94: 70 5.94 - 7.92: 14 7.92 - 9.90: 4 Bond angle restraints: 29739 Sorted by residual: angle pdb=" C THR C 303 " pdb=" CA THR C 303 " pdb=" CB THR C 303 " ideal model delta sigma weight residual 109.95 119.85 -9.90 1.99e+00 2.53e-01 2.48e+01 angle pdb=" CA THR C 303 " pdb=" CB THR C 303 " pdb=" OG1 THR C 303 " ideal model delta sigma weight residual 109.60 104.57 5.03 1.50e+00 4.44e-01 1.13e+01 angle pdb=" CA ARG A 151 " pdb=" C ARG A 151 " pdb=" O ARG A 151 " ideal model delta sigma weight residual 121.58 117.99 3.59 1.16e+00 7.43e-01 9.60e+00 angle pdb=" CA THR C 303 " pdb=" CB THR C 303 " pdb=" CG2 THR C 303 " ideal model delta sigma weight residual 110.50 115.73 -5.23 1.70e+00 3.46e-01 9.47e+00 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.63 -5.13 1.70e+00 3.46e-01 9.10e+00 ... (remaining 29734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 12370 24.14 - 48.28: 694 48.28 - 72.42: 76 72.42 - 96.56: 14 96.56 - 120.70: 6 Dihedral angle restraints: 13160 sinusoidal: 5298 harmonic: 7862 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.30 120.70 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.82 118.81 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.56 112.55 1 2.00e+01 2.50e-03 3.32e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2522 0.051 - 0.103: 632 0.103 - 0.154: 121 0.154 - 0.205: 5 0.205 - 0.256: 1 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA THR C 303 " pdb=" N THR C 303 " pdb=" C THR C 303 " pdb=" CB THR C 303 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE C 357 " pdb=" CA ILE C 357 " pdb=" CG1 ILE C 357 " pdb=" CG2 ILE C 357 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 163 " pdb=" CA ILE A 163 " pdb=" CG1 ILE A 163 " pdb=" CG2 ILE A 163 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 3278 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO D 164 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 321 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO G 322 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO G 322 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 322 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 335 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ARG B 335 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG B 335 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS B 336 " -0.011 2.00e-02 2.50e+03 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 453 2.70 - 3.25: 20497 3.25 - 3.80: 32732 3.80 - 4.35: 45981 4.35 - 4.90: 76661 Nonbonded interactions: 176324 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.148 2.170 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.208 3.040 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP F 56 " pdb=" NE2 HIS F 88 " model vdw 2.224 3.120 nonbonded pdb=" OD2 ASP E 244 " pdb=" NE2 GLN E 246 " model vdw 2.227 3.120 ... (remaining 176319 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.100 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.004 0.056 21924 Z= 0.184 Angle : 0.623 9.903 29739 Z= 0.312 Chirality : 0.046 0.256 3281 Planarity : 0.004 0.049 3827 Dihedral : 14.679 120.697 8126 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.17 % Allowed : 0.09 % Favored : 99.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.16), residues: 2691 helix: -0.86 (0.18), residues: 822 sheet: -0.14 (0.24), residues: 506 loop : -0.01 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 254 TYR 0.015 0.001 TYR B 306 PHE 0.012 0.001 PHE F 262 TRP 0.015 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00421 (21924) covalent geometry : angle 0.62333 (29739) hydrogen bonds : bond 0.24421 ( 870) hydrogen bonds : angle 8.60835 ( 2262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 256 time to evaluate : 0.927 Fit side-chains REVERT: A 97 ASP cc_start: 0.7698 (m-30) cc_final: 0.7349 (p0) REVERT: A 195 PHE cc_start: 0.7733 (m-80) cc_final: 0.7408 (m-80) REVERT: A 310 HIS cc_start: 0.7624 (p90) cc_final: 0.7386 (p-80) REVERT: A 464 LYS cc_start: 0.6948 (mmpt) cc_final: 0.6658 (mmmt) REVERT: C 246 GLN cc_start: 0.8808 (mp10) cc_final: 0.8457 (mp10) REVERT: E 326 LYS cc_start: 0.6715 (ptpp) cc_final: 0.6468 (mttp) outliers start: 4 outliers final: 1 residues processed: 259 average time/residue: 0.1613 time to fit residues: 63.9239 Evaluate side-chains 210 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 225 ASN F 162 ASN G 87 HIS G 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075830 restraints weight = 39953.788| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.65 r_work: 0.2976 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21924 Z= 0.149 Angle : 0.613 11.671 29739 Z= 0.302 Chirality : 0.046 0.173 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.757 107.864 3052 