Starting phenix.real_space_refine on Sun May 18 22:14:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zix_60132/05_2025/8zix_60132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zix_60132/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zix_60132/05_2025/8zix_60132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zix_60132/05_2025/8zix_60132.map" model { file = "/net/cci-nas-00/data/ceres_data/8zix_60132/05_2025/8zix_60132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zix_60132/05_2025/8zix_60132.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.02, per 1000 atoms: 0.57 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: 4.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.64 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: 6.34 Time building geometry restraints manager: 5.25 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: 0.03 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: 26.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.090 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.890 ------------------------------------------------------------------------------- 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 : 10.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP B 358 HIS 0.005 0.001 HIS A 103 PHE 0.012 0.001 PHE B 202 TYR 0.012 0.001 TYR E 145 ARG 0.006 0.000 ARG B 374 Details of bonding type rmsd hydrogen bonds : bond 0.16845 ( 766) hydrogen bonds : angle 6.63464 ( 2058) covalent geometry : bond 0.00450 (17946) covalent geometry : angle 0.70791 (24354) *********************** 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 : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8253 (tp30) cc_final: 0.7824 (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: 0.8223 (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: 0.5387 (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: 0.8874 (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: 0.3333 time to fit residues: 132.6878 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 : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 0.4980 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 89 HIS R 90 HIS R 94 ASN R 164 ASN R 175 HIS R 355 GLN A 61 GLN A 75 HIS 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 F 164 ASN F 175 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086187 restraints weight = 34670.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088743 restraints weight = 17207.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090413 restraints weight = 10160.183| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17946 Z= 0.167 Angle : 0.627 6.250 24354 Z= 0.314 Chirality : 0.045 0.141 2706 Planarity : 0.005 0.052 3114 Dihedral : 5.270 40.382 2496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.80 % Allowed : 9.93 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2214 helix: -0.46 (0.16), residues: 894 sheet: -1.95 (0.24), residues: 384 loop : -1.51 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 358 HIS 0.004 0.001 HIS B 163 PHE 0.012 0.001 PHE B 92 TYR 0.024 0.001 TYR F 168 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 766) hydrogen bonds : angle 5.31159 ( 2058) covalent geometry : bond 0.00392 (17946) covalent geometry : angle 0.62666 (24354) *********************** 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 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 229 MET cc_start: 0.7882 (tpp) cc_final: 0.7523 (tpt) REVERT: P 278 GLU cc_start: 0.8170 (tp30) cc_final: 0.7740 (tp30) REVERT: P 327 MET cc_start: 0.7195 (mmt) cc_final: 0.6916 (mmt) REVERT: R 59 GLU cc_start: 0.7173 (mp0) cc_final: 0.6815 (mp0) REVERT: R 168 TYR cc_start: 0.8230 (t80) cc_final: 0.7966 (t80) REVERT: R 362 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 377 PHE cc_start: 0.6010 (t80) cc_final: 0.5410 (m-80) REVERT: B 193 LYS cc_start: 0.8275 (ttpt) cc_final: 0.8001 (tppt) REVERT: B 332 ILE cc_start: 0.9074 (mm) cc_final: 0.8849 (mt) REVERT: F 115 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7471 (mmtt) REVERT: F 285 MET cc_start: 0.7416 (mmm) cc_final: 0.7143 (mmm) outliers start: 15 outliers final: 9 residues processed: 208 average time/residue: 0.2892 time to fit residues: 91.2198 Evaluate side-chains 185 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain R residue 372 VAL 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 45 VAL 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 60 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087120 restraints weight = 34541.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089680 restraints weight = 17238.