Starting phenix.real_space_refine on Sat Jun 14 08:44:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fju_50516/06_2025/9fju_50516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fju_50516/06_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_50516/06_2025/9fju_50516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fju_50516/06_2025/9fju_50516.map" model { file = "/net/cci-nas-00/data/ceres_data/9fju_50516/06_2025/9fju_50516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fju_50516/06_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-5710/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: 10.08, per 1000 atoms: 0.63 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: 4.02 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: 1.96 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: 5.00 Time building geometry restraints manager: 4.71 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.150 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.440 ------------------------------------------------------------------------------- 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 16324 Z= 0.198 Angle : 0.658 19.132 22198 Z= 0.311 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 Details of bonding type rmsd link_TRANS : bond 0.01340 ( 8) link_TRANS : angle 7.23200 ( 24) link_NAG-ASN : bond 0.01037 ( 2) link_NAG-ASN : angle 5.75031 ( 6) link_BETA1-4 : bond 0.00232 ( 2) link_BETA1-4 : angle 0.77683 ( 6) hydrogen bonds : bond 0.31045 ( 605) hydrogen bonds : angle 8.05070 ( 1581) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.79574 ( 4) covalent geometry : bond 0.00406 (16310) covalent geometry : angle 0.60691 (22158) *********************** 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 : 1.891 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: 0.2305 time to fit residues: 59.9029 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 : 1.636 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.099717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078541 restraints weight = 44219.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081234 restraints weight = 25649.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083081 restraints weight = 17363.975| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 16324 Z= 0.151 Angle : 0.659 10.598 22198 Z= 0.313 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 Details of bonding type rmsd link_TRANS : bond 0.00396 ( 8) link_TRANS : angle 1.74900 ( 24) link_NAG-ASN : bond 0.00398 ( 2) link_NAG-ASN : angle 6.59312 ( 6) link_BETA1-4 : bond 0.00199 ( 2) link_BETA1-4 : angle 3.80736 ( 6) hydrogen bonds : bond 0.05065 ( 605) hydrogen bonds : angle 5.67371 ( 1581) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.82459 ( 4) covalent geometry : bond 0.00334 (16310) covalent geometry : angle 0.64450 (22158) *********************** 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 : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8975 (mm) REVERT: B 213 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8474 (ttmm) REVERT: D 283 MET cc_start: 0.8546 (mmp) cc_final: 0.8131 (mmt) REVERT: F 16 MET cc_start: 0.8827 (mpp) cc_final: 0.8110 (mpp) outliers start: 55 outliers final: 34 residues processed: 222 average time/residue: 0.2771 time to fit residues: 96.4967 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 : 2.468 ------------------------------------------------------------------------------- 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: 7.9990 chunk 119 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS E 155 GLN E 180 GLN E 193 GLN F 96 GLN F 134 HIS F 252 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072334 restraints weight = 44753.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074764 restraints weight = 26858.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076466 restraints weight = 18712.443| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 16324 Z= 0.385 Angle : 0.878 13.514 22198 Z= 0.424 Chirality : 0.054 0.373 2498 Planarity : 0.006 0.069 2802 Dihedral : 11.493 136.849 2371 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.16 % Allowed : 20.83 % Favored : 73.00 % 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: -0.51 (0.19), residues: 1958 helix: -0.53 (0.18), residues: 752 sheet: 0.20 (0.29), residues: 340 loop : -0.17 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 1 HIS 0.013 0.002 HIS D 40 PHE 0.030 0.003 PHE C 127 TYR 0.029 0.002 TYR F 80 ARG 0.008 0.001 ARG B 177 Details of bonding type rmsd link_TRANS : bond 0.00293 ( 8) link_TRANS : angle 1.03827 ( 24) link_NAG-ASN : bond 0.00944 ( 2) link_NAG-ASN : angle 7.16966 ( 6) link_BETA1-4 : bond 0.00708 ( 2) link_BETA1-4 : angle 5.57317 ( 6) hydrogen bonds : bond 0.06156 ( 605) hydrogen bonds : angle 5.78994 ( 1581) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.27628 ( 4) covalent geometry : bond 0.00877 (16310) covalent geometry : angle 0.86529 (22158) *********************** 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 273 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 168 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (t-90) REVERT: B 213 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8504 (ttmm) REVERT: B 352 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8006 (t80) REVERT: C 163 VAL cc_start: 0.9183 (t) cc_final: 0.8895 (p) REVERT: C 226 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7020 (tm-30) REVERT: F 16 MET cc_start: 0.8947 (mpp) cc_final: 0.8111 (mpp) REVERT: F 112 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7559 (mm-30) REVERT: F 127 GLU cc_start: 0.7757 (mp0) cc_final: 0.7487 (mp0) outliers start: 105 outliers final: 65 residues processed: 254 average time/residue: 0.2303 time to fit residues: 92.5759 Evaluate side-chains 218 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 150 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 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 87 HIS 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 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 212 ILE 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 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 311 ASP Chi-restraints excluded: chain D residue 370 VAL 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: 30.0000 chunk 77 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 chunk 153 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.098185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076913 restraints weight = 44140.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079549 restraints weight = 25816.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081371 restraints weight = 17578.952| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16324 Z= 0.111 Angle : 0.654 11.091 22198 Z= 0.306 Chirality : 0.048 0.408 2498 Planarity : 0.004 0.046 2802 Dihedral : 10.774 134.809 2371 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.23 % Allowed : 23.65 % 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: -0.05 (0.19), residues: 1958 helix: 0.05 (0.20), residues: 736 sheet: 0.17 (0.29), residues: 348 loop : 0.00 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 194 HIS 0.006 0.001 HIS D 40 PHE 0.015 0.001 PHE E 6 TYR 0.014 0.001 TYR A 240 ARG 0.004 0.000 ARG E 79 Details of bonding type rmsd link_TRANS : bond 0.00223 ( 8) link_TRANS : angle 1.05931 ( 24) link_NAG-ASN : bond 0.00905 ( 2) link_NAG-ASN : angle 7.18523 ( 6) link_BETA1-4 : bond 0.00680 ( 2) link_BETA1-4 : angle 4.95099 ( 6) hydrogen bonds : bond 0.03696 ( 605) hydrogen bonds : angle 5.04073 ( 1581) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.96839 ( 4) covalent geometry : bond 0.00237 (16310) covalent geometry : angle 0.63738 (22158) *********************** 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 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8696 (mm) REVERT: B 213 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: B 269 MET cc_start: 0.7770 (tpp) cc_final: 0.7378 (tpp) REVERT: B 352 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7871 (t80) REVERT: D 119 MET cc_start: 0.8842 (tpp) cc_final: 0.8633 (tpp) REVERT: F 16 MET cc_start: 0.8894 (mpp) cc_final: 0.7819 (mpp) REVERT: F 50 LYS cc_start: 0.9288 (mtpp) cc_final: 0.8955 (mtmm) REVERT: F 112 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7490 (mm-30) outliers start: 55 outliers final: 36 residues processed: 222 average time/residue: 0.2525 time to fit residues: 88.3162 Evaluate side-chains 196 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 101 HIS 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 338 SER Chi-restraints excluded: chain B residue 352 PHE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 119 MET 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 374 CYS 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 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 67 VAL 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: 3.9990 chunk 162 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.095630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074438 restraints weight = 45060.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.076983 restraints weight = 26440.