Starting phenix.real_space_refine on Sat Jun 14 17:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwv_27761/06_2025/8dwv_27761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwv_27761/06_2025/8dwv_27761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwv_27761/06_2025/8dwv_27761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwv_27761/06_2025/8dwv_27761.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwv_27761/06_2025/8dwv_27761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwv_27761/06_2025/8dwv_27761.cif" } resolution = 3.6 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= 0.001 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 10450 2.51 5 N 2744 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 353, 2780 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2741 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 335} Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2754 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2749 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 347, 2749 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 336} Chain: "G" Number of atoms: 2737 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 345, 2737 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 334} Chain: "H" Number of atoms: 2719 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2719 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.18, per 1000 atoms: 0.68 Number of scatterers: 16480 At special positions: 0 Unit cell: (74.6929, 139.521, 305.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 3136 8.00 N 2744 7.00 C 10450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS H 361 " 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 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 44.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 185 through 197 removed outlier: 3.588A pdb=" N LEU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.133A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.514A pdb=" N GLU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.168A pdb=" N SER A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 4.502A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.604A pdb=" N MET A 269 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.617A pdb=" N ILE A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 removed outlier: 6.319A pdb=" N SER A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.699A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.772A pdb=" N SER A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.756A pdb=" N ASP B 63 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 145 through 148 Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.552A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.548A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.513A pdb=" N SER B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.226A pdb=" N VAL B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.787A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.541A pdb=" N LYS E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.542A pdb=" N GLY E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.572A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 255 removed outlier: 4.416A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.516A pdb=" N LEU E 273 " --> pdb=" O MET E 269 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 328 through 333 removed outlier: 4.189A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.596A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 360 removed outlier: 3.711A pdb=" N VAL E 349 " --> pdb=" O HIS E 345 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 358 " --> pdb=" O ARG E 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.926A pdb=" N ASP F 63 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 4.265A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.601A pdb=" N ASP F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 Processing helix chain 'F' and resid 215 through 222 Processing helix chain 'F' and resid 222 through 228 removed outlier: 3.734A pdb=" N MET F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 247 through 261 Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.618A pdb=" N SER F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 315 through 333 removed outlier: 6.059A pdb=" N SER F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP F 331 " --> pdb=" O TYR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.716A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.508A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 358 " --> pdb=" O ARG F 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.666A pdb=" N ARG G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 removed outlier: 4.197A pdb=" N ASP G 82 " --> pdb=" O GLU G 78 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'G' and resid 185 through 197 removed outlier: 4.201A pdb=" N GLU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 Processing helix chain 'G' and