Starting phenix.real_space_refine on Mon Jan 20 23:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fju_50516/01_2025/9fju_50516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fju_50516/01_2025/9fju_50516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fju_50516/01_2025/9fju_50516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fju_50516/01_2025/9fju_50516.map" model { file = "/net/cci-nas-00/data/ceres_data/9fju_50516/01_2025/9fju_50516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fju_50516/01_2025/9fju_50516.cif" } resolution = 3.84 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= 0.003 sd= 0.046 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 8 5.21 5 S 104 5.16 5 C 10084 2.51 5 N 2666 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15968 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2894 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1990 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 1 Chain: "F" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1990 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 1 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.80, per 1000 atoms: 0.61 Number of scatterers: 15968 At special positions: 0 Unit cell: (108.24, 80.08, 190.08, 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 104 16.00 P 12 15.00 Mg 8 11.99 O 3094 8.00 N 2666 7.00 C 10084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 209 " distance=2.03 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 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG K 1 " - " ASN E 18 " " NAG L 1 " - " ASN F 18 " TRANS " TRP G 1 " - " ALA G 7 " " DTH G 4 " - " ALA G 3 " " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 27 sheets defined 44.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.879A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.807A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.921A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.766A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.684A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.626A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.858A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.778A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.325A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.526A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.936A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.879A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.298A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.675A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.677A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.805A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.644A 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 267 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.575A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.799A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.509A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.527A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.855A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.798A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.839A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 3.787A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.776A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.917A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.502A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.626A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.744A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.816A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.847A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.765A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.524A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.598A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.631A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.973A pdb=" N MET D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.735A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.543A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.530A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.609A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.536A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.561A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.117A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 removed outlier: 4.365A pdb=" N ASN E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 removed outlier: 3.890A pdb=" N ARG E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.534A pdb=" N GLY E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 158 removed outlier: 4.347A pdb=" N GLU E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.905A pdb=" N SER E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.956A pdb=" N SER E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 Processing helix chain 'E' and resid 242 through 250 Processing helix chain 'F' and resid 12 through 17 removed outlier: 4.039A pdb=" N MET F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.740A pdb=" N VAL F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 