Starting phenix.real_space_refine on Thu Sep 18 14:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zix_60132/09_2025/8zix_60132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zix_60132/09_2025/8zix_60132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zix_60132/09_2025/8zix_60132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zix_60132/09_2025/8zix_60132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zix_60132/09_2025/8zix_60132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zix_60132/09_2025/8zix_60132.map" } resolution = 3.54 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 126 5.16 5 C 11076 2.51 5 N 2964 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "R" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.27 Number of scatterers: 17556 At special positions: 0 Unit cell: (97.94, 83, 220.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 12 15.00 O 3378 8.00 N 2964 7.00 C 11076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.37 Conformation dependent library (CDL) restraints added in 658.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 31 sheets defined 48.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'P' and resid 57 through 64 Processing helix chain 'P' and resid 80 through 95 Processing helix chain 'P' and resid 114 through 128 removed outlier: 4.043A pdb=" N ARG P 118 " --> pdb=" O PRO P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 147 removed outlier: 3.555A pdb=" N SER P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 177 Processing helix chain 'P' and resid 183 through 195 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 224 through 235 Processing helix chain 'P' and resid 254 through 259 Processing helix chain 'P' and resid 260 through 264 Processing helix chain 'P' and resid 265 through 270 Processing helix chain 'P' and resid 275 through 286 Processing helix chain 'P' and resid 291 through 298 removed outlier: 3.963A pdb=" N LEU P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 308 removed outlier: 3.944A pdb=" N TYR P 308 " --> pdb=" O THR P 305 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 323 Processing helix chain 'P' and resid 336 through 338 No H-bonds generated for 'chain 'P' and resid 336 through 338' Processing helix chain 'P' and resid 339 through 351 Processing helix chain 'P' and resid 352 through 357 removed outlier: 4.034A pdb=" N GLN P 355 " --> pdb=" O SER P 352 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN P 356 " --> pdb=" O THR P 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 360 through 368 Processing helix chain 'P' and resid 369 through 372 removed outlier: 4.006A pdb=" N VAL P 372 " --> pdb=" O PRO P 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 369 through 372' Processing helix chain 'R' and resid 57 through 64 Processing helix chain 'R' and resid 80 through 95 Processing helix chain 'R' and resid 114 through 128 removed outlier: 3.922A pdb=" N ARG R 118 " --> pdb=" O PRO R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 Processing helix chain 'R' and resid 183 through 195 Processing helix chain 'R' and resid 207 through 219 removed outlier: 3.525A pdb=" N CYS R 219 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 235 Processing helix chain 'R' and resid 254 through 259 Processing helix chain 'R' and resid 260 through 264 Processing helix chain 'R' and resid 265 through 270 Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.615A pdb=" N CYS R 287 " --> pdb=" O SER R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 298 removed outlier: 3.825A pdb=" N LEU R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 308 removed outlier: 3.981A pdb=" N TYR R 308 " --> pdb=" O THR R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 323 Processing helix chain 'R' and resid 336 through 338 No H-bonds generated for 'chain 'R' and resid 336 through 338' Processing helix chain 'R' and resid 339 through 350 Processing helix chain 'R' and resid 353 through 357 removed outlier: 4.133A pdb=" N GLN R 356 " --> pdb=" O THR R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 368 Processing helix chain 'R' and resid 369 through 372 removed outlier: 3.907A pdb=" N VAL R 372 " --> pdb=" O PRO R 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 369 through 372' Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.829A pdb=" N GLU A 102 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 114 through 128 removed outlier: 4.019A pdb=" N ARG A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.683A pdb=" N ILE A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.021A pdb=" N GLU A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 235 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.532A pdb=" N PHE A 268 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 270 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.670A pdb=" N CYS A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.070A pdb=" N TYR A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.929A