resid 222 through 230 removed outlier: 3.956A pdb=" N MET G 228 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE G 229 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 266 through 268 No H-bonds generated for 'chain 'G' and resid 266 through 268' Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.735A pdb=" N SER G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 314 through 333 removed outlier: 6.168A pdb=" N SER G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 removed outlier: 4.288A pdb=" N LYS G 339 " --> pdb=" O THR G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.580A pdb=" N VAL G 349 " --> pdb=" O HIS G 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 44 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.714A pdb=" N GLU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 4.017A pdb=" N ASN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 221 removed outlier: 3.982A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.755A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.737A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 269 through 281 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.739A pdb=" N SER H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 313 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 328 through 333 removed outlier: 4.087A pdb=" N LEU H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 345 Processing helix chain 'H' and resid 345 through 359 removed outlier: 3.511A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 38 removed outlier: 3.564A pdb=" N PHE A 32 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 34 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A 159 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 36 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 155 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.412A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.412A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 137 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 209 through 213 removed outlier: 8.393A pdb=" N ILE A 243 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS A 205 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.628A pdb=" N ILE B 137 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU B 86 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS B 135 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 213 removed outlier: 4.095A pdb=" N VAL B 241 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 205 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 29 through 38 removed outlier: 4.962A pdb=" N THR E 156 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 115 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 66 through 72 removed outlier: 7.015A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N AARG E 70 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB3, first strand: chain 'E' and resid 202 through 206 removed outlier: 4.020A pdb=" N PHE E 211 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.791A pdb=" N VAL F 164 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 68 through 72 removed outlier: 3.760A pdb=" N ASN F 72 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER F 85 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 206 Processing sheet with id=AB8, first strand: chain 'G' and resid 29 through 38 removed outlier: 3.948A pdb=" N CYS G 159 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP G 36 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE G 38 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 155 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 99 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.911A pdb=" N VAL G 71 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N AARG G 70 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 85 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU G 86 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE G 133 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AC2, first strand: chain 'H' and resid 29 through 35 Processing sheet with id=AC3, first strand: chain 'H' and resid 67 through 71 removed outlier: 3.573A pdb=" N TYR H 87 " --> pdb=" O AARG H 70 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU H 86 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LYS H 135 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LEU H 88 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N PHE H 133 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU H 90 " --> pdb=" O TRP H 131 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TRP H 131 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AC5, first strand: chain 'H' and resid 103 through 107 removed outlier: 3.597A pdb=" N LYS H 115 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 205 through 206 639 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5371 1.35 - 1.47: 3829 1.47 - 1.59: 7384 1.59 - 1.71: 0 1.71 - 1.83: 222 Bond restraints: 16806 Sorted by residual: bond pdb=" N GLN G 173 " pdb=" CA