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.61 % Allowed : 6.47 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2691 helix: -0.07 (0.19), residues: 810 sheet: -0.19 (0.23), residues: 520 loop : 0.18 (0.18), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.013 0.001 TYR B 306 PHE 0.010 0.001 PHE D 31 TRP 0.014 0.001 TRP D 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00361 (21924) covalent geometry : angle 0.61292 (29739) hydrogen bonds : bond 0.04253 ( 870) hydrogen bonds : angle 5.72923 ( 2262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8345 (m-30) cc_final: 0.7627 (p0) REVERT: A 310 HIS cc_start: 0.8010 (p90) cc_final: 0.7734 (p-80) REVERT: A 464 LYS cc_start: 0.7527 (mmpt) cc_final: 0.7302 (mmmt) REVERT: B 143 TYR cc_start: 0.6079 (t80) cc_final: 0.5859 (t80) REVERT: C 82 MET cc_start: 0.9027 (tpt) cc_final: 0.8740 (tpt) REVERT: C 122 ILE cc_start: 0.8654 (mt) cc_final: 0.8215 (mm) REVERT: E 326 LYS cc_start: 0.6935 (ptpp) cc_final: 0.6410 (mttp) REVERT: F 125 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7987 (mp0) REVERT: G 289 ILE cc_start: 0.8700 (mm) cc_final: 0.8498 (mm) outliers start: 14 outliers final: 11 residues processed: 233 average time/residue: 0.1645 time to fit residues: 58.9814 Evaluate side-chains 222 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 121 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 268 optimal weight: 0.4980 chunk 180 optimal weight: 0.8980 chunk 222 optimal weight: 0.0000 chunk 224 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS G 87 HIS G 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075634 restraints weight = 39876.861| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.64 r_work: 0.2968 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21924 Z= 0.144 Angle : 0.590 12.543 29739 Z= 0.286 Chirality : 0.046 0.155 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.572 103.149 3048 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.96 % Allowed : 9.00 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2691 helix: 0.23 (0.18), residues: 852 sheet: -0.16 (0.23), residues: 508 loop : 0.15 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 28 TYR 0.012 0.001 TYR B 306 PHE 0.016 0.001 PHE A 216 TRP 0.014 0.001 TRP D 340 HIS 0.008 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00354 (21924) covalent geometry : angle 0.58984 (29739) hydrogen bonds : bond 0.03645 ( 870) hydrogen bonds : angle 5.28969 ( 2262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8306 (m-30) cc_final: 0.7553 (p0) REVERT: A 182 GLN cc_start: 0.7345 (tp-100) cc_final: 0.7083 (pm20) REVERT: A 464 LYS cc_start: 0.7695 (mmpt) cc_final: 0.7450 (mmmt) REVERT: B 143 TYR cc_start: 0.6006 (t80) cc_final: 0.5647 (t80) REVERT: C 122 ILE cc_start: 0.8624 (mt) cc_final: 0.8171 (mm) outliers start: 22 outliers final: 14 residues processed: 242 average time/residue: 0.1620 time to fit residues: 60.6005 Evaluate side-chains 226 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 46 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 174 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 215 optimal weight: 0.0270 chunk 97 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS G 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.089869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.076499 restraints weight = 39829.771| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.65 r_work: 0.2988 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21924 Z= 0.111 Angle : 0.558 12.458 29739 Z= 0.268 Chirality : 0.044 0.152 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.298 100.737 3048 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.14 % Allowed : 10.44 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.17), residues: 2691 helix: 0.30 (0.18), residues: 906 sheet: -0.03 (0.24), residues: 510 loop : 0.26 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 28 TYR 0.011 0.001 TYR B 306 PHE 0.010 0.001 PHE D 31 TRP 0.012 0.001 TRP D 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00270 (21924) covalent geometry : angle 0.55767 (29739) hydrogen bonds : bond 0.03057 ( 870) hydrogen bonds : angle 5.01078 ( 2262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8299 (m-30) cc_final: 0.7584 (p0) REVERT: A 355 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 65 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8720 (pp) REVERT: B 143 TYR cc_start: 0.5947 (t80) cc_final: 0.5696 (t80) REVERT: B 260 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8779 (p) REVERT: C 122 ILE cc_start: 0.8562 (mt) cc_final: 0.8080 (mm) outliers start: 26 outliers final: 14 residues processed: 242 average time/residue: 0.1536 time to fit residues: 57.9738 Evaluate side-chains 