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078742 restraints weight = 18126.431| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16324 Z= 0.231 Angle : 0.709 11.517 22198 Z= 0.333 Chirality : 0.049 0.405 2498 Planarity : 0.004 0.046 2802 Dihedral : 10.748 134.727 2371 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.17 % Allowed : 23.18 % Favored : 72.65 % 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: -0.14 (0.19), residues: 1958 helix: 0.03 (0.19), residues: 728 sheet: 0.14 (0.29), residues: 352 loop : -0.12 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 194 HIS 0.008 0.001 HIS D 40 PHE 0.023 0.002 PHE E 82 TYR 0.015 0.001 TYR F 80 ARG 0.004 0.000 ARG B 177 Details of bonding type rmsd link_TRANS : bond 0.00110 ( 8) link_TRANS : angle 0.92148 ( 24) link_NAG-ASN : bond 0.00940 ( 2) link_NAG-ASN : angle 7.43380 ( 6) link_BETA1-4 : bond 0.00773 ( 2) link_BETA1-4 : angle 4.95891 ( 6) hydrogen bonds : bond 0.04268 ( 605) hydrogen bonds : angle 5.13800 ( 1581) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.94241 ( 4) covalent geometry : bond 0.00534 (16310) covalent geometry : angle 0.69354 (22158) *********************** 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 226 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.9103 (p0) cc_final: 0.8531 (p0) REVERT: A 293 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 213 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8815 (ttmm) REVERT: B 325 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8138 (tpt) REVERT: B 352 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7869 (t80) REVERT: D 305 MET cc_start: 0.8183 (mpp) cc_final: 0.7960 (mpp) REVERT: E 77 LYS cc_start: 0.7587 (mmtt) cc_final: 0.6939 (mmtm) REVERT: E 88 LYS cc_start: 0.9284 (mppt) cc_final: 0.8948 (mmtm) REVERT: F 16 MET cc_start: 0.8936 (mpp) cc_final: 0.7814 (mpp) REVERT: F 50 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8922 (mtmm) REVERT: F 112 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 180 GLN cc_start: 0.8726 (mt0) cc_final: 0.8469 (pt0) outliers start: 71 outliers final: 52 residues processed: 206 average time/residue: 0.2535 time to fit residues: 83.4694 Evaluate side-chains 205 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 34 ILE 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 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 122 ILE 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 325 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 119 MET 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 194 THR 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 25 ASP 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 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 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 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 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: 6.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.096164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075163 restraints weight = 44413.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077689 restraints weight = 26064.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079484 restraints weight = 17896.861| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16324 Z= 0.194 Angle : 0.687 11.545 22198 Z= 0.320 Chirality : 0.049 0.419 2498 Planarity : 0.004 0.047 2802 Dihedral : 10.510 134.973 2371 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.75 % Allowed : 22.65 % Favored : 72.59 % 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: -0.19 (0.19), residues: 1958 helix: 0.03 (0.19), residues: 732 sheet: 0.03 (0.29), residues: 352 loop : -0.14 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 194 HIS 0.008 0.001 HIS D 40 PHE 0.020 0.001 PHE E 82 TYR 0.013 0.001 TYR D 91 ARG 0.006 0.000 ARG F 213 Details of bonding type rmsd link_TRANS : bond 0.00079 ( 8) link_TRANS : angle 0.94564 ( 24) link_NAG-ASN : bond 0.00937 ( 2) link_NAG-ASN : angle 7.50947 ( 6) link_BETA1-4 : bond 0.00761 ( 2) link_BETA1-4 : angle 4.93978 ( 6) hydrogen bonds : bond 0.03919 ( 605) hydrogen bonds : angle 5.01836 ( 1581) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.95272 ( 4) covalent geometry : bond 0.00448 (16310) covalent geometry : angle 0.67057 (22158) *********************** 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 245 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 12 ASN cc_start: 0.8732 (t0) cc_final: 0.7762 (p0) REVERT: B 213 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8898 (ttmm) REVERT: C 80 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8534 (t0) REVERT: E 77 LYS cc_start: 0.7700 (mmtt) cc_final: 0.6989 (mmtm) REVERT: E 88 LYS cc_start: 0.9269 (mppt) cc_final: 0.8955 (mmtm) REVERT: F 16 MET cc_start: 0.8920 (mpp) cc_final: 0.7762 (mpp) REVERT: F 50 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8922 (mtmm) REVERT: F 112 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7547 (mm-30) REVERT: F 130 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7412 (mm) outliers start: 81 outliers final: 64 residues processed: 228 average time/residue: 0.2363 time to fit residues: 85.3772 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 159 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE 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 186 THR 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 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 298 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 119 MET 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 193 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 89 THR Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 119 MET 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 246 GLN 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 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 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 186 LEU Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 196 ILE 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: 0.8980 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076352 restraints weight = 45032.