GLN G 173 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.29e-02 6.01e+03 1.35e+01 bond pdb=" N SER G 171 " pdb=" CA SER G 171 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N ILE G 170 " pdb=" CA ILE G 170 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.30e-02 5.92e+03 7.58e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.35e+00 bond pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.95e+00 ... (remaining 16801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 22435 3.08 - 6.15: 212 6.15 - 9.23: 16 9.23 - 12.31: 1 12.31 - 15.38: 1 Bond angle restraints: 22665 Sorted by residual: angle pdb=" C MET B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 123.91 139.29 -15.38 1.66e+00 3.63e-01 8.59e+01 angle pdb=" O PHE E 43 " pdb=" C PHE E 43 " pdb=" N CYS E 44 " ideal model delta sigma weight residual 122.32 129.03 -6.71 1.15e+00 7.56e-01 3.40e+01 angle pdb=" CA PHE E 43 " pdb=" C PHE E 43 " pdb=" N CYS E 44 " ideal model delta sigma weight residual 117.07 110.83 6.24 1.21e+00 6.83e-01 2.66e+01 angle pdb=" CA ILE G 170 " pdb=" C ILE G 170 " pdb=" O ILE G 170 " ideal model delta sigma weight residual 121.58 116.63 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" N GLN G 173 " pdb=" CA GLN G 173 " pdb=" CB GLN G 173 " ideal model delta sigma weight residual 110.49 118.61 -8.12 1.69e+00 3.50e-01 2.31e+01 ... (remaining 22660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9257 17.89 - 35.79: 761 35.79 - 53.68: 154 53.68 - 71.58: 34 71.58 - 89.47: 19 Dihedral angle restraints: 10225 sinusoidal: 4089 harmonic: 6136 Sorted by residual: dihedral pdb=" CA VAL G 168 " pdb=" C VAL G 168 " pdb=" N ASN G 169 " pdb=" CA ASN G 169 " ideal model delta harmonic sigma weight residual -180.00 -108.12 -71.88 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CB CYS F 361 " pdb=" SG CYS F 361 " pdb=" SG CYS H 361 " pdb=" CB CYS H 361 " ideal model delta sinusoidal sigma weight residual -86.00 -173.37 87.37 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA SER G 171 " pdb=" C SER G 171 " pdb=" N GLY G 172 " pdb=" CA GLY G 172 " ideal model delta harmonic sigma weight residual 0.00 -41.89 41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 10222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2364 0.095 - 0.191: 125 0.191 - 0.286: 2 0.286 - 0.381: 3 0.381 - 0.477: 2 Chirality restraints: 2496 Sorted by residual: chirality pdb=" CA ARG E 198 " pdb=" N ARG E 198 " pdb=" C ARG E 198 " pdb=" CB ARG E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ARG E 45 " pdb=" N ARG E 45 " pdb=" C ARG E 45 " pdb=" CB ARG E 45 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 2493 not shown) Planarity restraints: 2911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 164 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C VAL G 164 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL G 164 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN G 165 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 361 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO F 362 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO F 362 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 362 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 43 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C PHE E 43 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE E 43 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS E 44 " 0.011 2.00e-02 2.50e+03 ... (remaining 2908 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 241 2.64 - 3.21: 15787 3.21 - 3.77: 24564 3.77 - 4.34: 32439 4.34 - 4.90: 53679 Nonbonded interactions: 126710 Sorted by model distance: nonbonded pdb=" OG1 THR G 25 " pdb=" O THR H 37 " model vdw 2.076 3.040 nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.081 3.040 nonbonded pdb=" OG SER G 298 " pdb=" OD1 ASN G 301 " model vdw 2.085 3.040 nonbonded pdb=" O LEU H 218 " pdb=" OG SER H 222 " model vdw 2.100 3.040 nonbonded pdb=" OG SER G 42 " pdb=" OD2 ASP G 153 " model vdw 2.108 3.040 ... (remaining 126705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'B' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'E' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 361)) selection = (chain 'F' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'G' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'H' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.190 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4687 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 0.047 16807 Z= 0.186 Angle : 0.740 15.384 22667 Z= 0.405 Chirality : 0.046 0.477 2496 Planarity : 0.004 0.072 2911 Dihedral : 14.514 89.471 6218 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.83 % Favored : 90.59 % Rotamer: Outliers : 0.28 % Allowed : 0.06 % Favored : 99.67 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.19), residues: 2072 helix: 0.86 (0.20), residues: 717 sheet: -1.10 (0.30), residues: 296 loop : -1.86 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 67 HIS 0.004 0.001 HIS B 214 PHE 