Starting phenix.real_space_refine on Sun May 18 01:40:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwv_27761/05_2025/8dwv_27761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwv_27761/05_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_27761/05_2025/8dwv_27761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwv_27761/05_2025/8dwv_27761.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwv_27761/05_2025/8dwv_27761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwv_27761/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.18, per 1000 atoms: 0.56 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: 3.49 Conformation dependent library (CDL) restraints added in 2.0 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: 1.74 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: 5.31 Time building geometry restraints manager: 4.17 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: 1.430 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: 0.150 Process input model: 34.960 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- 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 : 1.832 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: 0.2746 time to fit residues: 50.9413 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 : 1.870 ------------------------------------------------------------------------------- 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 = 0.046584 restraints weight = 148999.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.045859 restraints weight = 147425.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.045010 restraints weight = 169152.759| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 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 = 0.03 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 8.352 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 : 11.22 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 : 1.838 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: 0.7613 (mpp) cc_final: 0.7212 (mpp) REVERT: A 176 MET cc_start: 0.8338 (tpp) cc_final: 0.8018 (tmm) REVERT: A 233 MET cc_start: 0.6907 (tmm) cc_final: 0.6144 (tmm) REVERT: B 178 MET cc_start: 0.8186 (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: 0.8748 (tmm) cc_final: 0.8507 (tmm) REVERT: F 35 MET cc_start: 0.8784 (pmm) cc_final: 0.8191 (pmm) REVERT: F 228 MET cc_start: 0.8409 (ptt) cc_final: 0.7925 (tmm) REVERT: F 341 MET cc_start: 0.8862 (tpp) cc_final: 0.8657 (tpp) REVERT: H 48 MET cc_start: 0.8441 (mmm) cc_final: 0.8092 (mmm) REVERT: H 117 MET cc_start: 0.5385 (pmm) cc_final: 0.5141 (pmm) REVERT: H 288 MET cc_start: 0.8863 (ppp) cc_final: 0.8592 (ppp) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.2631 time to fit residues: 42.9298 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 : 1.725 ------------------------------------------------------------------------------- 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: 0.9980 chunk 91 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 A 345 HIS B 231 HIS H 26 GLN H 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.074191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.044456 restraints weight = 150624.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.043484 restraints weight = 140606.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.043591 restraints weight = 135460.788| |-----------------------------------------------------------------------------| 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) = 0.037 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.037 | | 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: 0.8093 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16807 Z= 0.197 Angle : 0.673 12.208 22667 Z= 0.359 Chirality : 0.043 0.352 2496 Planarity : 0.004 0.067 2911 Dihedral : 5.630 49.242 2216 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.06 % Favored : 91.46 % Rotamer: Outliers : 1.54 % Allowed : 9.70 % Favored : 88.76 % 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: -1.13 (0.18), residues: 2072 helix: 0.73 (0.19), residues: 774 sheet: -1.13 (0.29), residues: 329 loop : -1.88 