pdb=" N GLN A 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 356 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 369 through 372 removed outlier: 3.909A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'E' and resid 57 through 64 Processing helix chain 'E' and resid 80 through 95 Processing helix chain 'E' and resid 99 through 103 removed outlier: 4.215A pdb=" N GLU E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS E 103 " --> pdb=" O PRO E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 103' Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.811A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 207 through 219 Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 260 through 264 Processing helix chain 'E' and resid 265 through 270 removed outlier: 3.514A pdb=" N PHE E 268 " --> pdb=" O GLN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 350 Processing helix chain 'E' and resid 353 through 357 removed outlier: 3.925A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 368 Processing helix chain 'E' and resid 369 through 372 removed outlier: 4.262A pdb=" N VAL E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.966A pdb=" N GLU B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS B 103 " --> pdb=" O PRO B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 114 through 128 removed outlier: 3.978A pdb=" N ARG B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 204 through 219 removed outlier: 4.185A pdb=" N GLU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.518A pdb=" N LEU B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.842A pdb=" N THR B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.756A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 368 Processing helix chain 'B' and resid 369 through 372 removed outlier: 4.351A pdb=" N VAL B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 80 through 95 Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.871A pdb=" N GLU F 102 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS F 103 " --> pdb=" O PRO F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 103' Processing helix chain 'F' and resid 114 through 128 removed outlier: 3.829A pdb=" N ARG F 118 " --> pdb=" O PRO F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 207 through 219 removed outlier: 3.507A pdb=" N CYS F 219 " --> pdb=" O LYS F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 235 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 265 through 269 Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 291 through 297 removed outlier: 3.635A pdb=" N LEU F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.784A pdb=" N THR F 306 " --> pdb=" O GLY F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 339 through 350 Processing helix chain 'F' and resid 353 through 357 removed outlier: 3.656A pdb=" N GLN F 356 " --> pdb=" O THR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 368 Processing helix chain 'F' and resid 369 through 372 removed outlier: 4.108A pdb=" N VAL F 372 " --> pdb=" O PRO F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing sheet with id=AA1, first strand: chain 'P' and resid 31 through 34 removed outlier: 4.100A pdb=" N THR P 108 " --> pdb=" O CYS P 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 55 through 56 removed outlier: 3.612A pdb=" N ARG P 39 " --> pdb=" O THR P 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 178 through 180 removed outlier: 3.745A pdb=" N VAL P 154 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER P 157 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN P 299 " --> pdb=" O ILE P 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'P' and resid 240 through 244 removed outlier: 6.640A pdb=" N LYS P 240 " --> pdb=" O THR P 251 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR P 251 " --> pdb=" O LYS P 240 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR P 242 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL P 249 " --> pdb=" O TYR P 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'R' and resid 55 through 56 removed outlier: 3.641A pdb=" N ARG R 39 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 105 through 109 removed outlier: 6.792A pdb=" N THR R 105 " --> pdb=" O TYR R 135 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA R 137 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU R 107 " --> pdb=" O ALA R 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 178 through 180 removed outlier: 3.596A pdb=" N VAL R 154 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AB2, first strand: chain 'R' and resid 240 through 244 removed outlier: 6.578A pdb=" N LYS R 240 " --> pdb=" O THR R 251 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR R 251 " --> pdb=" O LYS R 240 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR R 242 " --> pdb=" O VAL R 249 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL R 249 " --> pdb=" O TYR R 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.031A pdb=" N THR A 108 