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.091371 restraints weight = 10221.603| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17946 Z= 0.127 Angle : 0.574 6.142 24354 Z= 0.284 Chirality : 0.043 0.140 2706 Planarity : 0.004 0.050 3114 Dihedral : 4.948 34.520 2496 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.27 % Allowed : 11.57 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2214 helix: 0.28 (0.17), residues: 894 sheet: -1.62 (0.25), residues: 384 loop : -1.11 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 88 HIS 0.004 0.001 HIS B 163 PHE 0.011 0.001 PHE E 92 TYR 0.023 0.001 TYR F 168 ARG 0.002 0.000 ARG B 374 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 766) hydrogen bonds : angle 4.98330 ( 2058) covalent geometry : bond 0.00295 (17946) covalent geometry : angle 0.57361 (24354) *********************** 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 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8097 (tp30) cc_final: 0.7706 (tp30) REVERT: P 327 MET cc_start: 0.7177 (mmt) cc_final: 0.6901 (mmt) REVERT: R 59 GLU cc_start: 0.7207 (mp0) cc_final: 0.6818 (mp0) REVERT: R 362 GLN cc_start: 0.7158 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 377 PHE cc_start: 0.5817 (t80) cc_final: 0.5410 (m-80) REVERT: E 49 MET cc_start: 0.4333 (mmp) cc_final: 0.4027 (mmp) REVERT: F 115 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7467 (mmtt) REVERT: F 229 MET cc_start: 0.7364 (mmm) cc_final: 0.7151 (mmm) outliers start: 24 outliers final: 15 residues processed: 220 average time/residue: 0.2974 time to fit residues: 99.7700 Evaluate side-chains 193 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 205 THR Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain A residue 19 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 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 Chi-restraints excluded: chain B residue 204 THR 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 102 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 GLN R 355 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084461 restraints weight = 35003.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087019 restraints weight = 17563.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088699 restraints weight = 10483.801| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17946 Z= 0.223 Angle : 0.655 6.491 24354 Z= 0.329 Chirality : 0.047 0.170 2706 Planarity : 0.005 0.048 3114 Dihedral : 5.290 43.428 2496 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.81 % Allowed : 12.79 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2214 helix: 0.21 (0.17), residues: 894 sheet: -1.46 (0.25), residues: 384 loop : -1.05 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 358 HIS 0.005 0.001 HIS A 103 PHE 0.013 0.002 PHE E 92 TYR 0.015 0.002 TYR F 168 ARG 0.004 0.001 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 766) hydrogen bonds : angle 5.13194 ( 2058) covalent geometry : bond 0.00525 (17946) covalent geometry : angle 0.65550 (24354) *********************** 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 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8208 (tp30) cc_final: 0.7787 (tp30) REVERT: P 327 MET cc_start: 0.7203 (mmt) cc_final: 0.6886 (mmt) REVERT: R 59 GLU cc_start: 0.7244 (mp0) cc_final: 0.6883 (mp0) REVERT: R 362 GLN cc_start: 0.7199 (tm-30) cc_final: 0.6947 (tm-30) REVERT: A 377 PHE cc_start: 0.6090 (t80) cc_final: 0.5661 (m-80) REVERT: B 14 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6812 (p0) REVERT: B 58 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6861 (t0) REVERT: F 115 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7480 (mmtt) REVERT: F 138 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8138 (tp) outliers start: 53 outliers final: 39 residues processed: 231 average time/residue: 0.2806 time to fit residues: 100.6124 Evaluate side-chains 218 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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 205 THR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 250 ILE 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 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 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 A residue 341 VAL 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 154 VAL 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 375 LYS Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain B residue 14 ASN 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 204 THR 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 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 3 optimal weight: 0.0060 chunk 53 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.099143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.088298 restraints weight = 34838.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090922 restraints weight = 17281.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092629 restraints weight = 10223.924| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17946 Z= 0.097 Angle : 0.540 6.196 24354 Z= 0.265 Chirality : 0.042 0.139 2706 Planarity : 0.004 0.047 3114 Dihedral : 4.746 29.595 2496 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.02 % Allowed : 13.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2214 helix: 0.70 (0.18), residues: 888 sheet: -1.32 (0.26), residues: 384 loop : -0.77 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P 88 HIS 0.004 0.001 HIS B 163 PHE 0.010 0.001 PHE R 33 TYR 0.026 0.001 TYR F 168 ARG 0.002 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 766) hydrogen bonds : angle 4.81203 ( 2058) covalent geometry : bond 0.00220 (17946) covalent geometry : angle 0.53990 (24354) *********************** 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 245 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 204 THR cc_start: 0.8478 (m) cc_final: 0.8177 (p) REVERT: P 278 GLU cc_start: 0.8061 (tp30) cc_final: 0.7676 (tp30) REVERT: P 327 MET cc_start: 0.7174 (mmt) cc_final: 0.6874 (mmt) REVERT: R 285 MET cc_start: 0.7440 (mmm) cc_final: 0.7188 (mmm) REVERT: R 316 GLN cc_start: 0.7738 (tt0) cc_final: 0.7486 (tt0) REVERT: A 168 TYR cc_start: 0.7954 (t80) cc_final: 0.7718 (t80) REVERT: A 377 