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 22 HIS 0.008 0.001 HIS F 214 PHE 0.021 0.002 PHE F 257 TYR 0.014 0.002 TYR F 123 ARG 0.006 0.001 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 632) hydrogen bonds : angle 5.55184 ( 1773) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.43006 ( 2) covalent geometry : bond 0.00409 (16806) covalent geometry : angle 0.67343 (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 122 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7756 (mpp) cc_final: 0.7241 (mpp) REVERT: A 233 MET cc_start: 0.7508 (tmm) cc_final: 0.7009 (tmm) REVERT: A 255 MET cc_start: 0.9158 (mmm) cc_final: 0.8717 (mtm) REVERT: B 35 MET cc_start: 0.5456 (tpt) cc_final: 0.5121 (mmp) REVERT: B 178 MET cc_start: 0.7941 (tpp) cc_final: 0.7579 (tpp) REVERT: B 228 MET cc_start: 0.9133 (ptm) cc_final: 0.8870 (ppp) REVERT: E 70 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8318 (ptm-80) REVERT: E 145 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8603 (tp30) REVERT: E 228 MET cc_start: 0.8067 (tmm) cc_final: 0.7587 (tmm) REVERT: E 341 MET cc_start: 0.9119 (tmm) cc_final: 0.8636 (tmm) REVERT: F 84 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8623 (mp) REVERT: G 117 MET cc_start: 0.6505 (ppp) cc_final: 0.6242 (ppp) REVERT: G 269 MET cc_start: 0.7536 (ppp) cc_final: 0.7300 (ppp) REVERT: H 24 TYR cc_start: 0.8677 (m-10) cc_final: 0.8380 (m-10) REVERT: H 26 GLN cc_start: 0.9552 (OUTLIER) cc_final: 0.9144 (pp30) REVERT: H 48 MET cc_start: 0.8606 (mmm) cc_final: 0.8111 (mmm) REVERT: H 117 MET cc_start: 0.6318 (pmm) cc_final: 0.6081 (pmm) REVERT: H 233 MET cc_start: 0.7617 (ppp) cc_final: 0.6589 (ppp) REVERT: H 288 MET cc_start: 0.9098 (ppp) cc_final: 0.8820 (ppp) outliers start: 28 outliers final: 10 residues processed: 115 average time/residue: 0.2534 time to fit residues: 46.4868 Evaluate side-chains 103 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain E residue 45 ARG 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 F residue 84 LEU 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 26 GLN 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: 5.9990 chunk 164 optimal weight: 50.0000 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.072323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.042427 restraints weight = 152531.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.041755 restraints weight = 143966.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.041434 restraints weight = 147520.587| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 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 = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16807 Z= 0.257 Angle : 0.738 13.764 22667 Z= 0.390 Chirality : 0.044 0.300 2496 Planarity : 0.005 0.061 2911 Dihedral : 5.759 39.062 2216 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.88 % Favored : 90.69 % Rotamer: Outliers : 1.82 % Allowed : 12.67 % Favored : 85.51 % 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: -1.39 (0.18), residues: 2072 helix: 0.49 (0.19), residues: 775 sheet: -1.24 (0.28), residues: 339 loop : -2.00 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 22 HIS 0.007 0.002 HIS F 214 PHE 0.027 0.002 PHE F 257 TYR 0.021 0.002 TYR F 123 ARG 0.006 0.001 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 632) hydrogen bonds : angle 5.78148 ( 1773) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.40196 ( 2) covalent geometry : bond 0.00539 (16806) covalent geometry : angle 0.73833 (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 121 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8649 (tpp) cc_final: 0.8423 (tmm) REVERT: A 233 MET cc_start: 0.8017 (tmm) cc_final: 0.7643 (tmm) REVERT: A 255 MET cc_start: 0.9123 (mmm) cc_final: 0.8652 (mtm) REVERT: B 35 MET cc_start: 0.6525 (tpt) cc_final: 0.6168 (mmp) REVERT: B 178 MET cc_start: 0.8028 (tpp) cc_final: 0.7740 (tpp) REVERT: E 63 ASP cc_start: 0.9362 (p0) cc_final: 0.9082 (m-30) REVERT: E 228 MET cc_start: 0.7977 (tmm) cc_final: 0.7448 (tmm) REVERT: F 310 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7906 (p0) REVERT: G 173 GLN cc_start: 0.9489 (mm110) cc_final: 0.9242 (mm-40) REVERT: H 24 TYR