Starting phenix.real_space_refine on Wed Jun 18 17:58:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo7_43366/06_2025/8vo7_43366_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo7_43366/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vo7_43366/06_2025/8vo7_43366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo7_43366/06_2025/8vo7_43366.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo7_43366/06_2025/8vo7_43366_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo7_43366/06_2025/8vo7_43366_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.08, per 1000 atoms: 0.66 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: 4.82 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.08 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: 8.74 Time building geometry restraints manager: 5.84 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 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: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 51.460 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.410 ------------------------------------------------------------------------------- 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 : 8.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (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 TRP 0.015 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.012 0.001 PHE F 262 TYR 0.015 0.001 TYR B 306 ARG 0.005 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.24421 ( 870) hydrogen bonds : angle 8.60835 ( 2262) covalent geometry : bond 0.00421 (21924) covalent geometry : angle 0.62333 (29739) *********************** 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 : 2.677 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: 0.3562 time to fit residues: 141.0188 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 : 2.324 ------------------------------------------------------------------------------- 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 227 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.088102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074658 restraints weight = 39826.507| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.62 r_work: 0.2953 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21924 Z= 0.198 Angle : 0.650 12.319 29739 Z= 0.320 Chirality : 0.048 0.189 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.917 108.540 3052 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.83 % Allowed : 6.73 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2691 helix: -0.18 (0.18), residues: 852 sheet: -0.26 (0.23), residues: 520 loop : 0.08 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.008 0.001 HIS G 87 PHE 0.013 0.001 PHE D 266 TYR 0.014 0.001 TYR B 306 ARG 0.004 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 870) hydrogen bonds : angle 5.74228 ( 2262) covalent geometry : bond 0.00489 (21924) covalent geometry : angle 0.64965 (29739) *********************** 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 239 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8380 (m-30) cc_final: 0.7604 (p0) REVERT: A 318 THR cc_start: 0.7133 (m) cc_final: 0.6529 (p) REVERT: B 143 TYR cc_start: 0.6158 (t80) cc_final: 0.5910 (t80) REVERT: C 82 MET cc_start: 0.9027 (tpt) cc_final: 0.8773 (tpt) REVERT: C 122 ILE cc_start: 0.8662 (mt) cc_final: 0.8240 (mm) outliers start: 19 outliers final: 16 residues processed: 235 average time/residue: 0.3467 time to fit residues: 125.8659 Evaluate side-chains 222 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 405 ASP 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 184 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 247 VAL 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 227 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 297 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 = 0.3317 r_free = 0.3317 target = 0.088676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075285 restraints weight = 39531.818| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.64 r_work: 0.2962 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21924 Z= 0.148 Angle : 0.594 12.839 29739 Z= 0.289 Chirality : 0.046 0.158 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.706 104.588 3048 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.22 % Allowed : 9.65 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2691 helix: 0.16 (0.18), residues: 852 sheet: -0.27 (0.23), residues: 518 loop : 0.13 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 340 HIS 0.008 0.001 HIS G 87 PHE 0.015 0.001 PHE A 216 TYR 0.013 0.001 TYR B 306 ARG 0.005 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 870) hydrogen bonds : angle 5.31101 ( 2262) covalent geometry : bond 0.00366 (21924) covalent geometry : angle 0.59408 (29739) *********************** 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 249 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 2.327 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8305 (m-30) cc_final: 0.7534 (p0) REVERT: A 182 GLN cc_start: 0.7365 (tp-100) cc_final: 0.7117 (pm20) REVERT: B 65 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 143 TYR cc_start: 0.6007 (t80) cc_final: 0.5691 (t80) REVERT: B 260 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8798 (p) REVERT: C 122 ILE cc_start: 0.8612 (mt) cc_final: 0.8168 (mm) REVERT: