Starting phenix.real_space_refine on Wed Mar 4 20:56:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwv_27761/03_2026/8dwv_27761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwv_27761/03_2026/8dwv_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dwv_27761/03_2026/8dwv_27761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwv_27761/03_2026/8dwv_27761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dwv_27761/03_2026/8dwv_27761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwv_27761/03_2026/8dwv_27761.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.99, per 1000 atoms: 0.24 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: 1.43 Conformation dependent library (CDL) restraints added in 610.6 milliseconds 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: 0.52 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: 2.60 Time building geometry restraints manager: 1.88 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG E 138 TYR 0.014 0.001 TYR E 327 PHE 0.022 0.002 PHE F 43 TRP 0.022 0.001 TRP H 67 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00380 (16806) covalent geometry : angle 0.73998 (22665) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.21954 ( 2) hydrogen bonds : bond 0.20159 ( 632) hydrogen bonds : angle 7.87446 ( 1773) *********************** 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 : 0.636 Fit side-chains 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: 0.1222 time to fit residues: 22.9206 Evaluate side-chains 97 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 3.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- 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 E 62 ASN E 360 GLN F 72 ASN G 72 ASN G 347 HIS H 26 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.078237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.047618 restraints weight = 146174.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.046572 restraints weight = 142691.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.046691 restraints weight = 129469.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.046410 restraints weight = 121301.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046455 restraints weight = 115315.831| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16807 Z= 0.138 Angle : 0.637 8.912 22667 Z= 0.337 Chirality : 0.043 0.312 2496 Planarity : 0.004 0.068 2911 Dihedral : 6.097 87.111 2220 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.72 % Favored : 91.65 % Rotamer: Outliers : 0.50 % Allowed : 6.56 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 2072 helix: 0.96 (0.19), residues: 756 sheet: -1.09 (0.30), residues: 328 loop : -1.90 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 139 TYR 0.015 0.001 TYR B 280 PHE 0.019 0.001 PHE F 257 TRP 0.015 0.001 TRP B 131 HIS 0.005 0.001 HIS E 214 Details of bonding type rmsd covalent geometry : bond 0.00289 (16806) covalent geometry : angle 0.63682 (22665) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.91822 ( 2) hydrogen bonds : bond 0.03447 ( 632) hydrogen bonds : angle 5.76540 ( 1773) *********************** 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 106 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7885 (tpp) cc_final: 0.7605 (tmm) REVERT: A 233 MET cc_start: 0.5610 (tmm) cc_final: 0.4871 (tmm) REVERT: B 117 MET cc_start: 0.8754 (mmm) cc_final: 0.8499 (tmm) REVERT: B 178 MET cc_start: 0.7969 (tpp) cc_final: 0.7284 (tpp) REVERT: B 228 MET cc_start: 0.8589 (ptm) cc_final: 0.8357 (ppp) REVERT: E 341 MET cc_start: 0.8853 (tmm) cc_final: 0.8530 (tmm) REVERT: F 35 MET cc_start: 0.8646 (pmm) cc_final: 0.8150 (pmm) REVERT: F 117 MET cc_start: 0.8705 (ppp) cc_final: 0.8174 (pmm) REVERT: F 341 MET cc_start: 0.8890 (tpp) cc_final: 0.8664 (tpp) REVERT: H 24 TYR cc_start: 0.8188 (m-10) cc_final: 0.7841 (m-10) REVERT: H 48 MET cc_start: 0.8208 (mmm) cc_final: 0.7624 (mmm) REVERT: H 288 MET cc_start: 0.8978 (ppp) cc_final: 0.8711 (ppp) outliers start: 9 outliers final: 4 residues processed: 102 average time/residue: 0.1142 time to fit residues: 18.7321 Evaluate side-chains 95 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 170 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 22 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 91 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN E 328 HIS F 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.076827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.046259 restraints weight = 149322.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.045492 restraints weight = 138385.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.045367 restraints weight = 135637.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.045228 restraints weight = 118297.