cc_start: 0.8493 (m-10) cc_final: 0.8281 (m-10) REVERT: H 48 MET cc_start: 0.9115 (mmm) cc_final: 0.8748 (mmm) REVERT: H 233 MET cc_start: 0.8589 (ppp) cc_final: 0.8107 (ppp) REVERT: H 288 MET cc_start: 0.9105 (ppp) cc_final: 0.8905 (ppp) outliers start: 33 outliers final: 19 residues processed: 113 average time/residue: 0.2449 time to fit residues: 45.0976 Evaluate side-chains 107 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN 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 B residue 266 LEU 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 48 MET Chi-restraints excluded: chain F residue 157 LEU 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 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 Chi-restraints excluded: chain H residue 244 ASN Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 7 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 154 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.072833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.043812 restraints weight = 153649.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.043004 restraints weight = 147048.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.042589 restraints weight = 138688.540| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16807 Z= 0.145 Angle : 0.673 16.135 22667 Z= 0.347 Chirality : 0.043 0.305 2496 Planarity : 0.003 0.041 2911 Dihedral : 5.363 32.146 2212 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.11 % Favored : 91.46 % Rotamer: Outliers : 1.76 % Allowed : 13.66 % Favored : 84.57 % Cbeta Deviations : 0.05 % 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: -1.16 (0.19), residues: 2072 helix: 0.84 (0.19), residues: 777 sheet: -1.35 (0.28), residues: 366 loop : -1.93 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 131 HIS 0.005 0.001 HIS F 214 PHE 0.021 0.001 PHE F 257 TYR 0.013 0.001 TYR F 123 ARG 0.004 0.000 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 632) hydrogen bonds : angle 5.33672 ( 1773) SS BOND : bond 0.00644 ( 1) SS BOND : angle 7.73910 ( 2) covalent geometry : bond 0.00311 (16806) covalent geometry : angle 0.66900 (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 121 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7982 (mpp) cc_final: 0.7602 (mpp) REVERT: A 255 MET cc_start: 0.9261 (mmm) cc_final: 0.8844 (mtm) REVERT: B 35 MET cc_start: 0.6283 (tpt) cc_final: 0.5865 (mmp) REVERT: B 178 MET cc_start: 0.8094 (tpp) cc_final: 0.7773 (tpp) REVERT: E 43 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9024 (t80) REVERT: E 63 ASP cc_start: 0.9199 (p0) cc_final: 0.8982 (m-30) REVERT: E 145 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8844 (tp30) REVERT: E 228 MET cc_start: 0.7803 (tmm) cc_final: 0.7479 (tmm) REVERT: E 341 MET cc_start: 0.9294 (tmm) cc_final: 0.8799 (tmm) REVERT: F 84 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8804 (mp) REVERT: F 233 MET cc_start: 0.8398 (pmm) cc_final: 0.8167 (pmm) REVERT: G 173 GLN cc_start: 0.9399 (mm110) cc_final: 0.9136 (mm110) REVERT: H 48 MET cc_start: 0.8935 (mmm) cc_final: 0.8592 (mmm) REVERT: H 233 MET cc_start: 0.8233 (ppp) cc_final: 0.7907 (ppp) REVERT: H 254 MET cc_start: 0.5882 (ptp) cc_final: 0.5541 (ptp) REVERT: H 274 LEU cc_start: 0.9069 (pp) cc_final: 0.8703 (tp) REVERT: H 288 MET cc_start: 0.9139 (ppp) cc_final: 0.8903 (ppp) outliers start: 32 outliers final: 16 residues processed: 118 average time/residue: 0.2443 time to fit residues: 46.9958 Evaluate side-chains 106 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 43 PHE 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 195 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE 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: 5.9990 chunk 128 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 13 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 overall best weight: 2.7284 ------------------------------------------------------------------------------- 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 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 = 0.4322 r_free = 0.4322 target = 0.072420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.043419 restraints weight = 153920.