Starting phenix.real_space_refine on Sun Aug 24 05:33:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxp_27772/08_2025/8dxp_27772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxp_27772/08_2025/8dxp_27772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dxp_27772/08_2025/8dxp_27772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxp_27772/08_2025/8dxp_27772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dxp_27772/08_2025/8dxp_27772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxp_27772/08_2025/8dxp_27772.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 11541 2.51 5 N 2756 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17465 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2501 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "E" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2498 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2490 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Time building chain proxies: 4.55, per 1000 atoms: 0.26 Number of scatterers: 17465 At special positions: 0 Unit cell: (125.4, 117.7, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 3021 8.00 N 2756 7.00 C 11541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 805.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4054 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 71.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 122 through 142 removed outlier: 3.510A pdb=" N TYR A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 151 through 167 removed outlier: 4.084A pdb=" N ILE A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.070A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 258 through 283 removed outlier: 3.728A pdb=" N TYR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 344 removed outlier: 4.262A pdb=" N ARG A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 367 through 378 Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.621A pdb=" N PHE A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.173A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.624A pdb=" N VAL B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 47 removed outlier: 5.080A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.621A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.886A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.701A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 165 removed outlier: 4.050A pdb=" N ILE B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.290A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 259 through 283 removed outlier: 3.521A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.559A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.504A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 405 removed outlier: 4.133A pdb=" N GLU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.614A pdb=" N VAL C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 4.193A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.759A pdb=" N LYS C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 126 " --> pdb=" O TRP C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'C' and resid 126 through 144 Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 232 through 253 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.556A pdb=" N VAL C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 313 through 343 removed outlier: 3.526A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.589A pdb=" N ARG C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.595A pdb=" N ALA C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.129A pdb=" N PHE C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.611A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 31 " --> pdb=" O PHE D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.730A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.639A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.879A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.734A pdb=" N SER D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 4.316A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.667A pdb=" N LYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 282 removed outlier: 3.918A pdb=" N MET D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 315 through 344 removed outlier: 4.332A pdb=" N ARG D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 359 removed outlier: 3.608A pdb=" N ARG D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 378 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.094A pdb=" N PHE D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 4.018A pdb=" N GLU D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.652A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.843A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 118 " --> pdb=" O MET E 114 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.501A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.605A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 176 Processing helix chain 'E' and resid 232 through 253 removed outlier: 3.516A pdb=" N GLU E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.937A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 removed outlier: 3.998A pdb=" N VAL E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 287' Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.798A pdb=" N PHE E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 removed outlier: 3.846A pdb=" N ARG E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.778A pdb=" N PHE E 372 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 373 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP E 381 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.139A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 405 Processing helix chain 'F' and resid 22 through 25 Processing helix chain 'F' and resid 26 through 49 Processing helix chain 'F' and resid 106 through 120 removed outlier: 4.236A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.693A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 167 removed outlier: 4.188A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 3.833A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 