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 105 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA A 137 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 107 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 55 through 56 removed outlier: 3.657A pdb=" N ARG A 39 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.523A pdb=" N MET A 178 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AB7, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.893A pdb=" N LYS A 240 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 251 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A 242 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 249 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 31 through 34 removed outlier: 4.106A pdb=" N THR E 108 " --> pdb=" O CYS E 12 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR E 105 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA E 137 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU E 107 " --> pdb=" O ALA E 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 55 through 56 removed outlier: 3.700A pdb=" N ARG E 39 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 178 through 180 removed outlier: 3.512A pdb=" N MET E 178 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 154 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 332 " --> pdb=" O ASN E 299 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 167 through 168 Processing sheet with id=AC3, first strand: chain 'E' and resid 240 through 244 removed outlier: 6.822A pdb=" N LYS E 240 " --> pdb=" O THR E 251 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR E 251 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR E 242 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL E 249 " --> pdb=" O TYR E 242 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.190A pdb=" N THR B 108 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 137 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 107 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.684A pdb=" N ARG B 39 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.501A pdb=" N VAL B 154 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AC8, first strand: chain 'B' and resid 240 through 244 removed outlier: 4.711A pdb=" N LEU B 244 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 34 removed outlier: 4.211A pdb=" N THR F 108 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA F 137 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU F 107 " --> pdb=" O ALA F 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 55 through 56 removed outlier: 3.543A pdb=" N ARG F 39 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 178 through 180 removed outlier: 6.893A pdb=" N ASN F 299 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 167 through 168 Processing sheet with id=AD4, first strand: chain 'F' and resid 240 through 244 removed outlier: 4.747A pdb=" N LEU F 244 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN F 248 " --> pdb=" O LEU F 244 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2058 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: 2.49 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5722 1.34 - 1.46: 3462 1.46 - 1.58: 8522 1.58 - 1.69: 18 1.69 - 1.81: 222 Bond restraints: 17946 Sorted by residual: bond pdb=" C HIS E 103 " pdb=" O HIS E 103 " ideal model delta sigma weight residual 1.246 1.235 0.011 9.20e-03 1.18e+04 1.42e+00 bond pdb=" C4 ADP P 401 " pdb=" C5 ADP P 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" C HIS R 103 " pdb=" O HIS R 103 " ideal model delta sigma weight residual 1.246 1.237 0.009 9.20e-03 1.18e+04 1.00e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" C4 ADP R 401 " pdb=" C5 ADP R 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.47e-01 ... (remaining 17941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 22714 1.26 - 2.52: 1328 2.52 - 3.78: 232 3.78 - 5.04: 55 5.04 - 6.30: 25 Bond angle restraints: 24354 Sorted by residual: angle pdb=" C MET F 307 " pdb=" N TYR F 308 " pdb=" CA TYR F 308 " ideal model delta sigma weight residual 120.49 115.83 4.66 1.42e+00 4.96e-01 1.08e+01 angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 113.20 110.33 2.87 9.60e-01 1.09e+00 8.94e+00 angle pdb=" N ILE B 66 " pdb=" CA ILE B 66 " pdb=" C ILE B 66 " ideal model delta sigma weight residual 113.20 110.54 2.66 9.60e-01 1.09e+00 7.68e+00 angle pdb=" N ILE F 66 " pdb=" CA ILE F 66 " pdb=" C ILE F 66 " ideal model delta sigma weight residual 113.20 110.58 2.62 9.60e-01 1.09e+00 7.46e+00 angle pdb=" N GLN P 43 " pdb=" CA GLN P 43 " pdb=" C GLN P 43 " ideal model delta sigma weight residual 111.14 113.99 -2.85 1.08e+00 8.57e-01 6.98e+00 ... (remaining 24349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 9681 17.11 - 34.22: 924 34.22 - 51.33: 153 51.33 - 68.43: 31 68.43 - 85.54: 11 Dihedral angle restraints: 10800 sinusoidal: 4368 harmonic: 6432 Sorted by residual: dihedral pdb=" CA CYS E 376 " pdb=" C CYS E 376 " pdb=" N PHE E 377 " pdb=" CA