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.045670 restraints weight = 114977.101| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16807 Z= 0.146 Angle : 0.622 12.210 22667 Z= 0.328 Chirality : 0.042 0.339 2496 Planarity : 0.003 0.066 2911 Dihedral : 5.492 56.954 2216 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.38 % Favored : 92.13 % Rotamer: Outliers : 1.05 % Allowed : 8.76 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 2072 helix: 1.10 (0.19), residues: 756 sheet: -1.02 (0.30), residues: 325 loop : -1.85 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 139 TYR 0.011 0.001 TYR B 280 PHE 0.019 0.001 PHE F 257 TRP 0.011 0.001 TRP E 338 HIS 0.005 0.001 HIS E 214 Details of bonding type rmsd covalent geometry : bond 0.00304 (16806) covalent geometry : angle 0.62216 (22665) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.63510 ( 2) hydrogen bonds : bond 0.03162 ( 632) hydrogen bonds : angle 5.32174 ( 1773) *********************** 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 114 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7533 (mpp) cc_final: 0.7011 (mpp) REVERT: A 233 MET cc_start: 0.6397 (tmm) cc_final: 0.6012 (tmm) REVERT: A 255 MET cc_start: 0.9128 (mmm) cc_final: 0.8732 (mtm) REVERT: B 117 MET cc_start: 0.8913 (mmm) cc_final: 0.8515 (tmm) REVERT: B 176 MET cc_start: 0.5301 (pmm) cc_final: 0.3881 (tmm) REVERT: E 228 MET cc_start: 0.8181 (tmm) cc_final: 0.7605 (tmm) REVERT: E 255 MET cc_start: 0.8342 (mtp) cc_final: 0.8088 (mtp) REVERT: E 341 MET cc_start: 0.8907 (tmm) cc_final: 0.8570 (tmm) REVERT: F 35 MET cc_start: 0.8707 (pmm) cc_final: 0.8320 (pmm) REVERT: G 117 MET cc_start: 0.6577 (ppp) cc_final: 0.6343 (ppp) REVERT: G 269 MET cc_start: 0.7748 (ppp) cc_final: 0.7536 (ppp) REVERT: H 24 TYR cc_start: 0.8221 (m-10) cc_final: 0.7990 (m-10) REVERT: H 48 MET cc_start: 0.8295 (mmm) cc_final: 0.7934 (mmm) REVERT: H 288 MET cc_start: 0.9094 (ppp) cc_final: 0.8849 (ppp) outliers start: 19 outliers final: 8 residues processed: 107 average time/residue: 0.1174 time to fit residues: 20.2273 Evaluate side-chains 100 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 187 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 312 HIS ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.072466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.043523 restraints weight = 153169.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.041923 restraints weight = 156437.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.041389 restraints weight = 167243.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.041393 restraints weight = 163302.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.041145 restraints weight = 146596.052| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 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 = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16807 Z= 0.318 Angle : 0.827 14.342 22667 Z= 0.433 Chirality : 0.046 0.273 2496 Planarity : 0.005 0.061 2911 Dihedral : 6.014 36.228 2216 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.12 % Favored : 90.40 % Rotamer: Outliers : 1.87 % Allowed : 10.91 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2072 helix: 0.27 (0.18), residues: 778 sheet: -1.32 (0.29), residues: 332 loop : -2.00 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 354 TYR 0.025 0.003 TYR F 123 PHE 0.034 0.003 PHE F 257 TRP 0.020 0.003 TRP B 131 HIS 0.009 0.002 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00667 (16806) covalent geometry : angle 0.82683 (22665) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.44295 ( 2) hydrogen bonds : bond 0.04142 ( 632) hydrogen bonds : angle 6.00821 ( 1773) *********************** 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 127 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7594 (mpp) cc_final: 0.7033 (mpp) REVERT: A 176 MET cc_start: 0.8615 (tpp) cc_final: 0.8346 (tmm) REVERT: A 233 MET cc_start: 0.8102 (tmm) cc_final: 0.7590 (tmm) REVERT: A 255 MET cc_start: 0.9042 (mmm) cc_final: 0.8615 (mtm) REVERT: B 178 MET cc_start: 0.7836 (tpp) cc_final: 0.7531 (tpp) REVERT: E 48 MET cc_start: 0.9126 (ppp) cc_final: 0.8896 (pmm) REVERT: E 63 ASP cc_start: 0.9389 (p0) cc_final: 0.9122 (m-30) REVERT: E 70 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8318 (ptm-80) REVERT: E 176 MET cc_start: 0.6318 (mmp) cc_final: 0.6066 (mmp) REVERT: E 228 MET cc_start: 0.7965 (tmm) cc_final: 0.7707 (tmm) REVERT: E 255 MET cc_start: 0.8378 (mtp) cc_final: 0.8133 (mtp) REVERT: F 84 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8624 (mp) REVERT: F 228 MET cc_start: 0.8406 (tmm) cc_final: 0.8101 (tmm) REVERT: H 24 TYR cc_start: 0.8367 (m-10) cc_final: 0.8130 (m-10) REVERT: H 48 MET cc_start: 0.8884 (mmm) cc_final: 0.8543 (mmm) REVERT: H 233 MET cc_start: 0.8483 (ppp) cc_final: 0.8157 (ppp) REVERT: H 254 MET cc_start: 0.5738 (ptp) cc_final: 0.5436 (ptp) REVERT: H 288 MET cc_start: 0.9109 (ppp) cc_final: 0.8896 (ppp) outliers start: 34 outliers final: 19 residues processed: 116 average time/residue: 0.1159 time to fit residues: 21.6987 Evaluate side-chains 108 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 A residue 345 HIS Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 168 VAL 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 173 GLN Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 187 optimal weight: 0.0000 chunk 102 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 147 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.073589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.044513 restraints weight = 151259.