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.042061 restraints weight = 163931.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.041949 restraints weight = 160044.388| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 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 = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16807 Z= 0.196 Angle : 0.694 10.964 22667 Z= 0.358 Chirality : 0.043 0.218 2496 Planarity : 0.004 0.064 2911 Dihedral : 5.408 28.851 2212 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.83 % Favored : 90.73 % Rotamer: Outliers : 1.65 % Allowed : 14.99 % Favored : 83.36 % 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: -1.17 (0.19), residues: 2072 helix: 0.79 (0.19), residues: 779 sheet: -1.40 (0.28), residues: 361 loop : -1.89 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 131 HIS 0.006 0.001 HIS F 214 PHE 0.024 0.002 PHE F 257 TYR 0.017 0.001 TYR F 123 ARG 0.005 0.000 ARG B 284 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 632) hydrogen bonds : angle 5.41452 ( 1773) SS BOND : bond 0.00467 ( 1) SS BOND : angle 5.15758 ( 2) covalent geometry : bond 0.00414 (16806) covalent geometry : angle 0.69281 (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 117 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7931 (tmm) cc_final: 0.7410 (tmm) REVERT: A 255 MET cc_start: 0.9282 (mmm) cc_final: 0.8878 (mtm) REVERT: B 35 MET cc_start: 0.6197 (tpt) cc_final: 0.5801 (mmp) REVERT: B 117 MET cc_start: 0.8914 (mmm) cc_final: 0.8331 (ttp) REVERT: B 178 MET cc_start: 0.8159 (tpp) cc_final: 0.7801 (tpp) REVERT: E 63 ASP cc_start: 0.9129 (p0) cc_final: 0.8919 (m-30) REVERT: E 70 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8200 (ptm-80) REVERT: E 145 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8868 (tp30) REVERT: E 175 THR cc_start: 0.5125 (OUTLIER) cc_final: 0.4380 (p) REVERT: E 228 MET cc_start: 0.7842 (tmm) cc_final: 0.7543 (tmm) REVERT: E 341 MET cc_start: 0.9238 (tmm) cc_final: 0.8833 (tmm) REVERT: F 84 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8781 (mp) REVERT: F 228 MET cc_start: 0.8555 (tmm) cc_final: 0.8293 (tmm) REVERT: F 233 MET cc_start: 0.8716 (pmm) cc_final: 0.8510 (pmm) REVERT: G 173 GLN cc_start: 0.9383 (mm110) cc_final: 0.9125 (mm110) REVERT: H 36 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.7064 (t60) REVERT: H 48 MET cc_start: 0.8964 (mmm) cc_final: 0.8631 (mmm) REVERT: H 233 MET cc_start: 0.8481 (ppp) cc_final: 0.8247 (ppp) REVERT: H 274 LEU cc_start: 0.9034 (pp) cc_final: 0.8527 (tt) REVERT: H 288 MET cc_start: 0.9212 (ppp) cc_final: 0.8996 (ppp) outliers start: 30 outliers final: 19 residues processed: 112 average time/residue: 0.2653 time to fit residues: 47.1576 Evaluate side-chains 110 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL 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 E residue 29 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 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 84 LEU 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 27 ILE 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 36 TRP Chi-restraints excluded: chain H residue 52 ILE 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: 0.0030 chunk 83 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 166 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 191 optimal weight: 50.0000 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN E 72 ASN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 147 ASN G 312 HIS H 196 ASN H 360 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.061364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.042788 restraints weight = 176699.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.042988 restraints weight = 122420.