removed outlier: 3.675A pdb=" N GLY F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 155 removed outlier: 3.743A pdb=" N ASN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR F 148 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'F' and resid 218 through 225 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 242 through 250 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.693A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.744A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 removed outlier: 3.942A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 357 " --> pdb=" O MET A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.676A pdb=" N LEU A 176 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.527A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.599A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.832A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.370A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.626A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.512A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 133 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.092A pdb=" N VAL E 67 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.711A pdb=" N LEU C 176 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.473A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.730A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 66 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 71 through 72 removed outlier: 3.505A pdb=" N ILE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.547A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 165 through 166 removed outlier: 3.688A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.775A pdb=" N VAL E 255 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 256 " --> pdb=" O ALA E 231 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 231 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 95 removed outlier: 3.653A pdb=" N SER E 90 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS E 117 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR E 94 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 115 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE E 128 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N MET E 164 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA E 129 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 193 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.611A pdb=" N LEU F 83 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN F 38 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 8 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL F 40 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR F 10 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU F 256 " --> pdb=" O ALA F 231 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 231 " --> pdb=" O GLU F 256 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 89 through 96 removed outlier: 6.569A pdb=" N VAL F 91 " --> pdb=" O SER F 119 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER F 119 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP F 93 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA F 114 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA F 132 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 116 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 128 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N MET F 164 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA F 129 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET F 166 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 131 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP F 168 " --> pdb=" O VAL F 131 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2625 1.31 - 1.43: 4350 1.43 - 1.56: 9127 1.56 - 1.69: 32 1.69 - 1.82: 176 Bond restraints: 16310 Sorted by residual: bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.475 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C7 NAG L 2 " pdb=" N2 NAG L 2 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C7 NAG L 1 " pdb=" N2 NAG L 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C7 NAG K 1 " pdb=" N2 NAG K 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.28e+01 ... (remaining 16305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21757 1.92 - 3.84: 298 3.84 - 5.76: 74 5.76 - 7.68: 24 7.68 - 9.60: 5 Bond angle restraints: 22158 Sorted by residual: angle pdb=" N ILE D 289 " pdb=" CA ILE D 289 " pdb=" C ILE D 289 " ideal model delta sigma weight residual 112.83 109.47 3.36 9.90e-01 1.02e+00 1.15e+01 angle pdb=" CB MET D 44 " pdb=" CG MET D 44 " pdb=" SD MET D 44 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 110.96 114.70 -3.74 1.19e+00 7.06e-01 9.87e+00 angle pdb=" CB LYS E 88 " pdb=" CG LYS E 88 " pdb=" CD LYS E 88 " ideal model delta sigma weight residual 111.30 118.31 -7.01 2.30e+00 1.89e-01 9.29e+00 angle pdb=" CA MET D 44 " pdb=" CB MET D 44 " pdb=" CG MET D 44 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.44e+00 ... (remaining 22153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 9213 28.57 - 57.14: 526 57.14 - 85.71: 54 85.71 - 114.28: 51 114.28 - 142.85: 4 Dihedral angle restraints: 9848 sinusoidal: 3984 harmonic: 5864 Sorted by residual: dihedral pdb=" CB CYS E 173 " pdb=" SG CYS E 173 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual -86.00 -161.59 75.59 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 157.15 142.85 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" CA TRP I 1 " pdb=" N TRP I 1 " pdb=" C ALA I 7 " pdb=" CA ALA I 7 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2203 0.068 - 0.136: 287 0.136 - 0.204: 6 0.204 - 0.272: 0 0.272 - 0.340: 2 Chirality restraints: 2498 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN F 18 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 18 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 2495 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP G 1 " -0.036 2.00e-02 2.50e+03 6.22e-02 3.86e+01 pdb=" CA ALA G 7 " -0.031 2.00e-02 2.50e+03 pdb=" C ALA G 7 " 0.107 2.00e-02 2.50e+03 pdb=" O ALA G 7 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " 0.022 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" CA ALA J 7 " 0.019 2.00e-02 2.50e+03 pdb=" C ALA J 7 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA J 7 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N TRP H 1 " 0.021 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" CA ALA H 7 " 0.018 2.00e-02 2.50e+03 pdb=" C ALA H 7 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA H 7 " 0.024 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 43 2.34 - 2.98: 8174 2.98 - 3.62: 24423 3.62 - 4.26: 36266 4.26 - 4.90: 59227 Nonbonded interactions: 128133 Sorted by model distance: nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.705 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.727 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.727 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.730 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.976 2.170 ... (remaining 128128 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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 group one per residue 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: 2.710 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: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.290 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.129 16310 Z= 0.271 Angle : 0.607 9.597 22158 Z= 0.280 Chirality : 0.044 0.340 2498 Planarity : 0.003 0.080 2802 Dihedral : 18.807 142.847 6050 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.18 % Allowed : 22.18 % Favored : 77.64 % 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 (0.19), residues: 1958 helix: -0.20 (0.20), residues: 674 sheet: 0.46 (0.29), residues: 374 loop : 0.40 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 194 HIS 0.007 0.001 HIS D 40 PHE 0.026 0.001 PHE C 255 TYR 0.011 0.001 TYR E 63 ARG 0.007 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 123 MET cc_start: 0.8524 (ttm) cc_final: 0.8315 (ttp) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 0.2473 time to fit residues: 63.9021 Evaluate side-chains 155 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.0010 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN C 371 HIS E 155 GLN F 57 GLN F 134 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.099755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078505 restraints weight = 44312.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081199 restraints weight = 25866.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083038 restraints weight = 17556.668| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16310 Z= 0.219 Angle : 0.644 10.059 22158 Z= 0.309 Chirality : 0.048 0.349 2498 Planarity : 0.004 0.050 2802 Dihedral : 13.343 132.802 2371 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.23 % Allowed : 20.31 % Favored : 76.47 % 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: 0.21 (0.19), residues: 1958 helix: 0.07 (0.19), residues: 712 sheet: 0.55 (0.29), residues: 354 loop : 0.22 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 194 HIS 0.007 0.001 HIS D 40 PHE 0.021 0.001 PHE E 6 TYR 0.013 0.001 TYR E 24 ARG 0.004 0.000 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8970 (mm) REVERT: B 213 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8452 (ttmm) REVERT: D 283 MET cc_start: 0.8562 (mmp) cc_final: 0.8161 (mmt) REVERT: F 16 MET cc_start: 0.8801 (mpp) cc_final: 0.8080 (mpp) outliers start: 55 outliers final: 34 residues processed: 222 average time/residue: 0.2460 time to fit residues: 85.6781 Evaluate side-chains 192 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS E 155 GLN E 170 ASN E 180 GLN E 193 GLN F 96 GLN F 134 HIS F 252 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072081 restraints weight = 44779.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074487 restraints weight = 26854.