0.022 0.002 PHE F 43 TYR 0.014 0.001 TYR E 327 ARG 0.006 0.000 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.20159 ( 632) hydrogen bonds : angle 7.87446 ( 1773) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.21954 ( 2) covalent geometry : bond 0.00380 (16806) covalent geometry : angle 0.73998 (22665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.2263 (tpt) cc_final: 0.1152 (tpt) REVERT: B 48 MET cc_start: 0.2399 (pmm) cc_final: 0.1542 (ppp) REVERT: B 176 MET cc_start: 0.6608 (tmm) cc_final: 0.5254 (mpp) REVERT: H 288 MET cc_start: 0.6949 (ppp) cc_final: 0.6560 (ppp) outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 0.2808 time to fit residues: 52.2825 Evaluate side-chains 98 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 62 ASN A 196 ASN B 239 ASN B 312 HIS E 62 ASN E 328 HIS E 347 HIS E 360 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN F 174 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 HIS ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.076264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.046582 restraints weight = 148999.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.045864 restraints weight = 147427.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.045002 restraints weight = 169329.136| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16807 Z= 0.212 Angle : 0.694 8.351 22667 Z= 0.368 Chirality : 0.044 0.317 2496 Planarity : 0.004 0.070 2911 Dihedral : 6.358 86.295 2220 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.72 % Favored : 91.70 % Rotamer: Outliers : 0.55 % Allowed : 7.60 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2072 helix: 0.76 (0.19), residues: 761 sheet: -1.16 (0.29), residues: 331 loop : -1.92 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 131 HIS 0.008 0.001 HIS A 214 PHE 0.023 0.002 PHE F 257 TYR 0.016 0.002 TYR B 280 ARG 0.007 0.001 ARG G 284 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 632) hydrogen bonds : angle 5.80572 ( 1773) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.86320 ( 2) covalent geometry : bond 0.00440 (16806) covalent geometry : angle 0.69427 (22665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7615 (mpp) cc_final: 0.7213 (mpp) REVERT: A 176 MET cc_start: 0.8337 (tpp) cc_final: 0.8019 (tmm) REVERT: A 233 MET cc_start: 0.6903 (tmm) cc_final: 0.6139 (tmm) REVERT: B 178 MET cc_start: 0.8188 (tpp) cc_final: 0.7442 (tpp) REVERT: B 228 MET cc_start: 0.9126 (ptm) cc_final: 0.8741 (ppp) REVERT: E 341 MET cc_start: 0.8751 (tmm) cc_final: 0.8503 (tmm) REVERT: F 35 MET cc_start: 0.8781 (pmm) cc_final: 0.8188 (pmm) REVERT: F 228 MET cc_start: 0.8394 (ptt) cc_final: 0.7924 (tmm) REVERT: F 341 MET cc_start: 0.8857 (tpp) cc_final: 0.8654 (tpp) REVERT: H 48 MET cc_start: 0.8434 (mmm) cc_final: 0.8085 (mmm) REVERT: H 117 MET cc_start: 0.5384 (pmm) cc_final: 0.5141 (pmm) REVERT: H 288 MET cc_start: 0.8864 (ppp) cc_final: 0.8593 (ppp) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.2624 time to fit residues: 42.8892 Evaluate side-chains 98 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 94 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 40 ASN B 231 HIS ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.075885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.045646 restraints weight = 148490.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.044571 restraints weight = 143048.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.044707 restraints weight = 131101.041| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16807 Z= 0.144 Angle : 0.625 11.216 22667 Z= 0.332 Chirality : 0.042 0.339 2496 Planarity : 0.004 0.066 2911 Dihedral : 5.568 52.408 2216 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.48 % Favored : 92.04 % Rotamer: Outliers : 1.16 % Allowed : 9.48 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.97 (0.19), residues: 2072 helix: 0.95 (0.19), residues: 770 sheet: -1.03 (0.30), residues: 324 loop : -1.86 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 131 HIS 0.006 0.001 HIS F 214 PHE 0.020 0.001 PHE F 257 TYR 0.012 0.001 TYR B 123 ARG 0.006 0.000 ARG B 284 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 632) hydrogen bonds : angle 5.39083 ( 1773) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.77192 ( 2) covalent geometry : bond 0.00302 (16806) covalent geometry : angle 0.62502 (22665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7661 (mpp) cc_final: 0.7142 (mpp) REVERT: A 233 MET cc_start: 0.7122 (tmm) cc_final: 0.6708 (tmm) REVERT: A 255 MET cc_start: 0.9107 (mmm) cc_final: 0.8795 (mtm) REVERT: B 178 MET cc_start: 0.7797 (tpp) cc_final: 0.7456 (tpp) REVERT: B 228 MET cc_start: 0.9099 (ptm) cc_final: 0.8853 (ppp) REVERT: E 228 MET cc_start: 0.8055 (tmm) cc_final: 0.7538 (tmm) REVERT: E 255 MET cc_start: 0.7872 (mtp) cc_final: 0.7515 (mtp) REVERT: E 341 MET cc_start: 0.8851 (tmm) cc_final: 0.8537 (tmm) REVERT: F 35 MET cc_start: 0.8770 (pmm) cc_final: 0.8442 (pmm) REVERT: F 233 MET cc_start: 0.8471 (pmm) cc_final: 0.8186 (pmm) REVERT: G 117 MET cc_start: 0.6194 (ppp) cc_final: 0.5915 (ppp) REVERT: G 269 MET cc_start: 0.7586 (ppp) cc_final: 0.7340 (ppp) REVERT: H 24 TYR cc_start: 0.8595 (m-10) cc_final: 0.8360 (m-10) REVERT: H 48 MET cc_start: 0.8499 (mmm) cc_final: 0.8128 (mmm) REVERT: H 117 MET cc_start: 0.5598 (pmm) cc_final: 0.5362 (pmm) REVERT: H 233 MET cc_start: 0.7512 (ppp) cc_final: 0.6737 (ppp) REVERT: H 288 MET cc_start: 0.9038 (ppp) cc_final: 0.8766 (ppp) outliers start: 21 outliers final: 8 residues processed: 110 average time/residue: 0.2452 time to fit residues: 44.0800 Evaluate side-chains 99 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 12 optimal weight: 10.0000 chunk 164 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 186 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 145 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 160 optimal weight: 50.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 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 = 0.4362 r_free = 0.4362 target = 0.073982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.044556 restraints weight = 149237.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.043576 restraints weight = 147787.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.043309 restraints weight = 135109.355| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16807 Z= 0.192 Angle : 0.669 13.690 22667 Z= 0.351 Chirality : 0.042 0.233 2496 Planarity : 0.004 0.062 2911 Dihedral : 5.390 35.118 2216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.64 % Favored : 90.93 % Rotamer: Outliers : 1.32 % Allowed : 11.52 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 2072 helix: 0.77 (0.19), residues: 773 sheet: -1.13 (0.28), residues: 349 loop : -1.90 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 131 HIS 0.006 0.001 HIS F 214 PHE 0.026 0.002 PHE H 251 TYR 0.014 0.001 TYR F 123 ARG 0.005 0.001 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 632) hydrogen bonds : angle 5.44505 ( 1773) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.32413 ( 2) covalent geometry : bond 0.00404 (16806) covalent geometry : angle 0.66927 (22665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7917 (mpp) cc_final: 0.7263 (mpp) REVERT: A 233 MET cc_start: 0.7503 (tmm) cc_final: 0.7067 (tmm) REVERT: A 255 MET cc_start: 0.9130 (mmm) cc_final: 0.8679 (mtm) REVERT: B 35 MET cc_start: 0.6177 (tpt) cc_final: 0.5882 (mmp) REVERT: B 178 MET cc_start: 0.7947 (tpp) cc_final: 0.7578 (tpp) REVERT: B 228 MET cc_start: 0.9104 (ptm) cc_final: 0.8889 (ppp) REVERT: E 48 MET cc_start: 0.8915 (ppp) cc_final: 0.8684 (pmm) REVERT: E 70 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8339 (ptm-80) REVERT: E 145 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8927 (tp30) REVERT: E 228 MET cc_start: 0.8016 (tmm) cc_final: 0.7471 (tmm) REVERT: E 341 MET cc_start: 0.9034 (tmm) cc_final: 0.8727 (tmm) REVERT: F 35 MET cc_start: 0.9034 (pmm) cc_final: 0.8827 (pmm) REVERT: F 84 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8602 (mp) REVERT: F 228 MET cc_start: 0.7936 (tmm) cc_final: 0.7646 (tmm) REVERT: F 233 MET cc_start: 0.8507 (pmm) cc_final: 0.8286 (pmm) REVERT: H 48 MET cc_start: 0.8759 (mmm) cc_final: 0.8448 (mmm) REVERT: H 117 MET cc_start: 0.6347 (pmm) cc_final: 0.6120 (pmm) REVERT: H 233 MET cc_start: 0.7182 (ppp) cc_final: 0.6217 (ppp) REVERT: H 288 MET cc_start: 0.9116 (ppp) cc_final: 0.8828 (ppp) outliers start: 24 outliers final: 12 residues processed: 111 average time/residue: 0.2511 time to fit residues: 44.4756 Evaluate side-chains 104 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 7 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 154 optimal weight: 30.0000 chunk 78 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.073077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.044022 restraints weight = 153358.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.043046 restraints weight = 143357.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.042574 restraints weight = 138965.791| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16807 Z= 0.180 Angle : 0.660 10.665 22667 Z= 0.346 Chirality : 0.042 0.179 2496 Planarity : 0.004 0.059 2911 Dihedral : 5.267 31.177 2212 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.11 % Favored : 91.51 % Rotamer: Outliers : 1.87 % Allowed : 12.95 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 2072 helix: 0.87 (0.19), residues: 775 sheet: -1.27 (0.28), residues: 353 loop : -1.90 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 22 HIS 0.006 0.001 HIS F 214 PHE 0.022 0.001 PHE F 257 TYR 0.016 0.001 TYR F 123 ARG 0.004 0.001 ARG G 121 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 632) hydrogen bonds : angle 5.34859 ( 1773) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.04699 ( 2) covalent geometry : bond 0.00379 (16806) covalent geometry : angle 0.65988 (22665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7868 (mpp) cc_final: 0.7665 (mpp) REVERT: A 176 MET cc_start: 0.8595 (tpp) cc_final: 0.8299 (tmm) REVERT: A 233 MET cc_start: 0.7857 (tmm) cc_final: 0.7629 (tmm) REVERT: A 255 MET cc_start: 0.9226 (mmm) cc_final: 0.8740 (mtm) REVERT: B 178 MET cc_start: 0.7956 (tpp) cc_final: 0.7648 (tpp) REVERT: E 63 ASP cc_start: 0.9258 (p0) cc_final: 0.9047 (m-30) REVERT: E 70 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8246 (ptm-80) REVERT: E 145 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8957 (tp30) REVERT: E 175 THR cc_start: 0.4619 (OUTLIER) cc_final: 0.4305 (p) REVERT: E 228 MET cc_start: 0.7839 (tmm) cc_final: 0.7498 (tmm) REVERT: E 341 MET cc_start: 0.8982 (tmm) cc_final: 0.8675 (tmm) REVERT: F 35 MET cc_start: 0.9159 (pmm) cc_final: 0.8878 (pmm) REVERT: F 228 MET cc_start: 0.8349 (tmm) cc_final: 0.7913 (tmm) REVERT: F 233 MET cc_start: 0.8709 (pmm) cc_final: 0.8456 (pmm) REVERT: H 48 MET cc_start: 0.9064 (mmm) cc_final: 0.8724 (mmm) REVERT: H 233 MET cc_start: 0.8632 (ppp) cc_final: 0.8380 (ppp) REVERT: H 274 LEU cc_start: 0.8914 (pp) cc_final: 0.8509 (tt) REVERT: H 288 MET cc_start: 0.9098 (ppp) cc_final: 0.8894 (ppp) outliers start: 34 outliers final: 16 residues processed: 119 average time/residue: 0.2590 time to fit residues: 50.0167 Evaluate side-chains 109 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 244 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 159 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 108 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.072643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.044233 restraints weight = 152444.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.042803 restraints weight = 157979.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.041944 restraints weight = 169967.567| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16807 Z= 0.175 Angle : 0.664 14.114 22667 Z= 0.343 Chirality : 0.043 0.239 2496 Planarity : 0.004 0.054 2911 Dihedral : 5.213 27.034 2210 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.64 % Favored : 90.97 % Rotamer: Outliers : 1.76 % Allowed : 13.88 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 2072 helix: 0.89 (0.19), residues: 772 sheet: -1.39 (0.29), residues: 335 loop : -1.86 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 131 HIS 0.005 0.001 HIS F 214 PHE 0.022 0.001 PHE F 257 TYR 0.014 0.001 TYR F 123 ARG 0.004 0.000 ARG F 284 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 632) hydrogen bonds : angle 5.30673 ( 1773) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.32380 ( 2) covalent geometry : bond 0.00371 (16806) covalent geometry : angle 0.66432 (22665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9239 (mmm) cc_final: 0.8798 (mtm) REVERT: B 117 MET cc_start: 0.8766 (mmm) cc_final: 0.8219 (ttp) REVERT: B 178 MET cc_start: 0.8031 (tpp) cc_final: 0.7717 (tpp) REVERT: B 341 MET cc_start: 0.9416 (tmm) cc_final: 0.9179 (tmm) REVERT: E 63 ASP cc_start: 0.9367 (p0) cc_final: 0.9034 (m-30) REVERT: E 70 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8080 (ptm-80) REVERT: E 145 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9151 (tp30) REVERT: E 176 MET cc_start: 0.6964 (mmp) cc_final: 0.6716 (mmp) REVERT: E 228 MET cc_start: 0.7845 (tmm) cc_final: 0.7521 (tmm) REVERT: F 35 MET cc_start: 0.9413 (pmm) cc_final: 0.9046 (pmm) REVERT: F 84 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8675 (mp) REVERT: F 228 MET cc_start: 0.8498 (tmm) cc_final: 0.8032 (tmm) REVERT: F 233 MET cc_start: 0.8764 (pmm) cc_final: 0.8519 (pmm) REVERT: H 274 LEU cc_start: 0.8706 (pp) cc_final: 0.8244 (tt) outliers start: 32 outliers final: 20 residues processed: 115 average time/residue: 0.2643 time to fit residues: 48.6797 Evaluate side-chains 110 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 174 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 166 optimal weight: 40.0000 chunk 49 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN ** F 72 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 = 0.4341 r_free = 0.4341 target = 0.072592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.043872 restraints weight = 151997.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.042385 restraints weight = 156989.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.042073 restraints weight = 161131.022| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16807 Z= 0.153 Angle : 0.669 14.148 22667 Z= 0.342 Chirality : 0.043 0.267 2496 Planarity : 0.003 0.056 2911 Dihedral : 5.133 25.362 2210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.30 % Favored : 91.26 % Rotamer: Outliers : 1.87 % Allowed : 14.