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.042649 restraints weight = 100982.746| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 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 = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16807 Z= 0.270 Angle : 0.789 12.633 22667 Z= 0.410 Chirality : 0.045 0.164 2496 Planarity : 0.005 0.064 2911 Dihedral : 5.907 29.309 2210 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.94 % Favored : 89.67 % Rotamer: Outliers : 2.31 % Allowed : 15.76 % Favored : 81.93 % 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: -1.59 (0.19), residues: 2072 helix: 0.33 (0.18), residues: 799 sheet: -1.60 (0.28), residues: 362 loop : -2.07 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 22 HIS 0.008 0.002 HIS F 214 PHE 0.029 0.002 PHE F 257 TYR 0.032 0.002 TYR F 123 ARG 0.006 0.001 ARG H 198 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 632) hydrogen bonds : angle 5.86562 ( 1773) SS BOND : bond 0.00923 ( 1) SS BOND : angle 3.55416 ( 2) covalent geometry : bond 0.00568 (16806) covalent geometry : angle 0.78793 (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 130 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.9256 (mmm) cc_final: 0.8781 (mtm) REVERT: B 35 MET cc_start: 0.6269 (tpt) cc_final: 0.5991 (mmp) REVERT: B 178 MET cc_start: 0.8837 (tpp) cc_final: 0.8439 (tpp) REVERT: B 341 MET cc_start: 0.9234 (tmm) cc_final: 0.9008 (tmm) REVERT: E 43 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8691 (t80) REVERT: E 145 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5635 (tp30) REVERT: E 228 MET cc_start: 0.8158 (tmm) cc_final: 0.7510 (tmm) REVERT: F 228 MET cc_start: 0.8578 (tmm) cc_final: 0.8187 (tmm) REVERT: F 233 MET cc_start: 0.9012 (pmm) cc_final: 0.8721 (pmm) REVERT: G 173 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7926 (mm110) REVERT: G 176 MET cc_start: 0.3533 (ppp) cc_final: 0.2299 (ppp) REVERT: H 36 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7278 (t60) REVERT: H 48 MET cc_start: 0.8795 (mmm) cc_final: 0.8383 (mmm) REVERT: H 274 LEU cc_start: 0.8861 (pp) cc_final: 0.8319 (tt) outliers start: 42 outliers final: 24 residues processed: 124 average time/residue: 0.2635 time to fit residues: 53.1382 Evaluate side-chains 113 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL 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 29 VAL Chi-restraints excluded: chain E residue 43 PHE 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 190 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 186 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 198 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4290 r_free = 0.4290 target = 0.070765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.042887 restraints weight = 157198.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.041800 restraints weight = 158287.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.041291 restraints weight = 156714.239| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 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 = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.6567 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= 0.208 Angle : 0.738 13.531 22667 Z= 0.379 Chirality : 0.044 0.167 2496 Planarity : 0.004 0.103 2911 Dihedral : 5.700 28.112 2210 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.56 % Favored : 90.06 % Rotamer: Outliers : 1.71 % Allowed : 17.13 % Favored : 81.16 % 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: -1.41 (0.19), residues: 2072 helix: 0.51 (0.19), residues: 796 sheet: -1.36 (0.29), residues: 348 loop : -2.07 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 22 HIS 0.006 0.001 HIS F 214 PHE 0.024 0.002 PHE F 257 TYR 0.022 0.002 TYR F 123 ARG 0.006 0.001 ARG F 139 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 632) hydrogen bonds : angle 5.63528 ( 1773) SS BOND : bond 0.00592 ( 1) SS BOND : angle 3.40893 ( 2) covalent geometry : bond 0.00444 (16806) covalent geometry : angle 0.73743 (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 117 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.769 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: 0.8456 (mpp) cc_final: 0.7646 (mpp) REVERT: A 255 MET cc_start: 0.9248 (mmm) cc_final: 0.8707 (mtm) REVERT: B 35 MET cc_start: 0.6218 (tpt) cc_final: 0.5764 (mmp) REVERT: B 178 MET cc_start: 0.8546 (tpp) cc_final: 0.8240 (tpp) REVERT: E 43 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9165 (t80) REVERT: E 145 GLU cc_start: 0.9428 (OUTLIER) cc_final: 0.9103 (tp30) REVERT: E 228 MET cc_start: 