PHE E 377 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LYS E 375 " pdb=" C LYS E 375 " pdb=" N CYS E 376 " pdb=" CA CYS E 376 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA CYS A 376 " pdb=" C CYS A 376 " pdb=" N PHE A 377 " pdb=" CA PHE A 377 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1297 0.027 - 0.053: 840 0.053 - 0.080: 310 0.080 - 0.106: 177 0.106 - 0.133: 82 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE F 167 " pdb=" N ILE F 167 " pdb=" C ILE F 167 " pdb=" CB ILE F 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE R 73 " pdb=" N ILE R 73 " pdb=" C ILE R 73 " pdb=" CB ILE R 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2703 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 244 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO E 245 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 245 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 245 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 244 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO A 245 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 244 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO F 245 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 245 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 245 " -0.027 5.00e-02 4.00e+02 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 349 2.67 - 3.23: 17314 3.23 - 3.79: 26822 3.79 - 4.34: 37567 4.34 - 4.90: 61337 Nonbonded interactions: 143389 Sorted by model distance: nonbonded pdb=" O SER B 302 " pdb=" OG1 THR B 306 " model vdw 2.114 3.040 nonbonded pdb=" O SER E 302 " pdb=" OG1 THR E 306 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASN B 14 " pdb=" NE1 TRP B 88 " model vdw 2.207 3.120 nonbonded pdb=" OE2 GLU R 197 " pdb=" NH1 ARG R 258 " model vdw 2.211 3.120 nonbonded pdb=" O LEU E 351 " pdb=" NE2 GLN E 355 " model vdw 2.219 3.120 ... (remaining 143384 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'P' selection = chain 'R' } 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: 8.830 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.210 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.005 0.043 17946 Z= 0.205 Angle : 0.708 6.296 24354 Z= 0.403 Chirality : 0.045 0.133 2706 Planarity : 0.005 0.053 3114 Dihedral : 13.610 85.543 6684 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.15), residues: 2214 helix: -1.85 (0.14), residues: 894 sheet: -2.46 (0.24), residues: 348 loop : -2.45 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 374 TYR 0.012 0.001 TYR E 145 PHE 0.012 0.001 PHE B 202 TRP 0.015 0.002 TRP B 358 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00450 (17946) covalent geometry : angle 0.70791 (24354) hydrogen bonds : bond 0.16845 ( 766) hydrogen bonds : angle 6.63464 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8253 (tp30) cc_final: 0.7825 (tp30) REVERT: P 327 MET cc_start: 0.7158 (mmt) cc_final: 0.6862 (mmt) REVERT: P 332 ILE cc_start: 0.8472 (mm) cc_final: 0.8224 (mm) REVERT: P 356 GLN cc_start: 0.7155 (pm20) cc_final: 0.6703 (mp10) REVERT: R 85 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 377 PHE cc_start: 0.5964 (t80) cc_final: 0.5386 (m-80) REVERT: B 193 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7979 (tppt) REVERT: B 332 ILE cc_start: 0.9083 (mm) cc_final: 0.8873 (mt) REVERT: F 115 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7515 (mmtt) REVERT: F 285 MET cc_start: 0.7399 (mmm) cc_final: 0.7105 (mmm) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1461 time to fit residues: 58.2252 Evaluate side-chains 189 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.0970 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 90 HIS P 94 ASN R 75 HIS R 90 HIS R 94 ASN R 164 ASN R 175 HIS R 355 GLN A 90 HIS A 94 ASN A 175 HIS E 61 GLN E 75 HIS E 89 HIS E 164 ASN E 175 HIS B 61 GLN B 75 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 175 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088250 restraints weight = 34359.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090824 restraints weight = 17026.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092516 restraints weight = 10037.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093639 restraints weight = 6695.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094403 restraints weight = 4891.802| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17946 Z= 0.110 Angle : 0.575 5.880 24354 Z= 0.285 Chirality : 0.043 0.144 2706 Planarity : 0.004 0.049 3114 Dihedral : 4.979 33.315 2496 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.58 % Allowed : 9.18 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.63 (0.17), residues: 2214 helix: -0.19 (0.16), residues: 888 sheet: -1.93 (0.24), residues: 384 loop : -1.46 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.024 0.001 TYR F 168 PHE 0.010 0.001 PHE R 33 TRP 0.009 0.002 TRP E 358 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00248 (17946) covalent geometry : angle 0.57471 (24354) hydrogen bonds : bond 