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078958 restraints weight = 26577.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080742 restraints weight = 18252.875| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16324 Z= 0.149 Angle : 0.668 11.559 22198 Z= 0.307 Chirality : 0.049 0.485 2498 Planarity : 0.004 0.048 2802 Dihedral : 10.249 134.015 2371 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.17 % Allowed : 23.59 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1958 helix: 0.11 (0.20), residues: 730 sheet: 0.05 (0.29), residues: 352 loop : -0.08 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 194 HIS 0.006 0.001 HIS D 40 PHE 0.025 0.001 PHE F 128 TYR 0.012 0.001 TYR D 91 ARG 0.007 0.000 ARG D 28 Details of bonding type rmsd link_TRANS : bond 0.00110 ( 8) link_TRANS : angle 0.97246 ( 24) link_NAG-ASN : bond 0.00929 ( 2) link_NAG-ASN : angle 7.74856 ( 6) link_BETA1-4 : bond 0.00774 ( 2) link_BETA1-4 : angle 4.97564 ( 6) hydrogen bonds : bond 0.03529 ( 605) hydrogen bonds : angle 4.89071 ( 1581) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.82922 ( 4) covalent geometry : bond 0.00342 (16310) covalent geometry : angle 0.65059 (22158) *********************** 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 239 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8756 (mm) REVERT: B 12 ASN cc_start: 0.8746 (t0) cc_final: 0.7843 (p0) REVERT: B 192 ILE cc_start: 0.9125 (tp) cc_final: 0.8861 (tp) REVERT: B 213 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8897 (ttmm) REVERT: B 237 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: B 352 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7905 (t80) REVERT: D 51 ASP cc_start: 0.7452 (p0) cc_final: 0.6997 (m-30) REVERT: E 77 LYS cc_start: 0.7737 (mmtt) cc_final: 0.6956 (mmtm) REVERT: E 88 LYS cc_start: 0.9274 (mppt) cc_final: 0.8951 (mmtm) REVERT: F 16 MET cc_start: 0.8876 (mpp) cc_final: 0.7826 (mpp) REVERT: F 50 LYS cc_start: 0.9263 (mtpp) cc_final: 0.8926 (mtmm) REVERT: F 112 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7567 (mm-30) REVERT: F 180 GLN cc_start: 0.8742 (mt0) cc_final: 0.8472 (pt0) outliers start: 71 outliers final: 58 residues processed: 223 average time/residue: 0.2229 time to fit residues: 79.4581 Evaluate side-chains 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 ILE 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 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 B residue 352 PHE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 123 MET 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 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 E residue 252 HIS 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: 3.9990 chunk 129 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.097455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076162 restraints weight = 44041.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078759 restraints weight = 25894.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080533 restraints weight = 17761.640| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16324 Z= 0.119 Angle : 0.655 11.551 22198 Z= 0.299 Chirality : 0.048 0.507 2498 Planarity : 0.003 0.048 2802 Dihedral : 10.009 132.543 2371 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.87 % Allowed : 24.12 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1958 helix: 0.19 (0.20), residues: 730 sheet: 0.09 (0.29), residues: 348 loop : -0.05 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 194 HIS 0.005 0.001 HIS D 40 PHE 0.026 0.001 PHE F 128 TYR 0.010 0.001 TYR E 151 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd link_TRANS : bond 0.00160 ( 8) link_TRANS : angle 1.00478 ( 24) link_NAG-ASN : bond 0.00788 ( 2) link_NAG-ASN : angle 7.87102 ( 6) link_BETA1-4 : bond 0.00696 ( 2) link_BETA1-4 : angle 5.10256 ( 6) hydrogen bonds : bond 0.03223 ( 605) hydrogen bonds : angle 4.78535 ( 1581) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.78287 ( 4) covalent geometry : bond 0.00270 (16310) covalent geometry : angle 0.63600 (22158) *********************** 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 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8816 (mm) REVERT: B 12 ASN cc_start: 0.8699 (t0) cc_final: 0.7885 (p0) REVERT: B 192 ILE cc_start: 