0.7684 (tmm) cc_final: 0.7450 (tmm) REVERT: F 72 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8143 (m110) REVERT: F 228 MET cc_start: 0.8538 (tmm) cc_final: 0.8235 (tmm) REVERT: F 233 MET cc_start: 0.8903 (pmm) cc_final: 0.8631 (pmm) REVERT: F 254 MET cc_start: 0.8963 (tmm) cc_final: 0.8205 (tmm) REVERT: G 173 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9293 (mm110) REVERT: G 176 MET cc_start: 0.4613 (ppp) cc_final: 0.3745 (ppp) REVERT: G 269 MET cc_start: 0.8009 (ppp) cc_final: 0.7762 (ppp) REVERT: H 35 MET cc_start: 0.8007 (pmm) cc_final: 0.7702 (pmm) REVERT: H 36 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.7349 (t60) REVERT: H 274 LEU cc_start: 0.9068 (pp) cc_final: 0.8657 (tt) outliers start: 31 outliers final: 22 residues processed: 115 average time/residue: 0.2539 time to fit residues: 47.2566 Evaluate side-chains 112 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 29 VAL Chi-restraints excluded: chain E residue 43 PHE 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 190 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 186 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 70 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.071933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.043908 restraints weight = 154755.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.042469 restraints weight = 159061.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.042117 restraints weight = 162410.394| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 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 = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16807 Z= 0.125 Angle : 0.707 16.995 22667 Z= 0.357 Chirality : 0.043 0.189 2496 Planarity : 0.004 0.106 2911 Dihedral : 5.320 25.328 2210 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.49 % Favored : 91.12 % Rotamer: Outliers : 1.43 % Allowed : 17.63 % Favored : 80.94 % 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: -1.09 (0.19), residues: 2072 helix: 0.90 (0.19), residues: 782 sheet: -1.43 (0.28), residues: 363 loop : -1.87 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 22 HIS 0.005 0.001 HIS B 347 PHE 0.022 0.001 PHE H 211 TYR 0.023 0.001 TYR B 83 ARG 0.004 0.000 ARG F 139 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 632) hydrogen bonds : angle 5.23482 ( 1773) SS BOND : bond 0.00434 ( 1) SS BOND : angle 3.22228 ( 2) covalent geometry : bond 0.00268 (16806) covalent geometry : angle 0.70628 (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 113 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8582 (mpp) cc_final: 0.7857 (mpp) REVERT: A 255 MET cc_start: 0.9234 (mmm) cc_final: 0.8695 (mtm) REVERT: B 83 TYR cc_start: 0.2823 (OUTLIER) cc_final: 0.2606 (t80) REVERT: B 178 MET cc_start: 0.8485 (tpp) cc_final: 0.8194 (tpp) REVERT: E 43 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8971 (t80) REVERT: E 228 MET cc_start: 0.7645 (tmm) cc_final: 0.7419 (tmm) REVERT: E 341 MET cc_start: 0.9470 (tmm) cc_final: 0.8836 (tmm) REVERT: F 228 MET cc_start: 0.8446 (tmm) cc_final: 0.8167 (tmm) REVERT: F 233 MET cc_start: 0.8834 (pmm) cc_final: 0.8563 (pmm) REVERT: F 254 MET cc_start: 0.8845 (tmm) cc_final: 0.8314 (tmm) REVERT: G 176 MET cc_start: 0.3846 (ppp) cc_final: 0.3034 (ppp) REVERT: G 269 MET cc_start: 0.8364 (ppp) cc_final: 0.8105 (ppp) REVERT: H 35 MET cc_start: 0.7655 (pmm) cc_final: 0.7329 (pmm) REVERT: H 36 TRP cc_start: 0.8665 (OUTLIER) cc_final: 0.7390 (t60) REVERT: H 274 LEU cc_start: 0.8799 (pp) cc_final: 0.8396 (tt) outliers start: 26 outliers final: 17 residues processed: 110 average time/residue: 0.2540 time to fit residues: 45.8257 Evaluate side-chains 105 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 83 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 43 PHE 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 F residue 195 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 52 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 197 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 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 = 0.4291 r_free = 0.4291 target = 0.070525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.042798 restraints weight = 158359.