0.03499 ( 766) hydrogen bonds : angle 5.18140 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 MET cc_start: 0.8291 (tpt) cc_final: 0.8033 (tpp) REVERT: P 229 MET cc_start: 0.7810 (tpp) cc_final: 0.7507 (tpt) REVERT: P 278 GLU cc_start: 0.8115 (tp30) cc_final: 0.7684 (tp30) REVERT: P 327 MET cc_start: 0.7213 (mmt) cc_final: 0.6974 (mmt) REVERT: P 356 GLN cc_start: 0.7149 (pm20) cc_final: 0.6689 (mp10) REVERT: R 59 GLU cc_start: 0.7111 (mp0) cc_final: 0.6746 (mp0) REVERT: R 168 TYR cc_start: 0.8237 (t80) cc_final: 0.7980 (t80) REVERT: R 182 LEU cc_start: 0.8217 (tp) cc_final: 0.7938 (tt) REVERT: R 362 GLN cc_start: 0.7115 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 377 PHE cc_start: 0.5737 (t80) cc_final: 0.5210 (m-80) REVERT: E 120 LYS cc_start: 0.7983 (tttp) cc_final: 0.7733 (mttm) REVERT: B 178 MET cc_start: 0.7604 (mmm) cc_final: 0.7377 (mmm) REVERT: B 229 MET cc_start: 0.7566 (mmm) cc_final: 0.7220 (mmm) REVERT: F 115 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7470 (mmtt) REVERT: F 285 MET cc_start: 0.7349 (mmm) cc_final: 0.7115 (mmm) outliers start: 11 outliers final: 7 residues processed: 231 average time/residue: 0.1349 time to fit residues: 47.6320 Evaluate side-chains 191 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 148 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 chunk 114 optimal weight: 0.0270 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087864 restraints weight = 34694.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090500 restraints weight = 17333.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092235 restraints weight = 10250.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093375 restraints weight = 6851.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094146 restraints weight = 5032.961| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17946 Z= 0.114 Angle : 0.556 5.884 24354 Z= 0.273 Chirality : 0.043 0.139 2706 Planarity : 0.004 0.044 3114 Dihedral : 4.784 32.438 2496 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.06 % Allowed : 11.25 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.84 (0.18), residues: 2214 helix: 0.45 (0.17), residues: 894 sheet: -1.55 (0.25), residues: 396 loop : -0.96 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 149 TYR 0.011 0.001 TYR F 168 PHE 0.011 0.001 PHE E 92 TRP 0.010 0.002 TRP B 358 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00264 (17946) covalent geometry : angle 0.55610 (24354) hydrogen bonds : bond 0.03172 ( 766) hydrogen bonds : angle 4.91222 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8153 (tp30) cc_final: 0.7717 (tp30) REVERT: P 327 MET cc_start: 0.7182 (mmt) cc_final: 0.6947 (mmt) REVERT: R 59 GLU cc_start: 0.7218 (mp0) cc_final: 0.6793 (mp0) REVERT: R 168 TYR cc_start: 0.8220 (t80) cc_final: 0.7980 (t80) REVERT: R 182 LEU cc_start: 0.8144 (tp) cc_final: 0.7925 (tt) REVERT: R 285 MET cc_start: 0.7437 (mmm) cc_final: 0.7158 (mmm) REVERT: R 316 GLN cc_start: 0.7752 (tt0) cc_final: 0.7484 (tt0) REVERT: A 377 PHE cc_start: 0.5743 (t80) cc_final: 0.5371 (m-80) REVERT: E 49 MET cc_start: 0.4236 (mmp) cc_final: 0.3927 (mmp) REVERT: E 377 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5588 (t80) REVERT: F 115 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7510 (mmtt) REVERT: F 229 MET cc_start: 0.7344 (mmm) cc_final: 0.7110 (mmm) outliers start: 20 outliers final: 14 residues processed: 215 average time/residue: 0.1192 time to fit residues: 40.1035 Evaluate side-chains 198 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain R residue 248 GLN Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain F residue 14 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087219 restraints weight = 34814.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089839 restraints weight = 17466.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.091550 restraints weight = 10374.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092625 restraints weight = 6983.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.093415 restraints weight = 5225.082| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17946 Z= 0.133 Angle : 0.567 6.012 24354 Z= 0.280 Chirality : 0.044 0.165 2706 Planarity : 0.004 0.041 3114 Dihedral : 4.795 33.877 2496 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.86 % Allowed : 11.78 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2214 helix: 0.59 (0.17), residues: 894 sheet: -1.39 (0.25), residues: 396 loop : -0.73 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.014 0.001 TYR A 168 PHE 0.012 0.001 PHE P 354 TRP 0.011 0.002 TRP B 358 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00312 (17946) covalent geometry : angle 0.56652 (24354) hydrogen bonds : bond 0.03265 ( 766) hydrogen bonds : angle 4.85295 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8157 (tp30) cc_final: 0.7728 (tp30) REVERT: P 327 MET cc_start: 0.7169 (mmt) cc_final: 0.6942 (mmt) REVERT: R 59 GLU cc_start: 0.7199 (mp0) cc_final: 0.6758 (mp0) REVERT: R 182 LEU cc_start: 0.8134 (tp) cc_final: 0.7919 (tt) REVERT: R 316 GLN cc_start: 0.7738 (tt0) cc_final: 0.7484 (tt0) REVERT: R 362 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 377 PHE cc_start: 0.5728 (t80) cc_final: 0.5416 (m-10) REVERT: E 49 MET cc_start: 0.4203 (mmp) cc_final: 0.3887 (mmp) REVERT: F 115 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7497 (mmtt) outliers start: 35 outliers final: 26 residues processed: 215 average time/residue: 0.1375 time to fit residues: 45.6881 Evaluate side-chains 203 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 12 CYS Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 248 GLN Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 171 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 211 optimal weight: 0.4980 chunk 178 optimal weight: 0.0270 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 overall best weight: 0.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088553 restraints weight = 34559.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091196 restraints weight = 17342.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092919 restraints weight = 10342.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094081 restraints weight = 6961.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094793 restraints weight = 5122.432| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17946 Z= 0.102 Angle : 0.533 5.859 24354 Z= 0.260 Chirality : 0.042 0.141 2706 Planarity : 0.004 0.041 3114 Dihedral : 4.609 29.893 2496 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.91 % Allowed : 12.90 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.26 (0.18), residues: 2214 helix: 0.83 (0.18), residues: 894 sheet: -1.25 (0.25), residues: 396 loop : -0.52 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.014 0.001 TYR A 168 PHE 0.009 0.001 PHE R 33 TRP 0.008 0.001 TRP R 81 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00234 (17946) covalent geometry : angle 0.53269 (24354) hydrogen bonds : bond 0.02897 ( 766) hydrogen bonds : angle 4.72649 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 192 MET cc_start: 0.8083 (mmm) cc_final: 0.7837 (tpp) REVERT: P 278 GLU cc_start: 0.8174 (tp30) cc_final: 0.7724 (tp30) REVERT: P 327 MET cc_start: 0.7057 (mmt) cc_final: 0.6828 (mmt) REVERT: R 285 MET cc_start: 0.7408 (mmm) cc_final: 0.7132 (mmm) REVERT: R 316 GLN cc_start: 0.7752 (tt0) cc_final: 0.7515 (tt0) REVERT: R 362 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6724 (tm-30) REVERT: B 45 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8405 (t) REVERT: F 115 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7494 (mmtt) outliers start: 36 outliers final: 23 residues processed: 235 average time/residue: 0.1288 time to fit residues: 47.2035 Evaluate side-chains 205 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 12 CYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 248 GLN Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 196 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085597 restraints weight = 34713.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088178 restraints weight = 17457.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089863 restraints weight = 10417.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090982 restraints weight = 7040.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091677 restraints weight = 5213.387| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17946 Z= 0.204 Angle : 0.628 6.309 24354 Z= 0.313 Chirality : 0.046 0.146 2706 Planarity : 0.004 0.043 3114 Dihedral : 5.013 38.205 2496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.44 % Allowed : 13.43 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.18), residues: 2214 helix: 0.61 (0.17), residues: 900 sheet: -1.20 (0.26), residues: 396 loop : -0.57 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 314 TYR 0.018 0.001 TYR A 168 PHE 0.014 0.002 PHE P 202 TRP 0.011 0.002 TRP A 358 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00481 (17946) covalent geometry : angle 0.62818 (24354) hydrogen bonds : bond 0.03766 ( 766) hydrogen bonds : angle 4.90522 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8208 (tp30) cc_final: 0.7777 (tp30) REVERT: P 327 MET cc_start: 0.7186 (mmt) cc_final: 0.6867 (mmt) REVERT: R 285 MET cc_start: 0.7334 (mmm) cc_final: 0.7025 (mmm) REVERT: R 362 GLN cc_start: 0.7154 (tm-30) cc_final: 0.6854 (tm-30) REVERT: R 377 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4265 (t80) REVERT: B 58 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6806 (t0) REVERT: F 115 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7513 (mmtt) REVERT: F 138 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7789 (tp) REVERT: F 223 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7153 (tt) outliers start: 46 outliers final: 37 residues processed: 230 average time/residue: 0.1411 time to fit residues: 49.7391 Evaluate side-chains 219 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 341 VAL Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 248 GLN Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 94 optimal weight: 1.9990 chunk 182 optimal weight: 0.0980 chunk 113 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 93 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 202 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089355 restraints weight = 34553.