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.043888 restraints weight = 141661.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.043401 restraints weight = 143255.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.043211 restraints weight = 147029.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.043713 restraints weight = 119917.834| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16807 Z= 0.123 Angle : 0.641 10.952 22667 Z= 0.335 Chirality : 0.043 0.191 2496 Planarity : 0.003 0.060 2911 Dihedral : 5.274 32.884 2212 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.63 % Favored : 91.99 % Rotamer: Outliers : 1.65 % Allowed : 12.51 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.19), residues: 2072 helix: 0.86 (0.19), residues: 774 sheet: -1.37 (0.29), residues: 346 loop : -1.86 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 138 TYR 0.011 0.001 TYR A 24 PHE 0.019 0.001 PHE F 257 TRP 0.012 0.001 TRP E 194 HIS 0.004 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00255 (16806) covalent geometry : angle 0.64133 (22665) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.19160 ( 2) hydrogen bonds : bond 0.02930 ( 632) hydrogen bonds : angle 5.33788 ( 1773) *********************** 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 116 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7909 (mpp) cc_final: 0.7532 (mpp) REVERT: A 255 MET cc_start: 0.9218 (mmm) cc_final: 0.8697 (mtm) REVERT: A 341 MET cc_start: 0.8167 (tmm) cc_final: 0.7948 (tmm) REVERT: B 117 MET cc_start: 0.8739 (mmm) cc_final: 0.8237 (ttp) REVERT: B 178 MET cc_start: 0.7897 (tpp) cc_final: 0.7555 (tpp) REVERT: E 70 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (ptm-80) REVERT: E 233 MET cc_start: 0.5010 (tpt) cc_final: 0.4633 (tpp) REVERT: E 255 MET cc_start: 0.8515 (mtp) cc_final: 0.8251 (mtp) REVERT: E 341 MET cc_start: 0.8934 (tmm) cc_final: 0.8564 (tmm) REVERT: F 228 MET cc_start: 0.8218 (tmm) cc_final: 0.7943 (tmm) REVERT: F 233 MET cc_start: 0.8928 (pmm) cc_final: 0.8680 (pmm) REVERT: F 254 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8033 (tmm) REVERT: G 117 MET cc_start: 0.7427 (ppp) cc_final: 0.7213 (ppp) REVERT: H 24 TYR cc_start: 0.7999 (m-10) cc_final: 0.7721 (m-10) REVERT: H 48 MET cc_start: 0.9087 (mmm) cc_final: 0.8718 (mmm) REVERT: H 233 MET cc_start: 0.8303 (ppp) cc_final: 0.7942 (ppp) REVERT: H 254 MET cc_start: 0.5597 (ptp) cc_final: 0.5258 (ptp) REVERT: H 274 LEU cc_start: 0.8967 (pp) cc_final: 0.8543 (tp) REVERT: H 288 MET cc_start: 0.9108 (ppp) cc_final: 0.8871 (ppp) outliers start: 30 outliers final: 12 residues processed: 111 average time/residue: 0.1101 time to fit residues: 20.2605 Evaluate side-chains 100 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 166 optimal weight: 50.0000 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.061486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.043082 restraints weight = 169959.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.042055 restraints weight = 158281.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.042186 restraints weight = 117281.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.042116 restraints weight = 101626.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.041952 restraints weight = 100226.722| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 16807 Z= 0.363 Angle : 0.864 15.107 22667 Z= 0.449 Chirality : 0.047 0.217 2496 Planarity : 0.005 0.060 2911 Dihedral : 6.052 31.386 2212 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.67 % Favored : 88.95 % Rotamer: Outliers : 2.31 % Allowed : 14.16 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 2072 helix: 0.11 (0.18), residues: 787 sheet: -1.53 (0.28), residues: 344 loop : -2.03 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 284 TYR 0.031 0.002 TYR F 123 PHE 0.035 0.003 PHE F 257 TRP 0.016 0.002 TRP B 22 HIS 0.012 0.002 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00759 (16806) covalent geometry : angle 0.86357 (22665) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.34232 ( 2) hydrogen bonds : bond 0.04243 ( 632) hydrogen bonds : angle 6.14276 ( 1773) *********************** 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 127 