253 removed outlier: 3.730A pdb=" N LEU F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 283 removed outlier: 4.663A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 263 " --> pdb=" O TYR F 259 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 342 Processing helix chain 'F' and resid 351 through 359 removed outlier: 3.526A pdb=" N ARG F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.593A pdb=" N PHE F 372 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 378 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.084A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 removed outlier: 3.688A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 49 removed outlier: 3.860A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.621A pdb=" N TYR G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.793A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 143 removed outlier: 3.741A pdb=" N ASN G 143 " --> pdb=" O MET G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 4.097A pdb=" N PHE G 148 " --> pdb=" O TRP G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 167 removed outlier: 3.557A pdb=" N ASP G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.928A pdb=" N SER G 176 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU G 177 " --> pdb=" O ARG G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 253 removed outlier: 3.626A pdb=" N ALA G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 245 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 281 removed outlier: 3.626A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 302 Processing helix chain 'G' and resid 313 through 341 Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 368 through 379 removed outlier: 4.019A pdb=" N PHE G 372 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 389 removed outlier: 3.884A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 392 No H-bonds generated for 'chain 'G' and resid 390 through 392' Processing helix chain 'G' and resid 393 through 405 removed outlier: 3.715A pdb=" N GLU G 397 " --> pdb=" O SER G 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 56 removed outlier: 3.551A pdb=" N ILE D 53 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.645A pdb=" N CYS F 308 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.817A pdb=" N ILE G 53 " --> pdb=" O ASN G 309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN G 309 " --> pdb=" O ILE G 53 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.03 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: 5178 1.34 - 1.46: 3268 1.46 - 1.57: 9264 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 17934 Sorted by residual: bond pdb=" N ASN F 368 " pdb=" CA ASN F 368 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C ASP C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.50e+00 bond pdb=" N PRO D 382 " pdb=" CA PRO D 382 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.37e+00 bond pdb=" CB LYS C 246 " pdb=" CG LYS C 246 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.69e-02 3.50e+03 9.09e-01 ... (remaining 17929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 23860 1.87 - 3.74: 312 3.74 - 5.62: 36 5.62 - 7.49: 1 7.49 - 9.36: 2 Bond angle restraints: 24211 Sorted by residual: angle pdb=" N TRP C 145 " pdb=" CA TRP C 145 " pdb=" C TRP C 145 " ideal model delta sigma weight residual 114.56 109.93 4.63 1.27e+00 6.20e-01 1.33e+01 angle pdb=" CB LYS C 246 " pdb=" CG LYS C 246 " pdb=" CD LYS C 246 " ideal model delta sigma weight residual 111.30 118.88 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" N LYS F 367 " pdb=" CA LYS F 367 " pdb=" C LYS F 367 " ideal model delta sigma weight residual 108.34 112.28 -3.94 1.31e+00 5.83e-01 9.03e+00 angle pdb=" C ASN G 368 " pdb=" CA ASN G 368 " pdb=" CB ASN G 368 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.08e+00 angle pdb=" CA TRP B 145 " pdb=" CB TRP B 145 " pdb=" CG TRP B 145 " ideal model delta sigma weight residual 113.60 118.77 -5.17 1.90e+00 2.77e-01 7.40e+00 ... (remaining 24206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9386 17.97 - 35.94: 983 35.94 - 53.91: 159 53.91 - 71.88: 16 71.88 - 89.85: 14 Dihedral angle restraints: 10558 sinusoidal: 4295 harmonic: 6263 Sorted by residual: dihedral pdb=" CA ASP B 25 " pdb=" C ASP B 25 " pdb=" N VAL B 26 " pdb=" CA VAL B 26 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU B 117 " pdb=" C GLU B 117 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU F 117 " pdb=" C GLU F 117 " pdb=" N ARG F 118 " pdb=" CA ARG F 118 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 10555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1735 0.030 - 0.060: 667 0.060 - 0.090: 163 0.090 - 0.119: 67 0.119 - 0.149: 11 Chirality restraints: 2643 Sorted by residual: chirality pdb=" CA ILE G 363 " pdb=" N ILE G 363 " pdb=" C ILE G 363 " pdb=" CB ILE G 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE C 53 " pdb=" N ILE C 53 " pdb=" C ILE C 53 " pdb=" CB ILE C 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 363 " pdb=" N ILE B 363 " pdb=" C ILE B 363 " pdb=" CB ILE B 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2640 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 145 " 0.023 2.00e-02 2.50e+03 1.51e-02 5.73e+00 pdb=" CG TRP B 145 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 145 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 145 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 145 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 145 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 145 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 242 " 0.008 2.00e-02 2.50e+03 1.15e-02 2.31e+00 pdb=" CG PHE F 242 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE F 242 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 242 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 242 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 242 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 242 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 260 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ALA C 260 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA C 260 " -0.009 2.00e-02 