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 2072 helix: 0.94 (0.19), residues: 776 sheet: -1.41 (0.29), residues: 350 loop : -1.77 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 22 HIS 0.005 0.001 HIS F 214 PHE 0.021 0.001 PHE F 257 TYR 0.014 0.001 TYR F 123 ARG 0.004 0.000 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 632) hydrogen bonds : angle 5.21444 ( 1773) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.45986 ( 2) covalent geometry : bond 0.00326 (16806) covalent geometry : angle 0.66937 (22665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7409 (mpp) cc_final: 0.7125 (mpp) REVERT: A 233 MET cc_start: 0.8413 (tmm) cc_final: 0.7993 (tmm) REVERT: A 255 MET cc_start: 0.9279 (mmm) cc_final: 0.8868 (mtm) REVERT: B 117 MET cc_start: 0.8527 (mmm) cc_final: 0.7983 (tmm) REVERT: B 178 MET cc_start: 0.8082 (tpp) cc_final: 0.7790 (tpp) REVERT: B 341 MET cc_start: 0.9408 (tmm) cc_final: 0.9176 (tmm) REVERT: E 43 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9216 (t80) REVERT: E 63 ASP cc_start: 0.9392 (p0) cc_final: 0.9080 (m-30) REVERT: E 70 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8009 (ptm-80) REVERT: E 175 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6090 (p) REVERT: E 233 MET cc_start: 0.6088 (tpt) cc_final: 0.4819 (tpp) REVERT: F 35 MET cc_start: 0.9415 (pmm) cc_final: 0.9088 (pmm) REVERT: F 84 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8828 (mp) REVERT: F 228 MET cc_start: 0.8510 (tmm) cc_final: 0.8024 (tmm) REVERT: F 233 MET cc_start: 0.8482 (pmm) cc_final: 0.8218 (pmm) REVERT: G 35 MET cc_start: 0.8567 (mmp) cc_final: 0.8357 (mmp) REVERT: G 178 MET cc_start: 0.5608 (tpp) cc_final: 0.5331 (tpp) REVERT: H 254 MET cc_start: 0.5699 (ptp) cc_final: 0.5424 (ptp) REVERT: H 274 LEU cc_start: 0.8910 (pp) cc_final: 0.8492 (tt) outliers start: 34 outliers final: 18 residues processed: 115 average time/residue: 0.2583 time to fit residues: 47.6883 Evaluate side-chains 109 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 198 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 72 ASN ** 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 = 0.4335 r_free = 0.4335 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.043413 restraints weight = 152186.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.042137 restraints weight = 156777.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.041796 restraints weight = 166323.301| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16807 Z= 0.162 Angle : 0.680 15.352 22667 Z= 0.347 Chirality : 0.042 0.162 2496 Planarity : 0.003 0.054 2911 Dihedral : 5.138 26.368 2210 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.35 % Favored : 91.22 % Rotamer: Outliers : 1.38 % Allowed : 15.65 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % 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: -0.99 (0.19), residues: 2072 helix: 0.87 (0.19), residues: 783 sheet: -1.20 (0.30), residues: 333 loop : -1.77 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 22 HIS 0.005 0.001 HIS F 214 PHE 0.021 0.001 PHE F 257 TYR 0.015 0.001 TYR F 123 ARG 0.005 0.000 ARG H 198 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 632) hydrogen bonds : angle 5.21758 ( 1773) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.37622 ( 2) covalent geometry : bond 0.00344 (16806) covalent geometry : angle 0.67991 (22665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9215 (mmm) cc_final: 0.8709 (mtm) REVERT: B 117 MET cc_start: 0.8699 (mmm) cc_final: 0.8070 (tmm) REVERT: B 178 MET cc_start: 0.8294 (tpp) cc_final: 0.7977 (tpp) REVERT: E 63 ASP cc_start: 0.9440 (p0) cc_final: 0.9082 (m-30) REVERT: E 70 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8167 (ptm-80) REVERT: E 175 THR cc_start: 0.6276 (OUTLIER) cc_final: 0.5847 (p) REVERT: E 341 MET cc_start: 0.9314 (tmm) cc_final: 0.8700 (tmm) REVERT: F 35 MET cc_start: 0.9006 (pmm) cc_final: 0.8766 (pmm) REVERT: F 84 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8800 (mp) REVERT: F 228 MET cc_start: 0.8384 (tmm) cc_final: 0.7922 (tmm) REVERT: F 233 MET cc_start: 0.8627 (pmm) cc_final: 0.8401 (pmm) REVERT: H 36 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7115 (t60) REVERT: H 274 LEU cc_start: 0.8955 (pp) cc_final: 0.8534 (tt) outliers start: 25 outliers final: 18 residues processed: 108 average time/residue: 0.3063 time to fit residues: 53.8412 Evaluate side-chains 109 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 70 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 192 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.071964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.043309 restraints weight = 152407.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.042121 restraints weight = 154664.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.041442 restraints weight = 168173.991| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16807 Z= 0.161 Angle : 0.691 16.747 22667 Z= 0.350 Chirality : 0.042 0.166 2496 Planarity : 0.003 0.051 2911 Dihedral : 5.156 27.006 2210 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.11 % Favored : 91.46 % Rotamer: Outliers : 1.60 % Allowed : 16.03 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 2072 helix: 0.88 (0.19), residues: 784 sheet: -1.19 (0.30), residues: 335 loop : -1.78 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 22 HIS 0.005 0.001 HIS F 214 PHE 0.021 0.001 PHE F 257 TYR 0.017 0.001 TYR F 123 ARG 0.004 0.000 ARG F 284 Details of bonding type rmsd hydrogen bonds : bond 