G 278 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8752 (m) outliers start: 28 outliers final: 15 residues processed: 242 average time/residue: 0.3417 time to fit residues: 128.9990 Evaluate side-chains 224 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 140 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.087737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074215 restraints weight = 40161.829| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.65 r_work: 0.2941 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21924 Z= 0.180 Angle : 0.612 13.657 29739 Z= 0.296 Chirality : 0.047 0.175 3281 Planarity : 0.004 0.052 3827 Dihedral : 7.695 104.496 3048 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.62 % Allowed : 11.14 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2691 helix: 0.22 (0.18), residues: 870 sheet: -0.22 (0.23), residues: 532 loop : 0.16 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.009 0.001 HIS G 87 PHE 0.012 0.001 PHE F 124 TYR 0.012 0.001 TYR B 306 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 870) hydrogen bonds : angle 5.15101 ( 2262) covalent geometry : bond 0.00447 (21924) covalent geometry : angle 0.61165 (29739) *********************** 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: 37 poor density : 212 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8363 (m-30) cc_final: 0.7565 (p0) REVERT: A 182 GLN cc_start: 0.7356 (tp-100) cc_final: 0.7086 (pm20) REVERT: A 318 THR cc_start: 0.7148 (m) cc_final: 0.6608 (p) REVERT: B 44 MET cc_start: 0.8822 (mtt) cc_final: 0.8443 (mtp) REVERT: B 65 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8795 (pp) REVERT: B 143 TYR cc_start: 0.6011 (t80) cc_final: 0.5641 (t80) REVERT: B 260 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8823 (p) REVERT: C 122 ILE cc_start: 0.8616 (mt) cc_final: 0.8141 (mm) REVERT: F 65 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8200 (pp) REVERT: F 107 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: G 278 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8758 (m) outliers start: 37 outliers final: 22 residues processed: 241 average time/residue: 0.3241 time to fit residues: 122.7435 Evaluate side-chains 233 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 193 HIS Chi-restraints excluded: chain A residue 296 LEU 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 C residue 357 ILE 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 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 57 GLU 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 101 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 415 GLN G 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.073946 restraints weight = 39839.282| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.63 r_work: 0.2936 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21924 Z= 0.181 Angle : 0.605 9.062 29739 Z= 0.294 Chirality : 0.047 0.170 3281 Planarity : 0.004 0.052 3827 Dihedral : 7.659 104.708 3048 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.92 % Allowed : 12.06 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2691 helix: 0.28 (0.18), residues: 870 sheet: -0.24 (0.23), residues: 532 loop : 0.15 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.008 0.001 HIS G 87 PHE 0.013 0.001 PHE F 124 TYR 0.011 0.001 TYR B 306 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 870) hydrogen bonds : angle 5.06127 ( 2262) covalent geometry : bond 0.00451 (21924) covalent geometry : angle 0.60521 (29739) *********************** 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 258 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 2.419 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8392 (m-30) cc_final: 0.7589 (p0) REVERT: A 182 GLN cc_start: 0.7365 (tp-100) cc_final: 0.7095 (pm20) REVERT: A 185 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7553 (mmp80) REVERT: A 318 THR cc_start: 0.7227 (m) cc_final: 0.6683 (p) REVERT: B 65 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 143 TYR cc_start: 0.6026 (t80) cc_final: 0.5607 (t80) REVERT: B 252 ASN cc_start: 0.8217 (m-40) cc_final: 0.8008 (m110) REVERT: B 260 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 122 ILE cc_start: 0.8624 (mt) cc_final: 0.8134 (mm) REVERT: E 9 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8451 (p) REVERT: E 72 GLU cc_start: 0.7566 (mp0) cc_final: 0.7329 (mp0) REVERT: F 65 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8227 (pp) REVERT: F 107 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: F 125 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: G 72 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: G 278 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8760 (m) outliers start: 44 outliers final: 28 residues processed: 249 average time/residue: 0.3289 time to fit residues: 129.3997 Evaluate side-chains 243 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 2.552 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 296 LEU 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 C residue 357 ILE 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 9 VAL Chi-restraints excluded: chain E residue 47 MET 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 247 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 57 GLU 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 