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092003 restraints weight = 17235.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093748 restraints weight = 10215.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094885 restraints weight = 6839.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.095684 restraints weight = 5036.595| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17946 Z= 0.094 Angle : 0.533 6.506 24354 Z= 0.259 Chirality : 0.042 0.142 2706 Planarity : 0.004 0.044 3114 Dihedral : 4.557 28.297 2496 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.96 % Allowed : 14.38 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.18), residues: 2214 helix: 0.95 (0.18), residues: 900 sheet: -0.70 (0.28), residues: 348 loop : -0.49 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.023 0.001 TYR F 168 PHE 0.010 0.001 PHE R 33 TRP 0.009 0.001 TRP A 358 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00211 (17946) covalent geometry : angle 0.53312 (24354) hydrogen bonds : bond 0.02733 ( 766) hydrogen bonds : angle 4.67569 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 MET cc_start: 0.8197 (tpt) cc_final: 0.7808 (tpp) REVERT: P 278 GLU cc_start: 0.8101 (tp30) cc_final: 0.7672 (tp30) REVERT: P 327 MET cc_start: 0.7050 (mmt) cc_final: 0.6768 (mmt) REVERT: R 285 MET cc_start: 0.7427 (mmm) cc_final: 0.7193 (mmm) REVERT: R 316 GLN cc_start: 0.7753 (tt0) cc_final: 0.7509 (tt0) REVERT: R 377 PHE cc_start: 0.5119 (OUTLIER) cc_final: 0.4225 (t80) REVERT: B 45 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8480 (t) REVERT: F 115 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7481 (mmtt) REVERT: F 223 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7152 (tt) outliers start: 37 outliers final: 31 residues processed: 234 average time/residue: 0.1404 time to fit residues: 50.3529 Evaluate side-chains 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 200 TYR Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 62 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.086214 restraints weight = 34589.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088784 restraints weight = 17357.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090469 restraints weight = 10344.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091601 restraints weight = 6972.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092297 restraints weight = 5139.562| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17946 Z= 0.174 Angle : 0.609 6.202 24354 Z= 0.301 Chirality : 0.045 0.140 2706 Planarity : 0.004 0.044 3114 Dihedral : 4.907 36.581 2496 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.44 % Allowed : 14.33 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.17 (0.18), residues: 2214 helix: 0.76 (0.18), residues: 900 sheet: -1.01 (0.26), residues: 390 loop : -0.43 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 149 TYR 0.025 0.001 TYR B 168 PHE 0.012 0.001 PHE P 202 TRP 0.010 0.002 TRP B 358 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00410 (17946) covalent geometry : angle 0.60883 (24354) hydrogen bonds : bond 0.03560 ( 766) hydrogen bonds : angle 4.82675 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8199 (tp30) cc_final: 0.7814 (tp30) REVERT: P 327 MET cc_start: 0.7045 (mmt) cc_final: 0.6725 (mmt) REVERT: R 229 MET cc_start: 0.7643 (tpp) cc_final: 0.7361 (tpp) REVERT: R 285 MET cc_start: 0.7332 (mmm) cc_final: 0.7084 (mmm) REVERT: R 377 PHE cc_start: 0.5279 (OUTLIER) cc_final: 0.4236 (t80) REVERT: B 58 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6824 (t0) REVERT: F 115 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7494 (mmtt) REVERT: F 192 MET cc_start: 0.7806 (ttm) cc_final: 0.7499 (ttm) REVERT: F 223 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7128 (tt) outliers start: 46 outliers final: 37 residues processed: 223 average time/residue: 0.1270 time to fit residues: 44.1601 Evaluate side-chains 217 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 205 THR Chi-restraints excluded: chain P residue 341 VAL Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 152 optimal weight: 0.0980 chunk 202 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.085074 restraints weight = 35039.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087628 restraints weight = 17642.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089316 restraints weight = 10545.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090428 restraints weight = 7131.