225 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN G 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073418 restraints weight = 39875.998| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.62 r_work: 0.2927 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21924 Z= 0.230 Angle : 0.651 14.119 29739 Z= 0.316 Chirality : 0.049 0.216 3281 Planarity : 0.004 0.053 3827 Dihedral : 7.552 102.945 3048 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.66 % Allowed : 11.66 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2691 helix: 0.26 (0.18), residues: 870 sheet: -0.21 (0.23), residues: 532 loop : 0.16 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 28 TYR 0.012 0.001 TYR A 111 PHE 0.017 0.002 PHE F 124 TRP 0.018 0.002 TRP D 340 HIS 0.014 0.002 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00575 (21924) covalent geometry : angle 0.65140 (29739) hydrogen bonds : bond 0.03866 ( 870) hydrogen bonds : angle 5.07692 ( 2262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8388 (m-30) cc_final: 0.7622 (p0) REVERT: A 182 GLN cc_start: 0.7384 (tp-100) cc_final: 0.7085 (pm20) REVERT: A 195 PHE cc_start: 0.7950 (m-80) cc_final: 0.7575 (m-80) REVERT: A 318 THR cc_start: 0.7257 (m) cc_final: 0.6713 (p) REVERT: B 65 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8790 (pp) REVERT: B 143 TYR cc_start: 0.6039 (t80) cc_final: 0.5595 (t80) REVERT: B 260 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 122 ILE cc_start: 0.8644 (mt) cc_final: 0.8163 (mm) REVERT: E 9 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8456 (p) REVERT: E 72 GLU cc_start: 0.7572 (mp0) cc_final: 0.7327 (mp0) REVERT: F 65 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8236 (pp) REVERT: F 107 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: G 287 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6350 (pt) outliers start: 38 outliers final: 19 residues processed: 242 average time/residue: 0.1495 time to fit residues: 57.0231 Evaluate side-chains 228 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 228 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 97 optimal weight: 0.0670 chunk 197 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 252 ASN G 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.074884 restraints weight = 39761.325| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.62 r_work: 0.2956 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21924 Z= 0.140 Angle : 0.580 8.390 29739 Z= 0.280 Chirality : 0.046 0.188 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.324 101.840 3048 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.40 % Allowed : 12.84 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2691 helix: 0.44 (0.18), residues: 870 sheet: -0.21 (0.23), residues: 520 loop : 0.20 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 28 TYR 0.011 0.001 TYR B 306 PHE 0.011 0.001 PHE D 31 TRP 0.014 0.001 TRP D 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00348 (21924) covalent geometry : angle 0.57968 (29739) hydrogen bonds : bond 0.03185 ( 870) hydrogen bonds : angle 4.93223 ( 2262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8319 (m-30) cc_final: 0.7575 (p0) REVERT: A 182 GLN cc_start: 0.7329 (tp-100) cc_final: 0.7084 (pm20) REVERT: A 185 ARG cc_start: 0.7869 (mmp80) cc_final: 0.7558 (mmp80) REVERT: A 318 THR cc_start: 0.7204 (m) cc_final: 0.6692 (p) REVERT: A 355 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 65 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8740 (pp) REVERT: B 143 TYR cc_start: 0.6004 (t80) cc_final: 0.5670 (t80) REVERT: B 260 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8802 (p) REVERT: C 122 ILE cc_start: 0.8578 (mt) cc_final: 0.8075 (mm) REVERT: E 9 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8414 (p) REVERT: E 72 GLU cc_start: 0.7553 (mp0) cc_final: 0.7315 (mp0) REVERT: F 65 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8217 (pp) REVERT: F 107 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: G 72 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7398 (mp0) outliers start: 32 outliers final: 18 residues processed: 238 average time/residue: 0.1647 time to fit residues: 60.9060 Evaluate side-chains 229 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 229 optimal weight: 0.1980 chunk 166 optimal weight: 1.9990 chunk 159 optimal weight: 0.0270 chunk 234 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.076316 restraints weight = 39554.332| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.62 r_work: 0.2984 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21924 Z= 0.102 Angle : 0.552 7.620 29739 Z= 0.266 Chirality : 0.044 0.170 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.059 100.250 3048 