2.50e+03 pdb=" N MET C 261 " -0.008 2.00e-02 2.50e+03 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4181 2.79 - 3.31: 17199 3.31 - 3.84: 27513 3.84 - 4.37: 30137 4.37 - 4.90: 52493 Nonbonded interactions: 131523 Sorted by model distance: nonbonded pdb=" NE2 HIS F 134 " pdb=" OH TYR F 279 " model vdw 2.258 3.120 nonbonded pdb=" O GLU G 352 " pdb=" OE1 GLN G 356 " model vdw 2.266 3.040 nonbonded pdb=" ND1 HIS F 314 " pdb=" OE2 GLU G 117 " model vdw 2.271 3.120 nonbonded pdb=" NH2 ARG A 58 " pdb=" OE1 GLU G 95 " model vdw 2.301 3.120 nonbonded pdb=" O ASN F 280 " pdb=" ND2 ASN F 280 " model vdw 2.303 3.120 ... (remaining 131518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'B' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'C' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 59 or resid 96 through 175 or resid 177 or resi \ d 235 through 405)) } 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: 3.190 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.003 0.047 17948 Z= 0.131 Angle : 0.553 9.361 24239 Z= 0.312 Chirality : 0.035 0.149 2643 Planarity : 0.003 0.031 2948 Dihedral : 14.487 89.846 6462 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.20), residues: 2055 helix: 1.76 (0.15), residues: 1304 sheet: -0.98 (0.48), residues: 119 loop : -2.54 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 58 TYR 0.019 0.001 TYR A 279 PHE 0.026 0.001 PHE F 242 TRP 0.040 0.001 TRP B 145 HIS 0.008 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00273 (17934) covalent geometry : angle 0.55316 (24211) SS BOND : bond 0.00244 ( 14) SS BOND : angle 0.47281 ( 28) hydrogen bonds : bond 0.15052 ( 1021) hydrogen bonds : angle 5.65929 ( 3024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.7578 (mtm) cc_final: 0.7215 (mtm) REVERT: G 356 GLN cc_start: 0.7399 (mp10) cc_final: 0.7110 (mp10) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.1385 time to fit residues: 70.0416 Evaluate side-chains 268 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS B 49 GLN B 157 HIS B 251 HIS C 106 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS E 265 GLN E 309 ASN E 398 ASN F 280 ASN F 398 ASN G 314 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.177253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139372 restraints weight = 28287.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136236 restraints weight = 24313.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137598 restraints weight = 19639.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138134 restraints weight = 14349.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138246 restraints weight = 13098.517| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17948 Z= 0.130 Angle : 0.555 11.381 24239 Z= 0.292 Chirality : 0.039 0.156 2643 Planarity : 0.003 0.048 2948 Dihedral : 4.027 26.466 2279 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.24 % Allowed : 10.33 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.20), residues: 2055 helix: 1.76 (0.15), residues: 1352 sheet: -0.60 (0.45), residues: 139 loop : -2.58 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 249 TYR 0.016 0.001 TYR F 279 PHE 0.058 0.002 PHE E 242 TRP 0.019 0.001 TRP E 170 HIS 0.008 0.001 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00283 (17934) covalent geometry : angle 0.55406 (24211) SS BOND : bond 0.00342 ( 14) SS BOND : angle 0.91030 ( 28) hydrogen bonds : bond 0.04347 ( 1021) hydrogen bonds : angle 4.10061 ( 3024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 306 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.6784 (ttp) cc_final: 0.6533 (ttt) REVERT: D 368 ASN cc_start: 0.8471 (m-40) cc_final: 0.7990 (m-40) REVERT: F 242 PHE cc_start: 0.7734 (m-80) cc_final: 0.7512 (m-80) REVERT: G 356 GLN cc_start: 0.7882 (mp10) cc_final: 0.7561 (mp10) REVERT: G 373 MET cc_start: 0.8568 (tpp) cc_final: 0.8325 (tpp) outliers start: 24 outliers final: 17 residues processed: 319 average time/residue: 0.1396 time to fit residues: 65.7998 Evaluate side-chains 287 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 192 optimal weight: 0.0170 chunk 24 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 144 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS C 106 GLN E 157 HIS E 265 GLN F 398 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.170491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133479 restraints weight = 28378.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129510 restraints weight = 36723.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131486 restraints weight = 32650.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131861 restraints weight = 19985.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132165 restraints weight = 18823.076| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17948 Z= 0.201 Angle : 0.591 10.442 24239 Z= 0.316 Chirality : 0.041 0.170 2643 Planarity : 0.003 0.039 2948 Dihedral : 4.110 26.772 2279 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.48 % Allowed : 13.79 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 2055 helix: 1.49 (0.14), residues: 1357 sheet: -0.65 (0.45), residues: 139 loop : -2.63 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 347 TYR 0.024 0.002 TYR A 330 PHE 0.022 0.002 PHE D 41 TRP 0.017 0.002 TRP B 145 HIS 0.007 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00473 (17934) covalent geometry : angle 0.59111 (24211) SS BOND : bond 0.00489 ( 14) SS BOND : angle 0.85216 ( 28) hydrogen bonds : bond 0.04900 ( 1021) hydrogen bonds : angle 4.09469 ( 3024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 373 MET cc_start: 0.8115 (ttp) cc_final: 0.7883 (tmm) REVERT: C 48 MET cc_start: 0.6856 (ttp) cc_final: 0.6555 (ttt) REVERT: D 259 TYR cc_start: 0.7410 (t80) cc_final: 0.6764 (t80) REVERT: D 387 ARG cc_start: 0.7336 (mtp180) cc_final: 0.7135 (tpp80) REVERT: G 140 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7210 (tp) outliers start: 48 outliers final: 34 residues processed: 317 average time/residue: 0.1420 time to fit residues: 67.4064 Evaluate side-chains 297 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 166 PHE Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 138 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 182 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN C 106 GLN E 157 HIS F 251 HIS F 398 ASN G 106 GLN G 121 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.176983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140526 restraints weight = 28389.