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076118 restraints weight = 18746.673| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 16310 Z= 0.635 Angle : 0.889 13.489 22158 Z= 0.433 Chirality : 0.055 0.374 2498 Planarity : 0.006 0.068 2802 Dihedral : 11.667 136.854 2371 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.04 % Allowed : 20.83 % Favored : 73.12 % 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: -0.54 (0.19), residues: 1958 helix: -0.58 (0.18), residues: 748 sheet: 0.19 (0.29), residues: 340 loop : -0.18 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 1 HIS 0.013 0.002 HIS D 40 PHE 0.031 0.003 PHE C 127 TYR 0.030 0.002 TYR F 80 ARG 0.007 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 166 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8534 (ttmm) REVERT: B 352 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7968 (t80) REVERT: C 163 VAL cc_start: 0.9208 (t) cc_final: 0.8933 (p) REVERT: F 16 MET cc_start: 0.8946 (mpp) cc_final: 0.8108 (mpp) REVERT: F 112 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7606 (mm-30) REVERT: F 127 GLU cc_start: 0.7743 (mp0) cc_final: 0.7471 (mp0) outliers start: 103 outliers final: 67 residues processed: 248 average time/residue: 0.2487 time to fit residues: 97.2208 Evaluate side-chains 218 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 121 HIS Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 20.0000 chunk 77 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076424 restraints weight = 44033.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079067 restraints weight = 25522.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080903 restraints weight = 17360.015| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16310 Z= 0.164 Angle : 0.640 10.003 22158 Z= 0.303 Chirality : 0.048 0.402 2498 Planarity : 0.004 0.044 2802 Dihedral : 10.834 135.165 2371 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.64 % Allowed : 23.42 % Favored : 72.95 % 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: -0.09 (0.19), residues: 1958 helix: 0.03 (0.20), residues: 736 sheet: 0.17 (0.29), residues: 348 loop : -0.04 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 194 HIS 0.007 0.001 HIS D 40 PHE 0.015 0.001 PHE E 6 TYR 0.027 0.001 TYR A 240 ARG 0.009 0.000 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8702 (mm) REVERT: B 213 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8670 (ttmm) REVERT: B 269 MET cc_start: 0.7829 (tpp) cc_final: 0.7414 (tpp) REVERT: B 352 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7907 (t80) REVERT: D 119 MET cc_start: 0.8859 (tpp) cc_final: 0.8622 (tpp) REVERT: F 16 MET cc_start: 0.8899 (mpp) cc_final: 0.7840 (mpp) REVERT: F 50 LYS cc_start: 0.9289 (mtpp) cc_final: 0.8954 (mtmm) REVERT: F 112 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7485 (mm-30) outliers start: 62 outliers final: 36 residues processed: 223 average time/residue: 0.2472 time to fit residues: 86.8223 Evaluate side-chains 193 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 165 optimal weight: 0.0970 chunk 173 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.096552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075009 restraints weight = 45053.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077611 restraints weight = 26377.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079405 restraints weight = 18072.684| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16310 Z= 0.243 Angle : 0.646 9.111 22158 Z= 0.304 Chirality : 0.048 0.406 2498 Planarity : 0.004 0.046 2802 Dihedral : 10.651 134.551 2371 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.64 % Allowed : 23.65 % Favored : 72.71 % 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: -0.04 (0.19), residues: 1958 helix: 0.11 (0.20), residues: 730 sheet: 0.19 (0.29), residues: 348 loop : -0.06 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 194 HIS 0.006 0.001 HIS D 40 PHE 0.013 0.001 PHE E 82 TYR 0.021 0.001 TYR A 240 ARG 0.003 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9105 (p0) cc_final: 0.8535 (p0) REVERT: A 293 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8745 (mm) REVERT: B 213 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8680 (ttmm) REVERT: B 269 MET cc_start: 0.7857 (tpp) cc_final: 0.7490 (tpp) REVERT: B 352 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7868 (t80) REVERT: D 305 MET cc_start: 0.8170 (mpp) cc_final: 0.7956 (mpp) REVERT: E 77 LYS cc_start: 0.7571 (mmtt) cc_final: 0.6934 (mmtm) REVERT: E 88 LYS cc_start: 0.9275 (mppt) cc_final: 0.8922 (mmtm) REVERT: F 16 MET cc_start: 0.8907 (mpp) cc_final: 0.7794 (mpp) REVERT: F 50 LYS cc_start: 0.9273 (mtpp) cc_final: 0.8921 (mtmm) REVERT: F 112 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7522 (mm-30) REVERT: F 133 LEU cc_start: 0.7418 (tp) cc_final: 0.7213 (tt) REVERT: F 180 GLN cc_start: 0.8734 (mt0) cc_final: 0.8459 (pt0) outliers start: 62 outliers final: 47 residues processed: 204 average time/residue: 0.2821 time to fit residues: 91.9274 Evaluate side-chains 204 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 106 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076071 restraints weight = 44454.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078691 restraints weight = 26047.