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.49 % Allowed : 13.19 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.17), residues: 2691 helix: 0.48 (0.18), residues: 906 sheet: -0.17 (0.23), residues: 520 loop : 0.27 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 28 TYR 0.011 0.001 TYR B 306 PHE 0.017 0.001 PHE A 195 TRP 0.011 0.001 TRP D 340 HIS 0.030 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00242 (21924) covalent geometry : angle 0.55229 (29739) hydrogen bonds : bond 0.02802 ( 870) hydrogen bonds : angle 4.80366 ( 2262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8253 (m-30) cc_final: 0.7544 (p0) REVERT: A 185 ARG cc_start: 0.7881 (mmp80) cc_final: 0.7610 (mmp80) REVERT: A 318 THR cc_start: 0.7202 (m) cc_final: 0.6706 (p) REVERT: A 355 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (m) REVERT: B 65 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 143 TYR cc_start: 0.5850 (t80) cc_final: 0.5623 (t80) REVERT: B 260 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8775 (p) REVERT: D 123 MET cc_start: 0.8674 (mmt) cc_final: 0.8332 (mmt) REVERT: E 9 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8373 (p) REVERT: E 72 GLU cc_start: 0.7491 (mp0) cc_final: 0.7250 (mp0) REVERT: F 65 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8270 (pp) REVERT: F 107 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: G 72 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7409 (mp0) outliers start: 34 outliers final: 21 residues processed: 242 average time/residue: 0.1455 time to fit residues: 55.3296 Evaluate side-chains 232 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 90 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 260 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 474 HIS G 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074216 restraints weight = 39811.411| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.62 r_work: 0.2943 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21924 Z= 0.181 Angle : 0.609 8.877 29739 Z= 0.295 Chirality : 0.047 0.208 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.222 100.240 3048 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 13.02 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2691 helix: 0.50 (0.18), residues: 870 sheet: -0.20 (0.22), residues: 542 loop : 0.20 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 28 TYR 0.011 0.001 TYR G 166 PHE 0.013 0.001 PHE F 124 TRP 0.016 0.002 TRP D 340 HIS 0.009 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00453 (21924) covalent geometry : angle 0.60905 (29739) hydrogen bonds : bond 0.03395 ( 870) hydrogen bonds : angle 4.88374 ( 2262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.812 Fit side-chains REVERT: A 97 ASP cc_start: 0.8296 (m-30) cc_final: 0.7565 (p0) REVERT: A 182 GLN cc_start: 0.7330 (tp-100) cc_final: 0.7078 (pm20) REVERT: A 318 THR cc_start: 0.7278 (m) cc_final: 0.6771 (p) REVERT: B 65 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8777 (pp) REVERT: B 143 TYR cc_start: 0.6035 (t80) cc_final: 0.5689 (t80) REVERT: B 260 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8825 (p) REVERT: E 72 GLU cc_start: 0.7573 (mp0) cc_final: 0.7323 (mp0) REVERT: F 65 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8226 (pp) REVERT: F 107 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: F 125 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: F 291 LYS cc_start: 0.8154 (tptt) cc_final: 0.7767 (tttm) REVERT: G 72 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7414 (mp0) outliers start: 45 outliers final: 23 residues processed: 242 average time/residue: 0.1533 time to fit residues: 57.6954 Evaluate side-chains 229 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 113 optimal weight: 1.9990 chunk 182 optimal weight: 0.0970 chunk 226 optimal weight: 0.8980 chunk 249 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 166 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 115 optimal weight: 0.0370 chunk 42 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS G 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075567 restraints weight = 39715.874| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.61 r_work: 0.2966 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21924 Z= 0.124 Angle : 0.571 7.997 29739 Z= 0.275 Chirality : 0.045 0.176 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.097 99.359 3048 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.57 % Allowed : 13.41 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2691 helix: 0.61 (0.18), residues: 870 sheet: -0.18 (0.23), residues: 520 loop : 0.23 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 28 TYR 0.010 0.001 TYR B 306 PHE 0.010 0.001 PHE D 31 TRP 0.013 0.001 