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8466 (mpp) cc_final: 0.8251 (mpp) REVERT: A 228 MET cc_start: 0.9183 (ppp) cc_final: 0.8974 (ppp) REVERT: A 233 MET cc_start: 0.7228 (tmm) cc_final: 0.6787 (tmm) REVERT: A 255 MET cc_start: 0.9072 (mmm) cc_final: 0.8622 (mtm) REVERT: A 341 MET cc_start: 0.8454 (tmm) cc_final: 0.8252 (tmm) REVERT: B 178 MET cc_start: 0.8381 (tpp) cc_final: 0.8037 (tpp) REVERT: E 176 MET cc_start: 0.5111 (mmp) cc_final: 0.4873 (mmt) REVERT: E 233 MET cc_start: 0.5713 (tpt) cc_final: 0.4765 (tpp) REVERT: E 255 MET cc_start: 0.8258 (mtp) cc_final: 0.7953 (mtp) REVERT: E 288 MET cc_start: 0.8779 (mtm) cc_final: 0.8542 (mtm) REVERT: H 24 TYR cc_start: 0.8024 (m-10) cc_final: 0.7694 (m-10) REVERT: H 48 MET cc_start: 0.8606 (mmm) cc_final: 0.8239 (mmm) REVERT: H 233 MET cc_start: 0.7991 (ppp) cc_final: 0.7659 (ppp) REVERT: H 288 MET cc_start: 0.9284 (ppp) cc_final: 0.9024 (ppp) outliers start: 42 outliers final: 26 residues processed: 118 average time/residue: 0.1168 time to fit residues: 22.4768 Evaluate side-chains 109 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 A residue 345 HIS 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 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 TRP Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 51 VAL 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 F residue 310 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 195 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN F 40 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.072667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.044537 restraints weight = 153400.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.043042 restraints weight = 159198.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.042376 restraints weight = 147984.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.042198 restraints weight = 133898.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.041938 restraints weight = 126865.259| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 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 = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16807 Z= 0.125 Angle : 0.692 12.161 22667 Z= 0.354 Chirality : 0.044 0.276 2496 Planarity : 0.004 0.113 2911 Dihedral : 5.375 25.718 2212 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.87 % Favored : 91.70 % Rotamer: Outliers : 1.21 % Allowed : 15.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 2072 helix: 0.80 (0.19), residues: 781 sheet: -1.29 (0.31), residues: 300 loop : -1.93 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 AARG E 70 TYR 0.013 0.001 TYR A 24 PHE 0.027 0.002 PHE H 211 TRP 0.015 0.002 TRP A 22 HIS 0.006 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00264 (16806) covalent geometry : angle 0.69251 (22665) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.22640 ( 2) hydrogen bonds : bond 0.02971 ( 632) hydrogen bonds : angle 5.37896 ( 1773) *********************** 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 108 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8154 (tmm) cc_final: 0.7688 (tmm) REVERT: A 255 MET cc_start: 0.9226 (mmm) cc_final: 0.8706 (mtm) REVERT: B 178 MET cc_start: 0.8227 (tpp) cc_final: 0.7944 (tpp) REVERT: E 43 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8991 (t80) REVERT: E 233 MET cc_start: 0.6052 (tpt) cc_final: 0.5048 (tpp) REVERT: F 84 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8910 (mp) REVERT: F 254 MET cc_start: 0.8871 (tmm) cc_final: 0.8273 (tmm) REVERT: H 24 TYR cc_start: 0.7872 (m-10) cc_final: 0.7646 (m-10) REVERT: H 274 LEU cc_start: 0.8795 (pp) cc_final: 0.8412 (tt) outliers start: 22 outliers final: 15 residues processed: 104 average time/residue: 0.1064 time to fit residues: 18.5614 Evaluate side-chains 101 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 29 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 175 THR 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 117 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN G 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.072016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.043500 restraints weight = 154929.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.042216 restraints weight = 175104.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.041499 restraints weight = 172182.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.041633 restraints weight = 150247.