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080497 restraints weight = 17818.386| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16310 Z= 0.186 Angle : 0.627 8.256 22158 Z= 0.292 Chirality : 0.048 0.421 2498 Planarity : 0.003 0.048 2802 Dihedral : 10.315 132.986 2371 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.81 % Allowed : 23.30 % Favored : 72.89 % 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 (0.19), residues: 1958 helix: 0.21 (0.20), residues: 732 sheet: 0.19 (0.29), residues: 348 loop : -0.03 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 194 HIS 0.005 0.001 HIS D 40 PHE 0.012 0.001 PHE E 82 TYR 0.018 0.001 TYR A 240 ARG 0.005 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8778 (mm) REVERT: B 213 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8790 (ttmm) REVERT: B 352 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 176 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8706 (mt) REVERT: D 51 ASP cc_start: 0.7447 (p0) cc_final: 0.7026 (m-30) REVERT: E 77 LYS cc_start: 0.7594 (mmtt) cc_final: 0.6988 (mmtm) REVERT: E 88 LYS cc_start: 0.9279 (mppt) cc_final: 0.8919 (mmtm) REVERT: F 16 MET cc_start: 0.8858 (mpp) cc_final: 0.7790 (mpp) REVERT: F 50 LYS cc_start: 0.9262 (mtpp) cc_final: 0.8925 (mtmm) REVERT: F 112 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7540 (mm-30) outliers start: 65 outliers final: 48 residues processed: 216 average time/residue: 0.2352 time to fit residues: 80.9048 Evaluate side-chains 214 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 113 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074866 restraints weight = 44552.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077386 restraints weight = 26101.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079086 restraints weight = 17941.508| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16310 Z= 0.309 Angle : 0.688 9.266 22158 Z= 0.322 Chirality : 0.049 0.504 2498 Planarity : 0.004 0.045 2802 Dihedral : 10.291 132.977 2371 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.17 % Allowed : 23.47 % Favored : 72.36 % 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: -0.09 (0.19), residues: 1958 helix: 0.13 (0.20), residues: 730 sheet: 0.02 (0.29), residues: 356 loop : -0.08 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 194 HIS 0.008 0.001 HIS D 40 PHE 0.014 0.001 PHE C 127 TYR 0.017 0.001 TYR A 240 ARG 0.004 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 161 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9128 (p0) cc_final: 0.8683 (p0) REVERT: A 293 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 12 ASN cc_start: 0.8709 (t0) cc_final: 0.7844 (p0) REVERT: B 213 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8855 (ttmm) REVERT: B 237 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 80 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8538 (t0) REVERT: D 51 ASP cc_start: 0.7508 (p0) cc_final: 0.7038 (m-30) REVERT: E 77 LYS cc_start: 0.7672 (mmtt) cc_final: 0.6959 (mmtm) REVERT: F 16 MET cc_start: 0.8894 (mpp) cc_final: 0.7771 (mpp) REVERT: F 50 LYS cc_start: 0.9243 (mtpp) cc_final: 0.8920 (mtmm) REVERT: F 112 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7572 (mm-30) REVERT: F 180 GLN cc_start: 0.8736 (mt0) cc_final: 0.8466 (pt0) outliers start: 71 outliers final: 58 residues processed: 215 average time/residue: 0.2415 time to fit residues: 82.3450 Evaluate side-chains 218 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 156 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 150 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 188 optimal weight: 20.0000 chunk 60 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.098292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077075 restraints weight = 44066.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079713 restraints weight = 25747.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081516 restraints weight = 17555.680| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16310 Z= 0.150 Angle : 0.634 9.331 22158 Z= 0.293 Chirality : 0.048 0.503 2498 Planarity : 0.003 0.049 2802 Dihedral : 9.901 132.097 2371 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.11 % Allowed : 24.77 % Favored : 72.12 % 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: 0.10 (0.19), residues: 1958 helix: 0.30 (0.20), residues: 730 sheet: 0.16 (0.29), residues: 348 loop : -0.01 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 194 HIS 0.004 0.001 HIS D 40 PHE 0.017 0.001 PHE F 82 TYR 0.015 0.001 TYR A 240 ARG 0.009 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9122 (p0) cc_final: 0.8694 (p0) REVERT: A 293 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8893 (mm) REVERT: B 12 ASN cc_start: 0.8680 (t0) cc_final: 0.7817 (p0) REVERT: B 192 ILE cc_start: 0.9014 (tp) cc_final: 0.8766 (tp) REVERT: B 205 GLU cc_start: 0.7773 (mp0) cc_final: 0.7538 (mp0) REVERT: B 213 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8827 (ttmm) REVERT: B 237 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: B 352 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7844 (t80) REVERT: C 176 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8517 (mt) REVERT: E 77 LYS cc_start: 0.7715 (mmtt) cc_final: 0.6971 (mmtm) REVERT: E 245 MET cc_start: 0.8256 (pmm) cc_final: 0.8048 (pmm) REVERT: F 16 MET cc_start: 0.8850 (mpp) cc_final: 0.7848 (mpp) REVERT: F 50 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8907 (mtmm) REVERT: F 180 GLN cc_start: 0.8731 (mt0) cc_final: 0.8435 (pt0) outliers start: 53 outliers final: 43 residues processed: 219 average time/residue: 0.2429 time to fit residues: 84.0770 Evaluate side-chains 212 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 128 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076450 restraints weight = 44813.