0.9051 (tp) cc_final: 0.8790 (tp) REVERT: B 205 GLU cc_start: 0.7813 (mp0) cc_final: 0.7459 (mp0) REVERT: B 213 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: B 237 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: B 352 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7920 (t80) REVERT: C 176 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8550 (mt) REVERT: D 325 MET cc_start: 0.8588 (mmt) cc_final: 0.8366 (mmt) REVERT: E 77 LYS cc_start: 0.7704 (mmtt) cc_final: 0.6958 (mmtm) REVERT: E 245 MET cc_start: 0.8237 (pmm) cc_final: 0.8025 (pmm) REVERT: F 16 MET cc_start: 0.8827 (mpp) cc_final: 0.7822 (mpp) REVERT: F 36 LEU cc_start: 0.8770 (mm) cc_final: 0.8386 (mm) REVERT: F 50 LYS cc_start: 0.9292 (mtpp) cc_final: 0.8916 (mtmm) REVERT: F 112 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7566 (mm-30) REVERT: F 180 GLN cc_start: 0.8736 (mt0) cc_final: 0.8452 (pt0) outliers start: 66 outliers final: 56 residues processed: 222 average time/residue: 0.2421 time to fit residues: 85.0447 Evaluate side-chains 225 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 164 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 186 THR 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 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 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 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 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 192 ILE Chi-restraints excluded: chain C residue 193 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 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 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 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 Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 128 optimal weight: 5.9990 chunk 193 optimal weight: 0.0010 chunk 22 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.095129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073842 restraints weight = 44338.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076363 restraints weight = 26084.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078108 restraints weight = 17946.809| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16324 Z= 0.245 Angle : 0.743 11.612 22198 Z= 0.347 Chirality : 0.050 0.515 2498 Planarity : 0.004 0.045 2802 Dihedral : 10.191 132.720 2370 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.58 % Allowed : 23.88 % 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: -0.31 (0.19), residues: 1958 helix: -0.11 (0.19), residues: 750 sheet: -0.14 (0.28), residues: 356 loop : -0.11 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 181 HIS 0.009 0.001 HIS D 40 PHE 0.018 0.002 PHE F 128 TYR 0.015 0.001 TYR D 91 ARG 0.008 0.001 ARG F 213 Details of bonding type rmsd link_TRANS : bond 0.00126 ( 8) link_TRANS : angle 0.93533 ( 24) link_NAG-ASN : bond 0.00860 ( 2) link_NAG-ASN : angle 7.98407 ( 6) link_BETA1-4 : bond 0.00868 ( 2) link_BETA1-4 : angle 5.05138 ( 6) hydrogen bonds : bond 0.04118 ( 605) hydrogen bonds : angle 5.05905 ( 1581) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.88573 ( 4) covalent geometry : bond 0.00564 (16310) covalent geometry : angle 0.72617 (22158) *********************** 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 237 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 159 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8778 (mm) REVERT: B 12 ASN cc_start: 0.8787 (t0) cc_final: 0.8106 (p0) REVERT: B 213 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8941 (ttmm) REVERT: B 237 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: D 51 ASP cc_start: 0.7555 (p0) cc_final: 0.7060 (m-30) REVERT: D 325 MET cc_start: 0.8632 (mmt) cc_final: 0.8369 (mmt) REVERT: E 77 LYS cc_start: 0.7757 (mmtt) cc_final: 0.6933 (mmtm) REVERT: E 245 MET cc_start: 0.8269 (pmm) cc_final: 0.8033 (pmm) REVERT: F 16 MET cc_start: 0.8840 (mpp) cc_final: 0.7839 (mpp) REVERT: F 36 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8338 (mm) REVERT: F 50 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8904 (mtmm) REVERT: F 112 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 180 GLN cc_start: 0.8749 (mt0) cc_final: 0.8484 (pt0) outliers start: 78 outliers final: 66 residues processed: 220 average time/residue: 0.2829 time to fit residues: 99.7039 Evaluate side-chains 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 157 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 257 CYS 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 75 ILE 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 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 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 192 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 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 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 248 ILE 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 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 116 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: 0.9990 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** ** D 40 HIS ** 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 = 0.3702 r_free = 0.3702 target = 0.098946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077252 restraints weight = 44837.