PHE cc_start: 0.5743 (t80) cc_final: 0.5517 (m-10) REVERT: B 14 ASN cc_start: 0.7006 (OUTLIER) cc_final: 0.6765 (p0) REVERT: B 58 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6812 (t0) REVERT: F 115 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7431 (mmtt) REVERT: F 223 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7135 (tt) outliers start: 38 outliers final: 26 residues processed: 241 average time/residue: 0.2815 time to fit residues: 104.3388 Evaluate side-chains 209 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 341 VAL Chi-restraints excluded: chain R residue 243 GLU 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 154 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain E residue 79 THR 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 14 ASN 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 204 THR 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 223 LEU 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 36 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.096642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085888 restraints weight = 34763.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.088440 restraints weight = 17428.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090115 restraints weight = 10378.732| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17946 Z= 0.178 Angle : 0.611 6.244 24354 Z= 0.304 Chirality : 0.045 0.141 2706 Planarity : 0.004 0.046 3114 Dihedral : 5.024 39.020 2496 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.71 % Allowed : 14.17 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2214 helix: 0.59 (0.17), residues: 894 sheet: -1.23 (0.26), residues: 384 loop : -0.73 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 88 HIS 0.004 0.001 HIS B 163 PHE 0.012 0.001 PHE E 202 TYR 0.015 0.001 TYR B 168 ARG 0.003 0.000 ARG P 64 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 766) hydrogen bonds : angle 4.92504 ( 2058) covalent geometry : bond 0.00420 (17946) covalent geometry : angle 0.61069 (24354) *********************** 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 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8160 (tp30) cc_final: 0.7765 (tp30) REVERT: P 327 MET cc_start: 0.7150 (mmt) cc_final: 0.6825 (mmt) REVERT: R 229 MET cc_start: 0.7675 (tpp) cc_final: 0.7359 (tpp) REVERT: R 285 MET cc_start: 0.7364 (mmm) cc_final: 0.7057 (mmm) REVERT: R 362 GLN cc_start: 0.7145 (tm-30) cc_final: 0.6887 (tm-30) REVERT: R 377 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4320 (t80) REVERT: E 301 MET cc_start: 0.7294 (mmt) cc_final: 0.7084 (mmt) REVERT: B 14 ASN cc_start: 0.7148 (OUTLIER) cc_final: 0.6835 (p0) REVERT: B 58 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6862 (t0) REVERT: F 115 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7491 (mmtt) REVERT: F 138 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7846 (tp) outliers start: 51 outliers final: 40 residues processed: 230 average time/residue: 0.2761 time to fit residues: 98.3997 Evaluate side-chains 219 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 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 244 LEU 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 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 203 VAL 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 14 ASN 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 128 THR Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 192 MET 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 97 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.097849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087081 restraints weight = 34586.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089653 restraints weight = 17229.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091363 restraints weight = 10254.898| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17946 Z= 0.131 Angle : 0.569 6.143 24354 Z= 0.281 Chirality : 0.044 0.143 2706 Planarity : 0.004 0.047 3114 Dihedral : 4.868 34.372 2496 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.76 % Allowed : 14.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2214 helix: 0.72 (0.18), residues: 894 sheet: -1.14 (0.26), residues: 384 loop : -0.57 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P 88 HIS 0.004 0.001 HIS B 163 PHE 0.009 0.001 PHE E 92 TYR 0.018 0.001 TYR A 168 ARG 0.002 0.000 ARG P 64 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 766) hydrogen bonds : angle 4.82894 ( 2058) covalent geometry : bond 0.00306 (17946) covalent geometry : angle 0.56927 (24354) *********************** 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: 52 poor density : 186 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: P 204 THR cc_start: 0.8352 (m) cc_final: 0.8035 (p) REVERT: P 278 GLU cc_start: 0.8089 (tp30) cc_final: 0.7727 (tp30) REVERT: P 327 MET cc_start: 0.7170 (mmt) cc_final: 0.6846 (mmt) REVERT: R 229 MET cc_start: 0.7692 (tpp) cc_final: 0.7216 (tpp) REVERT: R 285 MET cc_start: 0.7396 (mmm) cc_final: 0.7126 (mmm) REVERT: R 362 GLN cc_start: 0.7129 (tm-30) cc_final: 0.6843 (tm-30) REVERT: R 377 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.4248 (t80) REVERT: A 168 TYR cc_start: 0.7911 (t80) cc_final: 0.7685 (t80) REVERT: E 301 MET cc_start: 0.7263 (mmt) cc_final: 0.7032 (mmt) REVERT: B 14 ASN cc_start: 0.7116 (OUTLIER) cc_final: 0.6797 (p0) REVERT: B 58 