216 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 0.0060 chunk 106 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 115 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 = 0.3304 r_free = 0.3304 target = 0.087930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074457 restraints weight = 39632.402| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.62 r_work: 0.2946 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21924 Z= 0.147 Angle : 0.584 8.547 29739 Z= 0.282 Chirality : 0.046 0.165 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.508 103.149 3048 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 12.84 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2691 helix: 0.40 (0.18), residues: 870 sheet: -0.21 (0.23), residues: 530 loop : 0.18 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.009 0.001 HIS G 87 PHE 0.011 0.001 PHE D 31 TYR 0.011 0.001 TYR B 306 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 870) hydrogen bonds : angle 4.95899 ( 2262) covalent geometry : bond 0.00366 (21924) covalent geometry : angle 0.58366 (29739) *********************** 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 257 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8311 (m-30) cc_final: 0.7571 (p0) REVERT: A 182 GLN cc_start: 0.7375 (tp-100) cc_final: 0.7099 (pm20) REVERT: A 318 THR cc_start: 0.7233 (m) cc_final: 0.6698 (p) REVERT: B 65 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 143 TYR cc_start: 0.5996 (t80) cc_final: 0.5636 (t80) REVERT: B 252 ASN cc_start: 0.8171 (m-40) cc_final: 0.7954 (m110) REVERT: B 260 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8813 (p) REVERT: E 9 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8423 (p) REVERT: E 72 GLU cc_start: 0.7589 (mp0) cc_final: 0.7358 (mp0) REVERT: F 65 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8233 (pp) REVERT: F 107 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: F 125 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: G 72 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: G 278 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8751 (m) outliers start: 43 outliers final: 27 residues processed: 250 average time/residue: 0.3253 time to fit residues: 127.7069 Evaluate side-chains 243 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 221 VAL 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 274 ILE 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 D residue 260 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 232 SER 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 Chi-restraints excluded: chain G residue 298 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 226 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 D 115 ASN G 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074403 restraints weight = 39738.033| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.62 r_work: 0.2943 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21924 Z= 0.157 Angle : 0.588 8.483 29739 Z= 0.284 Chirality : 0.046 0.197 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.455 102.699 3048 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 13.06 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2691 helix: 0.44 (0.18), residues: 870 sheet: -0.22 (0.23), residues: 530 loop : 0.19 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.009 0.001 HIS G 87 PHE 0.012 0.001 PHE D 31 TYR 0.011 0.001 TYR B 306 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 870) hydrogen bonds : angle 4.92692 ( 2262) covalent geometry : bond 0.00392 (21924) covalent geometry : angle 0.58840 (29739) *********************** 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 259 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 2.840 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8316 (m-30) cc_final: 0.7574 (p0) REVERT: A 182 GLN cc_start: 0.7353 (tp-100) cc_final: 0.7074 (pm20) REVERT: A 318 THR cc_start: 0.7260 (m) cc_final: 0.6742 (p) REVERT: B 65 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (pp) REVERT: B 143 TYR cc_start: 0.6011 (t80) cc_final: 0.5675 (t80) REVERT: B 252 ASN cc_start: 0.8181 (m-40) cc_final: 0.7966 (m110) REVERT: B 260 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8820 (p) REVERT: D 298 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.7999 (t) REVERT: E 9 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8408 (p) REVERT: E 72 GLU cc_start: 0.7597 (mp0) cc_final: 0.7360 (mp0) REVERT: F 65 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8239 (pp) REVERT: F 107 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: F 125 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: G 72 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: G 278 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8750 (m) outliers start: 48 outliers final: 30 residues processed: 254 average time/residue: 0.4387 time to fit residues: 180.0525 Evaluate side-chains 247 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 4.851 ------------------------------------------------------------------------------- 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 221 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 34 ILE 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 274 ILE 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 D residue 260 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 