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080064 restraints weight = 24941.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081971 restraints weight = 16615.266| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16324 Z= 0.150 Angle : 0.694 11.587 22198 Z= 0.318 Chirality : 0.049 0.517 2498 Planarity : 0.004 0.047 2802 Dihedral : 9.983 133.095 2370 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.70 % Allowed : 24.59 % Favored : 71.71 % 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: -0.17 (0.19), residues: 1958 helix: 0.09 (0.20), residues: 730 sheet: -0.08 (0.29), residues: 352 loop : -0.11 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 194 HIS 0.007 0.001 HIS D 40 PHE 0.022 0.001 PHE F 128 TYR 0.011 0.001 TYR D 91 ARG 0.005 0.000 ARG D 28 Details of bonding type rmsd link_TRANS : bond 0.00113 ( 8) link_TRANS : angle 0.99670 ( 24) link_NAG-ASN : bond 0.00801 ( 2) link_NAG-ASN : angle 7.95590 ( 6) link_BETA1-4 : bond 0.00739 ( 2) link_BETA1-4 : angle 5.05951 ( 6) hydrogen bonds : bond 0.03507 ( 605) hydrogen bonds : angle 4.92066 ( 1581) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.83603 ( 4) covalent geometry : bond 0.00347 (16310) covalent geometry : angle 0.67660 (22158) ********************** 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 227 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8776 (mm) REVERT: B 12 ASN cc_start: 0.8717 (t0) cc_final: 0.8074 (p0) REVERT: B 192 ILE cc_start: 0.9056 (tp) cc_final: 0.8799 (tp) REVERT: B 213 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8892 (ttmm) REVERT: B 237 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: D 325 MET cc_start: 0.8626 (mmt) cc_final: 0.8384 (mmt) REVERT: E 77 LYS cc_start: 0.7744 (mmtt) cc_final: 0.6961 (mmtm) REVERT: E 245 MET cc_start: 0.8297 (pmm) cc_final: 0.8045 (pmm) REVERT: F 16 MET cc_start: 0.8823 (mpp) cc_final: 0.7831 (mpp) REVERT: F 36 LEU cc_start: 0.8571 (mm) cc_final: 0.8104 (mm) REVERT: F 50 LYS cc_start: 0.9280 (mtpp) cc_final: 0.8900 (mtmm) REVERT: F 112 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7552 (mm-30) REVERT: F 180 GLN cc_start: 0.8738 (mt0) cc_final: 0.8462 (pt0) outliers start: 63 outliers final: 59 residues processed: 213 average time/residue: 0.2334 time to fit residues: 80.0043 Evaluate side-chains 223 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 186 THR 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 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 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 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 45 VAL 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 192 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 194 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 25 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 89 THR 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 311 ASP Chi-restraints excluded: chain D residue 345 ILE 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 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: 5.9990 chunk 81 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 102 optimal weight: 0.0270 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077715 restraints weight = 43272.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080314 restraints weight = 24928.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082125 restraints weight = 16851.136| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16324 Z= 0.103 Angle : 0.676 14.080 22198 Z= 0.306 Chirality : 0.048 0.520 2498 Planarity : 0.003 0.049 2802 Dihedral : 9.596 130.904 2370 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.88 % Allowed : 25.41 % Favored : 71.71 % 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: 0.27 (0.20), residues: 722 sheet: 0.03 (0.29), residues: 348 loop : -0.00 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 194 HIS 0.004 0.001 HIS D 40 PHE 0.028 0.001 PHE F 82 TYR 0.010 0.001 TYR E 151 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd link_TRANS : bond 0.00225 ( 8) link_TRANS : angle 1.04325 ( 24) link_NAG-ASN : bond 0.00784 ( 2) link_NAG-ASN : angle 8.01849 ( 6) link_BETA1-4 : bond 0.00638 ( 2) link_BETA1-4 : angle 5.20969 ( 6) hydrogen bonds : bond 0.02890 ( 605) hydrogen bonds : angle 4.72533 ( 1581) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.75475 ( 4) covalent geometry : bond 0.00227 (16310) covalent geometry : angle 0.65660 (22158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.06 seconds wall clock time: 86 minutes 2.69 seconds (5162.69 seconds total)