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.041537 restraints weight = 129937.029| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 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 = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16807 Z= 0.178 Angle : 0.716 11.303 22667 Z= 0.365 Chirality : 0.043 0.166 2496 Planarity : 0.004 0.095 2911 Dihedral : 5.392 26.348 2210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.98 % Favored : 90.64 % Rotamer: Outliers : 1.27 % Allowed : 16.20 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 2072 helix: 0.84 (0.19), residues: 781 sheet: -1.64 (0.27), residues: 368 loop : -1.87 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 284 TYR 0.016 0.001 TYR F 123 PHE 0.021 0.002 PHE H 211 TRP 0.012 0.002 TRP F 22 HIS 0.008 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00379 (16806) covalent geometry : angle 0.71644 (22665) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.29255 ( 2) hydrogen bonds : bond 0.03150 ( 632) hydrogen bonds : angle 5.42575 ( 1773) *********************** 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 106 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8114 (mpp) cc_final: 0.7839 (mpp) REVERT: A 255 MET cc_start: 0.9237 (mmm) cc_final: 0.8720 (mtm) REVERT: B 178 MET cc_start: 0.8438 (tpp) cc_final: 0.8126 (tpp) REVERT: E 233 MET cc_start: 0.6386 (tpt) cc_final: 0.5306 (tpp) REVERT: E 341 MET cc_start: 0.9318 (tmm) cc_final: 0.8677 (tmm) REVERT: F 84 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8864 (mp) REVERT: F 254 MET cc_start: 0.8854 (tmm) cc_final: 0.8131 (tmm) REVERT: G 117 MET cc_start: 0.6712 (ppp) cc_final: 0.6482 (ppp) REVERT: G 178 MET cc_start: 0.6740 (tpp) cc_final: 0.6368 (tpp) REVERT: H 36 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7134 (t60) REVERT: H 48 MET cc_start: 0.8252 (mmm) cc_final: 0.7812 (mmm) REVERT: H 274 LEU cc_start: 0.9084 (pp) cc_final: 0.8739 (tt) outliers start: 23 outliers final: 15 residues processed: 105 average time/residue: 0.1107 time to fit residues: 19.1365 Evaluate side-chains 100 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain 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 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 110 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 178 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 overall best weight: 2.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.071313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.042972 restraints weight = 156564.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.041679 restraints weight = 169268.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.041397 restraints weight = 171414.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.041451 restraints weight = 147775.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.041363 restraints weight = 141011.390| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16807 Z= 0.196 Angle : 0.756 17.714 22667 Z= 0.381 Chirality : 0.045 0.545 2496 Planarity : 0.004 0.094 2911 Dihedral : 5.495 26.761 2210 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.75 % Favored : 89.86 % Rotamer: Outliers : 1.38 % Allowed : 16.53 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 2072 helix: 0.77 (0.19), residues: 782 sheet: -1.65 (0.28), residues: 368 loop : -1.88 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 284 TYR 0.021 0.001 TYR F 123 PHE 0.023 0.002 PHE F 257 TRP 0.013 0.002 TRP B 131 HIS 0.010 0.001 HIS E 214 Details of bonding type rmsd covalent geometry : bond 0.00419 (16806) covalent geometry : angle 0.75559 (22665) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.18555 ( 2) hydrogen bonds : bond 0.03259 ( 632) hydrogen bonds : angle 5.50540 ( 1773) *********************** 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 109 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8295 (mpp) cc_final: 0.7394 (mpp) REVERT: A 255 MET cc_start: 0.9194 (mmm) cc_final: 0.8622 (mtm) REVERT: B 178 MET cc_start: 0.8433 (tpp) cc_final: 0.8133 (tpp) REVERT: E 43 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.9150 (t80) REVERT: E 175 THR cc_start: 0.5478 (OUTLIER) cc_final: 0.4834 (p) REVERT: E 228 MET cc_start: 0.8752 (tmm) cc_final: 0.8319 (tmm) REVERT: E 233 MET cc_start: 0.6216 (tpt) cc_final: 0.5121 (tpp) REVERT: F 84 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8856 (mp) REVERT: F 254 MET cc_start: 0.8928 (tmm) cc_final: 0.8269 (tmm) REVERT: F 255 MET cc_start: 0.8402 (tpp) cc_final: 0.6936 (tpp) REVERT: G 176 MET cc_start: 0.3323 (ppp) cc_final: 0.2584 (ppp) REVERT: H 36 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.7094 (t60) REVERT: H 48 MET cc_start: 0.8544 (mmm) cc_final: 0.8203 (mmm) REVERT: H 274 LEU cc_start: 0.9089 (pp) cc_final: 0.8754 (tt) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.1156 time to fit residues: 20.0017 Evaluate side-chains 103 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain 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 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 86 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 28 optimal weight: 30.0000 chunk 154 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 chunk 50 optimal weight: 0.0570 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 ASN H 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.071837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.043474 restraints weight = 155467.