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6839 (t0) REVERT: F 115 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7482 (mmtt) REVERT: F 169 GLU cc_start: 0.6804 (tp30) cc_final: 0.6576 (mm-30) REVERT: F 223 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7134 (tt) outliers start: 52 outliers final: 42 residues processed: 232 average time/residue: 0.2718 time to fit residues: 98.4064 Evaluate side-chains 225 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 200 TYR 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 250 ILE 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 154 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 249 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 203 VAL 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 14 ASN 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 128 THR Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 180 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 216 optimal weight: 0.5980 chunk 181 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.098476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087724 restraints weight = 34433.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090323 restraints weight = 17203.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092029 restraints weight = 10232.637| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2227 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= 0.119 Angle : 0.558 6.450 24354 Z= 0.275 Chirality : 0.043 0.142 2706 Planarity : 0.004 0.045 3114 Dihedral : 4.759 32.837 2496 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.71 % Allowed : 14.65 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2214 helix: 0.79 (0.18), residues: 894 sheet: -1.06 (0.26), residues: 384 loop : -0.48 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 88 HIS 0.003 0.001 HIS B 163 PHE 0.009 0.001 PHE E 92 TYR 0.017 0.001 TYR A 168 ARG 0.002 0.000 ARG P 64 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 766) hydrogen bonds : angle 4.77340 ( 2058) covalent geometry : bond 0.00277 (17946) covalent geometry : angle 0.55842 (24354) *********************** 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 242 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 2.260 Fit side-chains revert: symmetry clash REVERT: P 204 THR cc_start: 0.8458 (m) cc_final: 0.8120 (p) REVERT: P 278 GLU cc_start: 0.8095 (tp30) cc_final: 0.7757 (tp30) REVERT: P 327 MET cc_start: 0.7160 (mmt) cc_final: 0.6844 (mmt) REVERT: R 229 MET cc_start: 0.7684 (tpp) cc_final: 0.7254 (tpp) REVERT: R 285 MET cc_start: 0.7380 (mmm) cc_final: 0.7146 (mmm) REVERT: R 316 GLN cc_start: 0.7739 (tt0) cc_final: 0.7475 (tt0) REVERT: R 362 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6890 (tm-30) REVERT: R 377 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4303 (t80) REVERT: A 168 TYR cc_start: 0.7955 (t80) cc_final: 0.7749 (t80) REVERT: E 301 MET cc_start: 0.7279 (mmt) cc_final: 0.7016 (mmt) REVERT: B 14 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6792 (p0) REVERT: B 58 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6815 (t0) REVERT: F 115 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7475 (mmtt) REVERT: F 223 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7109 (tt) outliers start: 51 outliers final: 42 residues processed: 234 average time/residue: 0.2714 time to fit residues: 99.0919 Evaluate side-chains 229 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 200 TYR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 243 GLU 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 243 GLU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 250 ILE 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 154 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 249 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 203 VAL 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 377 PHE Chi-restraints excluded: chain B residue 14 ASN 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 B residue 372 VAL Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 192 MET 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 186 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** R 355 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084461 restraints weight = 35353.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086975 restraints weight = 17782.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088673 restraints weight = 10624.082| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17946 Z= 0.252 Angle : 0.681 6.782 24354 Z= 0.342 Chirality : 0.048 0.154 2706 Planarity : 0.005 0.045 3114 Dihedral : 5.336 44.510 2496 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.92 % Allowed : 14.92 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2214 helix: 0.42 (0.17), residues: 894 sheet: -1.12 (0.26), residues: 384 loop : -0.68 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP P 88 HIS 0.006 0.001 HIS A 103 PHE 0.017 0.002 PHE A 202 TYR 0.019 0.002 TYR B 168 ARG 0.005 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 766) hydrogen bonds : angle 5.07068 ( 2058) covalent geometry : bond 0.00593 (17946) covalent geometry : angle 0.68055 (24354) *********************** 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 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8201 (tp30) cc_final: 0.7816 (tp30) REVERT: R 229 MET cc_start: 0.7688 (tpp) cc_final: 0.7281 (tpp) REVERT: R 285 MET cc_start: 