232 SER 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 Chi-restraints excluded: chain G residue 298 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 209 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 115 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 = 0.3270 r_free = 0.3270 target = 0.086603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073181 restraints weight = 39593.161| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.60 r_work: 0.2909 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21924 Z= 0.199 Angle : 0.620 8.922 29739 Z= 0.300 Chirality : 0.048 0.195 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.527 104.633 3048 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.27 % Allowed : 12.84 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2691 helix: 0.37 (0.18), residues: 870 sheet: -0.24 (0.22), residues: 542 loop : 0.14 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.009 0.001 HIS G 87 PHE 0.013 0.001 PHE F 124 TYR 0.011 0.001 TYR B 306 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 870) hydrogen bonds : angle 4.96333 ( 2262) covalent geometry : bond 0.00498 (21924) covalent geometry : angle 0.61954 (29739) *********************** 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 256 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 2.526 Fit side-chains REVERT: A 97 ASP cc_start: 0.8314 (m-30) cc_final: 0.7575 (p0) REVERT: A 182 GLN cc_start: 0.7347 (tp-100) cc_final: 0.7084 (pm20) REVERT: A 318 THR cc_start: 0.7270 (m) cc_final: 0.6745 (p) REVERT: B 65 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8779 (pp) REVERT: B 143 TYR cc_start: 0.6272 (t80) cc_final: 0.5649 (t80) REVERT: B 252 ASN cc_start: 0.8228 (m-40) cc_final: 0.8018 (m110) REVERT: B 260 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8830 (p) REVERT: D 298 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8013 (t) REVERT: E 9 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8418 (t) REVERT: E 72 GLU cc_start: 0.7630 (mp0) cc_final: 0.7383 (mp0) REVERT: F 65 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8264 (pp) REVERT: F 107 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: F 125 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: F 291 LYS cc_start: 0.8236 (tptt) cc_final: 0.7774 (ttpp) REVERT: G 72 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: G 278 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8706 (m) REVERT: G 287 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6312 (pt) REVERT: G 327 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8494 (mp) outliers start: 52 outliers final: 33 residues processed: 248 average time/residue: 0.3504 time to fit residues: 138.7764 Evaluate side-chains 249 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 221 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain B residue 34 ILE 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 274 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET 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 D residue 260 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 232 SER 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 247 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 104 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 Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 9 optimal weight: 2.9990 chunk 183 optimal weight: 0.0870 chunk 118 optimal weight: 0.9980 chunk 262 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 260 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 115 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 = 0.3315 r_free = 0.3315 target = 0.088482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074974 restraints weight = 39564.217| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.60 r_work: 0.2956 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21924 Z= 0.130 Angle : 0.578 8.151 29739 Z= 0.280 Chirality : 0.045 0.163 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.327 101.801 3048 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 13.28 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2691 helix: 0.52 (0.18), residues: 870 sheet: -0.19 (0.23), residues: 530 loop : 0.18 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.009 0.001 HIS G 87 PHE 0.011 0.001 PHE D 31 TYR 0.010 0.001 TYR B 306 ARG 0.007 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 870) hydrogen bonds : angle 4.85416 ( 2262) covalent geometry : bond 0.00320 (21924) covalent geometry : angle 0.57817 (29739) *********************** 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 256 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 2.507 Fit side-chains REVERT: A 97 ASP cc_start: 0.8225 (m-30) cc_final: 0.7535 (p0) REVERT: A 318 THR cc_start: 0.7262 (m) cc_final: 0.6749 (p) REVERT: A 355 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 65 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8782 (pp) REVERT: B 143 TYR cc_start: 0.6195 (t80) cc_final: 0.5684 (t80) REVERT: B 252 ASN cc_start: 0.8151 (m-40) cc_final: 0.7944 (m110) REVERT: B 260 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8808 (p) REVERT: C 246 GLN cc_start: 0.8909 (mp10) cc_final: 0.8597 (mp10) REVERT: D 298 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.7994 (t) REVERT: E 72 GLU cc_start: 0.7615 (mp0) cc_final: 0.7388 (mp0) REVERT: F 65 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8226 (pp) REVERT: F 107 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: F 125 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: F 291 LYS cc_start: 0.8120 (tptt) cc_final: 0.7722 (tttm) REVERT: G 72 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: G 278 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8755 (m) REVERT: G 327 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8487 (mp) outliers start: 46 outliers final: 29 residues processed: 249 average time/residue: 0.3222 time to fit residues: 126.2700 Evaluate side-chains 243 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 34 ILE 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 274 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET 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 260 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 232 SER 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 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 104 LEU 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 Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 173 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 185 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 chunk 259 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 115 ASN E 296 ASN G 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075030 restraints weight = 39774.969| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.61 r_work: 0.2960 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21924 Z= 0.132 Angle : 0.578 8.139 29739 Z= 0.279 Chirality : 0.046 0.160 3281 Planarity : 0.004 0.050 3827 Dihedral : 7.190 100.173 3048 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 13.59 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2691 helix: 0.58 (0.18), residues: 870 sheet: -0.11 (0.23), residues: 520 loop : 0.17 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.009 0.001 HIS G 87 PHE 0.011 0.001 PHE D 31 TYR 0.012 0.001 TYR G 166 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 870) hydrogen bonds : angle 4.80504 ( 2262) covalent geometry : bond 0.00328 (21924) covalent geometry : angle 0.57848 (29739) ********************** 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 252 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 2.369 Fit side-chains REVERT: A 97 ASP cc_start: 0.8265 (m-30) cc_final: 0.7538 (p0) REVERT: A 182 GLN cc_start: 0.7337 (tp-100) cc_final: 0.7113 (pm20) REVERT: A 355 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8526 (m) REVERT: B 65 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8744 (pp) REVERT: B 143 TYR cc_start: 0.6195 (t80) cc_final: 0.5615 (t80) REVERT: B 252 ASN cc_start: 0.8175 (m-40) cc_final: 0.7966 (m110) REVERT: B 260 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 246 GLN cc_start: 0.8955 (mp10) cc_final: 0.8642 (mp10) REVERT: D 298 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.7988 (t) REVERT: E 72 GLU cc_start: 0.7601 (mp0) cc_final: 0.7352 (mp0) REVERT: F 65 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8226 (pp) REVERT: F 107 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: F 125 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: F 291 LYS cc_start: 0.8182 (tptt) cc_final: 0.7793 (tttm) REVERT: G 72 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: G 278 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8804 (m) REVERT: G 327 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 43 outliers final: 30 residues processed: 247 average time/residue: 0.3439 time to fit residues: 134.5392 Evaluate side-chains 245 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 34 ILE 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 274 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET 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 260 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 232 SER 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 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 104 LEU 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 Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 16 optimal weight: 0.0050 chunk 28 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 115 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 = 0.3322 r_free = 0.3322 target = 0.088867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075387 restraints weight = 39678.764| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.62 r_work: 0.2945 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21924 Z= 0.128 Angle : 0.573 8.144 29739 Z= 0.276 Chirality : 0.045 0.154 3281 Planarity : 0.004 0.049 3827 Dihedral : 7.089 98.837 3048 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 13.67 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2691 helix: 0.63 (0.18), residues: 870 sheet: -0.10 (0.23), residues: 510 loop : 0.19 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.010 0.001 HIS G 87 PHE 0.011 0.001 PHE D 31 TYR 0.010 0.001 TYR B 306 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 870) hydrogen bonds : angle 4.76155 ( 2262) covalent geometry : bond 0.00317 (21924) covalent geometry : angle 0.57290 (29739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12622.20 seconds wall clock time: 220 minutes 42.55 seconds (13242.55 seconds total)