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.042057 restraints weight = 152410.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.041721 restraints weight = 139536.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.041633 restraints weight = 119162.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.041576 restraints weight = 115810.238| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 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 = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6160 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= 0.137 Angle : 0.726 16.462 22667 Z= 0.364 Chirality : 0.044 0.457 2496 Planarity : 0.004 0.091 2911 Dihedral : 5.306 25.242 2210 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.74 % Favored : 90.88 % Rotamer: Outliers : 1.05 % Allowed : 17.25 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.19), residues: 2072 helix: 0.96 (0.19), residues: 784 sheet: -1.30 (0.29), residues: 349 loop : -1.81 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 284 TYR 0.014 0.001 TYR F 123 PHE 0.020 0.001 PHE F 257 TRP 0.018 0.001 TRP A 22 HIS 0.010 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00295 (16806) covalent geometry : angle 0.72642 (22665) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.28130 ( 2) hydrogen bonds : bond 0.02975 ( 632) hydrogen bonds : angle 5.25857 ( 1773) ********************** 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 103 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7976 (mpp) cc_final: 0.7151 (mpp) REVERT: A 255 MET cc_start: 0.9222 (mmm) cc_final: 0.8684 (mtm) REVERT: B 178 MET cc_start: 0.8437 (tpp) cc_final: 0.8181 (tpp) REVERT: E 43 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.8984 (t80) REVERT: E 175 THR cc_start: 0.5186 (OUTLIER) cc_final: 0.4645 (p) REVERT: E 228 MET cc_start: 0.8611 (tmm) cc_final: 0.8150 (tmm) REVERT: E 233 MET cc_start: 0.5731 (tpt) cc_final: 0.4626 (tpp) REVERT: F 84 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8858 (mp) REVERT: F 254 MET cc_start: 0.8854 (tmm) cc_final: 0.8087 (tmm) REVERT: F 255 MET cc_start: 0.8239 (tpp) cc_final: 0.7101 (tpp) REVERT: G 117 MET cc_start: 0.7433 (ppp) cc_final: 0.6106 (ppp) REVERT: G 173 GLN cc_start: 0.9505 (mm110) cc_final: 0.9243 (mm-40) REVERT: G 176 MET cc_start: 0.2944 (ppp) cc_final: 0.2371 (ppp) REVERT: H 36 TRP cc_start: 0.8287 (OUTLIER) cc_final: 0.7022 (t60) REVERT: H 48 MET cc_start: 0.8622 (mmm) cc_final: 0.8353 (mmm) REVERT: H 274 LEU cc_start: 0.8706 (pp) cc_final: 0.8367 (tt) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.1183 time to fit residues: 19.8025 Evaluate side-chains 101 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL 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 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 254 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 36 TRP 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 28 optimal weight: 30.0000 chunk 167 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.070674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.042351 restraints weight = 157598.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.041083 restraints weight = 165158.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.040829 restraints weight = 170685.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.040447 restraints weight = 179659.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040588 restraints weight = 139436.030| |-----------------------------------------------------------------------------| 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) = 0.033 | | 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) = 0.033 | | 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: 0.8237 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16807 Z= 0.222 Angle : 0.791 15.777 22667 Z= 0.399 Chirality : 0.045 0.451 2496 Planarity : 0.004 0.094 2911 Dihedral : 5.611 29.627 2210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.33 % Favored : 89.29 % Rotamer: Outliers : 0.94 % Allowed : 17.58 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.19), residues: 2072 helix: 0.69 (0.19), residues: 793 sheet: -1.57 (0.29), residues: 352 loop : -1.86 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 284 TYR 0.025 0.002 TYR F 123 PHE 0.024 0.002 PHE F 257 TRP 0.013 0.002 TRP B 131 HIS 0.010 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00474 (16806) covalent geometry : angle 0.79109 (22665) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.14270 ( 2) hydrogen bonds : bond 0.03377 ( 632) hydrogen bonds : angle 5.52866 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5764.52 seconds wall clock time: 99 minutes 12.26 seconds (5952.26 seconds total)