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079185 restraints weight = 25193.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.081063 restraints weight = 16897.638| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16310 Z= 0.352 Angle : 0.709 9.647 22158 Z= 0.333 Chirality : 0.050 0.508 2498 Planarity : 0.004 0.046 2802 Dihedral : 10.041 131.618 2370 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.70 % Allowed : 24.77 % Favored : 71.54 % 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: -0.09 (0.19), residues: 1958 helix: 0.12 (0.20), residues: 736 sheet: -0.02 (0.29), residues: 356 loop : -0.03 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 194 HIS 0.016 0.001 HIS D 40 PHE 0.025 0.002 PHE E 82 TYR 0.017 0.001 TYR A 240 ARG 0.007 0.001 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8784 (mm) REVERT: B 12 ASN cc_start: 0.8766 (t0) cc_final: 0.8064 (p0) REVERT: B 28 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7348 (ptp90) REVERT: B 213 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: B 237 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: B 352 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7972 (t80) REVERT: E 77 LYS cc_start: 0.7718 (mmtt) cc_final: 0.6923 (mmtm) REVERT: F 16 MET cc_start: 0.8840 (mpp) cc_final: 0.7860 (mpp) REVERT: F 50 LYS cc_start: 0.9291 (mtpp) cc_final: 0.8918 (mtmm) REVERT: F 180 GLN cc_start: 0.8742 (mt0) cc_final: 0.8467 (pt0) outliers start: 63 outliers final: 54 residues processed: 207 average time/residue: 0.2443 time to fit residues: 79.7866 Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 HIS Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 157 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 161 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076658 restraints weight = 44314.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079232 restraints weight = 25723.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081019 restraints weight = 17490.351| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16310 Z= 0.211 Angle : 0.669 10.711 22158 Z= 0.310 Chirality : 0.049 0.510 2498 Planarity : 0.004 0.047 2802 Dihedral : 9.897 131.827 2370 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.40 % Allowed : 25.47 % Favored : 71.13 % 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: -0.01 (0.19), residues: 1958 helix: 0.24 (0.20), residues: 724 sheet: 0.02 (0.29), residues: 348 loop : -0.05 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 194 HIS 0.013 0.001 HIS D 40 PHE 0.025 0.001 PHE E 82 TYR 0.015 0.001 TYR A 240 ARG 0.006 0.000 ARG D 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9133 (p0) cc_final: 0.8687 (p0) REVERT: A 293 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8810 (mm) REVERT: B 12 ASN cc_start: 0.8724 (t0) cc_final: 0.8051 (p0) REVERT: B 192 ILE cc_start: 0.9113 (tp) cc_final: 0.8845 (tp) REVERT: B 213 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8947 (ttmm) REVERT: B 237 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 352 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7899 (t80) REVERT: C 176 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8681 (mt) REVERT: E 77 LYS cc_start: 0.7715 (mmtt) cc_final: 0.6933 (mmtm) REVERT: E 245 MET cc_start: 0.8203 (pmm) cc_final: 0.7954 (pmm) REVERT: F 16 MET cc_start: 0.8888 (mpp) cc_final: 0.7907 (mpp) REVERT: F 36 LEU cc_start: 0.8675 (mm) cc_final: 0.8332 (mm) REVERT: F 50 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8896 (mtmm) REVERT: F 180 GLN cc_start: 0.8713 (mt0) cc_final: 0.8429 (pt0) outliers start: 58 outliers final: 49 residues processed: 213 average time/residue: 0.2398 time to fit residues: 81.0106 Evaluate side-chains 216 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 68 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076114 restraints weight = 44346.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.078723 restraints weight = 26109.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080455 restraints weight = 17923.382| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16310 Z= 0.189 Angle : 0.666 13.662 22158 Z= 0.306 Chirality : 0.048 0.514 2498 Planarity : 0.003 0.047 2802 Dihedral : 9.722 130.201 2370 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.23 % Allowed : 25.41 % Favored : 71.36 % 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 (0.19), residues: 1958 helix: 0.29 (0.20), residues: 724 sheet: 0.07 (0.29), residues: 348 loop : -0.02 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 194 HIS 0.011 0.001 HIS D 40 PHE 0.023 0.001 PHE E 82 TYR 0.014 0.001 TYR A 240 ARG 0.006 0.000 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3956.88 seconds wall clock time: 73 minutes 50.94 seconds (4430.94 seconds total)