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.091142 restraints weight = 5298.068| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17946 Z= 0.213 Angle : 0.649 6.949 24354 Z= 0.323 Chirality : 0.046 0.148 2706 Planarity : 0.004 0.044 3114 Dihedral : 5.170 40.226 2496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.76 % Allowed : 14.23 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2214 helix: 0.56 (0.17), residues: 900 sheet: -1.05 (0.26), residues: 390 loop : -0.56 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 149 TYR 0.028 0.002 TYR B 168 PHE 0.013 0.002 PHE E 202 TRP 0.011 0.002 TRP F 342 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00502 (17946) covalent geometry : angle 0.64905 (24354) hydrogen bonds : bond 0.03857 ( 766) hydrogen bonds : angle 4.96622 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.8236 (tpt) cc_final: 0.7862 (tpp) REVERT: P 278 GLU cc_start: 0.8206 (tp30) cc_final: 0.7819 (tp30) REVERT: P 327 MET cc_start: 0.7169 (mmt) cc_final: 0.6844 (mmt) REVERT: R 229 MET cc_start: 0.7650 (tpp) cc_final: 0.7339 (tpp) REVERT: R 285 MET cc_start: 0.7353 (mmm) cc_final: 0.7115 (mmm) REVERT: B 357 MET cc_start: 0.7663 (mtp) cc_final: 0.7395 (mtm) REVERT: F 115 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7485 (mmtt) REVERT: F 192 MET cc_start: 0.7908 (ttm) cc_final: 0.7567 (ttm) REVERT: F 223 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7148 (tt) outliers start: 52 outliers final: 41 residues processed: 223 average time/residue: 0.1256 time to fit residues: 43.7059 Evaluate side-chains 216 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 341 VAL Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 141 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087717 restraints weight = 34294.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090298 restraints weight = 17181.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091994 restraints weight = 10247.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093130 restraints weight = 6896.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093884 restraints weight = 5080.626| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17946 Z= 0.116 Angle : 0.566 7.205 24354 Z= 0.277 Chirality : 0.043 0.143 2706 Planarity : 0.004 0.044 3114 Dihedral : 4.777 31.775 2496 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 15.02 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.11 (0.18), residues: 2214 helix: 0.87 (0.18), residues: 894 sheet: -0.99 (0.26), residues: 384 loop : -0.45 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 149 TYR 0.023 0.001 TYR B 168 PHE 0.009 0.001 PHE R 33 TRP 0.011 0.002 TRP E 358 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00270 (17946) covalent geometry : angle 0.56647 (24354) hydrogen bonds : bond 0.03092 ( 766) hydrogen bonds : angle 4.77313 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8110 (tp30) cc_final: 0.7728 (tp30) REVERT: P 327 MET cc_start: 0.7085 (mmt) cc_final: 0.6833 (mmt) REVERT: R 285 MET cc_start: 0.7447 (mmm) cc_final: 0.7234 (mmm) REVERT: R 316 GLN cc_start: 0.7708 (tt0) cc_final: 0.7442 (tt0) REVERT: R 377 PHE cc_start: 0.5251 (OUTLIER) cc_final: 0.4259 (t80) REVERT: E 49 MET cc_start: 0.4106 (mmp) cc_final: 0.3873 (mmp) REVERT: F 115 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7463 (mmtt) REVERT: F 192 MET cc_start: 0.7798 (ttm) cc_final: 0.7481 (ttm) REVERT: F 223 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7164 (tt) outliers start: 38 outliers final: 34 residues processed: 222 average time/residue: 0.1307 time to fit residues: 44.6174 Evaluate side-chains 219 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 203 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain R residue 377 PHE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 198 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.087224 restraints weight = 34691.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.089819 restraints weight = 17383.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091529 restraints weight = 10350.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092658 restraints weight = 6960.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093421 restraints weight = 5141.898| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17946 Z= 0.132 Angle : 0.579 7.094 24354 Z= 0.284 Chirality : 0.044 0.142 2706 Planarity : 0.004 0.051 3114 Dihedral : 4.793 33.386 2496 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.23 % Allowed : 14.92 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.07 (0.18), residues: 2214 helix: 0.87 (0.18), residues: 894 sheet: -0.94 (0.26), residues: 384 loop : -0.42 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 149 TYR 0.025 0.001 TYR B 168 PHE 0.009 0.001 PHE E 92 TRP 0.011 0.002 TRP E 358 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00312 (17946) covalent geometry : angle 0.57874 (24354) hydrogen bonds : bond 0.03222 ( 766) hydrogen bonds : angle 4.78417 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.05 seconds wall clock time: 44 minutes 19.37 seconds (2659.37 seconds total)