TRP D 340 HIS 0.009 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00306 (21924) covalent geometry : angle 0.57122 (29739) hydrogen bonds : bond 0.02962 ( 870) hydrogen bonds : angle 4.80163 ( 2262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.984 Fit side-chains REVERT: A 97 ASP cc_start: 0.8238 (m-30) cc_final: 0.7543 (p0) REVERT: A 182 GLN cc_start: 0.7325 (tp-100) cc_final: 0.7112 (pm20) REVERT: A 355 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8474 (m) REVERT: B 65 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8757 (pp) REVERT: B 143 TYR cc_start: 0.6003 (t80) cc_final: 0.5673 (t80) REVERT: B 260 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8795 (p) REVERT: C 246 GLN cc_start: 0.8878 (mp10) cc_final: 0.8599 (mp10) REVERT: E 72 GLU cc_start: 0.7505 (mp0) cc_final: 0.7266 (mp0) REVERT: F 65 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8208 (pp) REVERT: F 107 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: F 125 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: F 291 LYS cc_start: 0.8198 (tptt) cc_final: 0.7813 (tttm) REVERT: G 72 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7418 (mp0) outliers start: 36 outliers final: 25 residues processed: 234 average time/residue: 0.1566 time to fit residues: 57.5763 Evaluate side-chains 233 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 128 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 115 optimal weight: 0.0970 chunk 194 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS G 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075231 restraints weight = 39770.264| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.62 r_work: 0.2960 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21924 Z= 0.137 Angle : 0.581 8.137 29739 Z= 0.279 Chirality : 0.046 0.181 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.074 99.109 3048 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.57 % Allowed : 13.50 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2691 helix: 0.61 (0.18), residues: 870 sheet: -0.14 (0.23), residues: 530 loop : 0.22 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 28 TYR 0.010 0.001 TYR A 111 PHE 0.011 0.001 PHE D 31 TRP 0.014 0.001 TRP D 340 HIS 0.009 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00340 (21924) covalent geometry : angle 0.58081 (29739) hydrogen bonds : bond 0.03034 ( 870) hydrogen bonds : angle 4.78450 ( 2262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.878 Fit side-chains REVERT: A 97 ASP cc_start: 0.8243 (m-30) cc_final: 0.7543 (p0) REVERT: A 182 GLN cc_start: 0.7300 (tp-100) cc_final: 0.7089 (pm20) REVERT: A 355 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 65 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8766 (pp) REVERT: B 143 TYR cc_start: 0.6123 (t80) cc_final: 0.5620 (t80) REVERT: B 260 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8806 (p) REVERT: C 246 GLN cc_start: 0.8892 (mp10) cc_final: 0.8615 (mp10) REVERT: E 72 GLU cc_start: 0.7515 (mp0) cc_final: 0.7283 (mp0) REVERT: F 65 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8227 (pp) REVERT: F 107 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: F 125 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: F 291 LYS cc_start: 0.8202 (tptt) cc_final: 0.7822 (tttm) REVERT: G 72 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7432 (mp0) outliers start: 36 outliers final: 26 residues processed: 236 average time/residue: 0.1580 time to fit residues: 58.1283 Evaluate side-chains 234 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 247 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 183 optimal weight: 0.1980 chunk 29 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS G 87 HIS G 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076790 restraints weight = 39554.983| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.58 r_work: 0.2990 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21924 Z= 0.108 Angle : 0.557 8.355 29739 Z= 0.266 Chirality : 0.045 0.164 3281 Planarity : 0.004 0.053 3827 Dihedral : 6.908 97.692 3048 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.53 % Allowed : 13.81 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2691 helix: 0.58 (0.18), residues: 906 sheet: -0.11 (0.23), residues: 520 loop : 0.26 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 28 TYR 0.010 0.001 TYR B 306 PHE 0.010 0.001 PHE D 31 TRP 0.012 0.001 TRP B 79 HIS 0.009 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00264 (21924) covalent geometry : angle 0.55687 (29739) hydrogen bonds : bond 0.02746 ( 870) hydrogen bonds : angle 4.70523 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5659.39 seconds wall clock time: 97 minutes 37.17 seconds (5857.17 seconds total)