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.041284 restraints weight = 177120.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.041046 restraints weight = 173599.134| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 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 = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16807 Z= 0.232 Angle : 0.785 17.295 22667 Z= 0.400 Chirality : 0.045 0.337 2496 Planarity : 0.004 0.102 2911 Dihedral : 5.609 30.685 2210 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.65 % Favored : 89.96 % Rotamer: Outliers : 1.16 % Allowed : 18.35 % Favored : 80.50 % 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: -1.35 (0.19), residues: 2072 helix: 0.64 (0.19), residues: 789 sheet: -1.49 (0.29), residues: 337 loop : -2.02 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 22 HIS 0.008 0.001 HIS F 214 PHE 0.024 0.002 PHE B 257 TYR 0.026 0.002 TYR F 123 ARG 0.005 0.001 ARG F 284 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 632) hydrogen bonds : angle 5.56793 ( 1773) SS BOND : bond 0.00417 ( 1) SS BOND : angle 2.80851 ( 2) covalent geometry : bond 0.00492 (16806) covalent geometry : angle 0.78468 (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 105 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8807 (mpp) cc_final: 0.8382 (mpp) REVERT: A 255 MET cc_start: 0.9169 (mmm) cc_final: 0.8559 (mtm) REVERT: B 83 TYR cc_start: 0.3237 (OUTLIER) cc_final: 0.2934 (t80) REVERT: B 178 MET cc_start: 0.8523 (tpp) cc_final: 0.8212 (tpp) REVERT: E 228 MET cc_start: 0.7715 (tmm) cc_final: 0.7275 (tmm) REVERT: E 288 MET cc_start: 0.9058 (mtm) cc_final: 0.8769 (mtm) REVERT: E 341 MET cc_start: 0.9411 (tmm) cc_final: 0.8891 (tmm) REVERT: F 228 MET cc_start: 0.8262 (tmm) cc_final: 0.8021 (tmm) REVERT: F 254 MET cc_start: 0.8937 (tmm) cc_final: 0.8224 (tmm) REVERT: F 255 MET cc_start: 0.7878 (tpp) cc_final: 0.6861 (tpp) REVERT: G 269 MET cc_start: 0.7946 (ppp) cc_final: 0.7685 (ppp) REVERT: H 35 MET cc_start: 0.8218 (pmm) cc_final: 0.7922 (pmm) REVERT: H 36 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.7349 (t60) REVERT: H 274 LEU cc_start: 0.9094 (pp) cc_final: 0.8704 (tt) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.2584 time to fit residues: 43.5597 Evaluate side-chains 102 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 B residue 83 TYR Chi-restraints excluded: chain E residue 29 VAL 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 195 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 244 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 177 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 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 = 0.4336 r_free = 0.4336 target = 0.071647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.043921 restraints weight = 155516.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.042260 restraints weight = 162671.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.041827 restraints weight = 158769.241| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 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 = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16807 Z= 0.127 Angle : 0.724 17.786 22667 Z= 0.365 Chirality : 0.043 0.220 2496 Planarity : 0.004 0.098 2911 Dihedral : 5.262 26.230 2210 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.35 % Favored : 91.26 % Rotamer: Outliers : 1.16 % Allowed : 18.40 % Favored : 80.44 % 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: -1.01 (0.19), residues: 2072 helix: 1.03 (0.19), residues: 774 sheet: -1.53 (0.28), residues: 362 loop : -1.78 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 22 HIS 0.006 0.001 HIS F 231 PHE 0.020 0.001 PHE F 257 TYR 0.017 0.001 TYR B 83 ARG 0.004 0.000 ARG F 284 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 632) hydrogen bonds : angle 5.18783 ( 1773) SS BOND : bond 0.00249 ( 1) SS BOND : angle 2.66955 ( 2) covalent geometry : bond 0.00274 (16806) covalent geometry : angle 0.72400 (22665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8702.00 seconds wall clock time: 151 minutes 49.98 seconds (9109.98 seconds total)