0.7360 (mmm) cc_final: 0.7116 (mmm) REVERT: R 362 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 373 HIS cc_start: 0.7221 (m-70) cc_final: 0.6955 (m-70) REVERT: E 301 MET cc_start: 0.7326 (mmt) cc_final: 0.7030 (mmt) REVERT: B 14 ASN cc_start: 0.7140 (OUTLIER) cc_final: 0.6719 (p0) REVERT: B 58 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6867 (t0) REVERT: F 115 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7459 (mmtt) REVERT: F 138 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7772 (tp) REVERT: F 168 TYR cc_start: 0.8176 (t80) cc_final: 0.7948 (t80) outliers start: 55 outliers final: 45 residues processed: 230 average time/residue: 0.2698 time to fit residues: 97.3807 Evaluate side-chains 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 243 GLU Chi-restraints excluded: chain P residue 250 ILE 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 250 ILE 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 154 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 249 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 66 ILE 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 203 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 251 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 B residue 14 ASN 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 204 THR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 372 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 128 THR Chi-restraints excluded: chain F residue 138 ILE 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 45 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** P 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087102 restraints weight = 34596.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089657 restraints weight = 17380.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.091363 restraints weight = 10398.000| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17946 Z= 0.128 Angle : 0.579 7.034 24354 Z= 0.286 Chirality : 0.044 0.143 2706 Planarity : 0.004 0.047 3114 Dihedral : 4.924 34.890 2496 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.76 % Allowed : 15.13 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2214 helix: 0.70 (0.18), residues: 894 sheet: -1.09 (0.26), residues: 384 loop : -0.56 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 88 HIS 0.003 0.001 HIS B 163 PHE 0.010 0.001 PHE R 33 TYR 0.022 0.001 TYR E 168 ARG 0.002 0.000 ARG P 64 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 766) hydrogen bonds : angle 4.85666 ( 2058) covalent geometry : bond 0.00297 (17946) covalent geometry : angle 0.57898 (24354) ********************** 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 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: P 278 GLU cc_start: 0.8070 (tp30) cc_final: 0.7707 (tp30) REVERT: P 327 MET cc_start: 0.7154 (mmt) cc_final: 0.6836 (mmt) REVERT: R 229 MET cc_start: 0.7712 (tpp) cc_final: 0.7208 (tpp) REVERT: R 285 MET cc_start: 0.7421 (mmm) cc_final: 0.7205 (mmm) REVERT: R 362 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 168 TYR cc_start: 0.7872 (t80) cc_final: 0.7663 (t80) REVERT: A 373 HIS cc_start: 0.7177 (m-70) cc_final: 0.6924 (m-70) REVERT: E 301 MET cc_start: 0.7291 (mmt) cc_final: 0.7009 (mmt) REVERT: B 14 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6792 (p0) REVERT: F 115 LYS cc_start: 0.7741 (mtpt) cc_final: 0.7442 (mmtt) outliers start: 52 outliers final: 44 residues processed: 231 average time/residue: 0.2673 time to fit residues: 96.4033 Evaluate side-chains 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 243 GLU Chi-restraints excluded: chain P residue 250 ILE 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 250 ILE 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 154 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 249 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 66 ILE 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 203 VAL 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 14 ASN 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 180 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 372 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 128 THR 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 174 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.099038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088240 restraints weight = 34316.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090844 restraints weight = 17116.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092539 restraints weight = 10176.518| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17946 Z= 0.111 Angle : 0.559 7.094 24354 Z= 0.274 Chirality : 0.043 0.142 2706 Planarity : 0.004 0.045 3114 Dihedral : 4.722 31.537 2496 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.23 % Allowed : 16.08 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2214 helix: 0.92 (0.18), residues: 888 sheet: -1.04 (0.26), residues: 384 loop : -0.45 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 88 HIS 0.003 0.001 HIS B 163 PHE 0.009 0.001 PHE R 33 TYR 0.020 0.001 TYR E 168 ARG 0.002 0.000 ARG P 64 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 766) hydrogen bonds : angle 4.75973 ( 2058) covalent geometry : bond 0.00258 (17946) covalent geometry : angle 0.55907 (24354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4827.86 seconds wall clock time: 87 minutes 28.14 seconds (5248.14 seconds total)