0.02965 ( 632) hydrogen bonds : angle 5.19894 ( 1773) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.41697 ( 2) covalent geometry : bond 0.00345 (16806) covalent geometry : angle 0.69133 (22665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9190 (mmm) cc_final: 0.8744 (mtm) REVERT: B 117 MET cc_start: 0.8492 (mmm) cc_final: 0.7889 (tmm) REVERT: B 178 MET cc_start: 0.8231 (tpp) cc_final: 0.7961 (tpp) REVERT: B 341 MET cc_start: 0.9415 (tmm) cc_final: 0.9165 (tmm) REVERT: E 43 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.9096 (t80) REVERT: E 63 ASP cc_start: 0.9346 (p0) cc_final: 0.9029 (m-30) REVERT: E 175 THR cc_start: 0.6632 (OUTLIER) cc_final: 0.6219 (p) REVERT: E 228 MET cc_start: 0.8342 (tmm) cc_final: 0.7971 (tmm) REVERT: F 35 MET cc_start: 0.9375 (pmm) cc_final: 0.9081 (pmm) REVERT: F 228 MET cc_start: 0.8591 (tmm) cc_final: 0.8048 (tmm) REVERT: F 233 MET cc_start: 0.8511 (pmm) cc_final: 0.8243 (pmm) REVERT: G 176 MET cc_start: 0.2396 (ppp) cc_final: 0.1855 (ppp) REVERT: G 254 MET cc_start: -0.1112 (tpt) cc_final: -0.1319 (ttt) REVERT: H 36 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7120 (t60) REVERT: H 274 LEU cc_start: 0.8610 (pp) cc_final: 0.8180 (tt) outliers start: 29 outliers final: 21 residues processed: 111 average time/residue: 0.2716 time to fit residues: 48.5777 Evaluate side-chains 112 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN G 120 GLN G 312 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.070814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.042606 restraints weight = 157028.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.041483 restraints weight = 162116.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.040866 restraints weight = 161750.119| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16807 Z= 0.237 Angle : 0.765 15.267 22667 Z= 0.394 Chirality : 0.044 0.163 2496 Planarity : 0.004 0.061 2911 Dihedral : 5.527 29.888 2210 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.41 % Favored : 90.15 % Rotamer: Outliers : 1.38 % Allowed : 16.47 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2072 helix: 0.63 (0.19), residues: 791 sheet: -1.23 (0.30), residues: 334 loop : -1.98 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 22 HIS 0.008 0.001 HIS F 214 PHE 0.024 0.002 PHE F 257 TYR 0.028 0.002 TYR F 123 ARG 0.007 0.001 ARG F 284 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 632) hydrogen bonds : angle 5.57167 ( 1773) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.43322 ( 2) covalent geometry : bond 0.00503 (16806) covalent geometry : angle 0.76491 (22665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8366 (mpp) cc_final: 0.7862 (mpp) REVERT: A 255 MET cc_start: 0.9229 (mmm) cc_final: 0.8723 (mtm) REVERT: B 178 MET cc_start: 0.8585 (tpp) cc_final: 0.8268 (tpp) REVERT: E 63 ASP cc_start: 0.9135 (p0) cc_final: 0.8843 (m-30) REVERT: E 175 THR cc_start: 0.6440 (OUTLIER) cc_final: 0.6080 (p) REVERT: E 228 MET cc_start: 0.8735 (tmm) cc_final: 0.8238 (tmm) REVERT: F 228 MET cc_start: 0.8302 (tmm) cc_final: 0.7895 (tmm) REVERT: F 233 MET cc_start: 0.8964 (pmm) cc_final: 0.8739 (pmm) REVERT: G 108 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7150 (m-40) REVERT: H 36 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.7273 (t60) REVERT: H 274 LEU cc_start: 0.8903 (pp) cc_final: 0.8507 (tt) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.3300 time to fit residues: 57.1853 Evaluate side-chains 110 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 177 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 176 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN H 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.071955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.044377 restraints weight = 154748.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.042882 restraints weight = 169565.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.042027 restraints weight = 163381.197| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16807 Z= 0.126 Angle : 0.713 18.180 22667 Z= 0.360 Chirality : 0.043 0.199 2496 Planarity : 0.003 0.049 2911 Dihedral : 5.179 26.949 2210 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.54 % Favored : 91.07 % Rotamer: Outliers : 1.32 % Allowed : 16.64 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % 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: -0.94 (0.19), residues: 2072 helix: 0.89 (0.19), residues: 783 sheet: -1.13 (0.30), residues: 349 loop : -1.74 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 22 HIS 0.004 0.001 HIS E 214 PHE 0.020 0.001 PHE F 257 TYR 0.012 0.001 TYR F 123 ARG 0.004 0.000 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 632) hydrogen bonds : angle 5.19858 ( 1773) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.40288 ( 2) covalent geometry : bond 0.00268 (16806) covalent geometry : angle 0.71309 (22665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9531.29 seconds wall clock time: 166 minutes 37.65 seconds (9997.65 seconds total)