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137422 restraints weight = 38602.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139538 restraints weight = 31788.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139749 restraints weight = 19712.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140103 restraints weight = 17328.494| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17948 Z= 0.117 Angle : 0.515 11.232 24239 Z= 0.272 Chirality : 0.038 0.160 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.961 26.209 2279 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.86 % Allowed : 16.06 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 2055 helix: 1.66 (0.15), residues: 1363 sheet: -0.50 (0.45), residues: 139 loop : -2.56 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.014 0.001 TYR F 279 PHE 0.020 0.001 PHE G 248 TRP 0.022 0.001 TRP F 145 HIS 0.010 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00258 (17934) covalent geometry : angle 0.51510 (24211) SS BOND : bond 0.00261 ( 14) SS BOND : angle 0.61270 ( 28) hydrogen bonds : bond 0.03893 ( 1021) hydrogen bonds : angle 3.78888 ( 3024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7016 (tmm) cc_final: 0.6488 (tmm) REVERT: B 248 PHE cc_start: 0.6784 (t80) cc_final: 0.6578 (t80) REVERT: C 48 MET cc_start: 0.6749 (ttp) cc_final: 0.6459 (ttt) REVERT: D 259 TYR cc_start: 0.7481 (t80) cc_final: 0.6692 (t80) REVERT: D 279 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.5061 (t80) REVERT: D 376 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7164 (mtm) REVERT: F 145 TRP cc_start: 0.7897 (p-90) cc_final: 0.7690 (p-90) REVERT: G 140 LEU cc_start: 0.7569 (tt) cc_final: 0.7106 (tp) REVERT: G 373 MET cc_start: 0.8358 (tpp) cc_final: 0.8093 (tpp) outliers start: 36 outliers final: 23 residues processed: 309 average time/residue: 0.1381 time to fit residues: 64.0279 Evaluate side-chains 288 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 166 PHE Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 53 optimal weight: 0.0970 chunk 195 optimal weight: 0.0170 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 94 optimal weight: 0.5980 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 ASN E 134 HIS E 157 HIS F 375 HIS G 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138576 restraints weight = 28073.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136821 restraints weight = 27580.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138522 restraints weight = 24882.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138504 restraints weight = 16110.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138826 restraints weight = 14874.183| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17948 Z= 0.106 Angle : 0.497 12.269 24239 Z= 0.264 Chirality : 0.037 0.157 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.853 26.160 2279 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.58 % Allowed : 16.84 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 2055 helix: 1.76 (0.15), residues: 1352 sheet: -0.38 (0.47), residues: 139 loop : -2.51 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 347 TYR 0.014 0.001 TYR B 279 PHE 0.033 0.001 PHE G 372 TRP 0.034 0.001 TRP C 145 HIS 0.012 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00227 (17934) covalent geometry : angle 0.49708 (24211) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.51003 ( 28) hydrogen bonds : bond 0.03513 ( 1021) hydrogen bonds : angle 3.64207 ( 3024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6959 (tmm) cc_final: 0.6431 (tmm) REVERT: C 48 MET cc_start: 0.6839 (ttp) cc_final: 0.6518 (ttt) REVERT: D 242 PHE cc_start: 0.7019 (m-80) cc_final: 0.6761 (m-80) REVERT: D 279 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5123 (t80) REVERT: D 369 ASP cc_start: 0.7347 (p0) cc_final: 0.7123 (t70) REVERT: D 376 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7076 (mtm) REVERT: E 49 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7920 (tp-100) outliers start: 50 outliers final: 32 residues processed: 312 average time/residue: 0.1386 time to fit residues: 65.1255 Evaluate side-chains 299 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 370 PHE Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 375 HIS Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 126 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 157 HIS E 309 ASN F 251 HIS F 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142122 restraints weight = 28142.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139536 restraints weight = 35876.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141467 restraints weight = 28844.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141719 restraints weight = 18666.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141850 restraints weight = 18250.396| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17948 Z= 0.118 Angle : 0.515 11.768 24239 Z= 0.271 Chirality : 0.038 0.157 2643 Planarity : 0.003 0.031 2948 Dihedral : 3.830 25.908 2279 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.74 % Allowed : 17.41 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.20), residues: 2055 helix: 1.71 (0.15), residues: 1352 sheet: -0.29 (0.47), residues: 138 loop : -2.51 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.015 0.001 TYR A 330 PHE 0.035 0.001 PHE G 372 TRP 0.042 0.001 TRP C 145 HIS 0.018 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00269 (17934) covalent geometry : angle 0.51476 (24211) SS BOND : bond 0.00273 ( 14) SS BOND : angle 0.54048 ( 28) hydrogen bonds : bond 0.03642 ( 1021) hydrogen bonds : angle 3.63502 ( 3024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6906 (tmm) cc_final: 0.6448 (tmm) REVERT: C 48 MET cc_start: 0.7036 (ttp) cc_final: 0.6649 (ttt) REVERT: D 242 PHE cc_start: 0.7125 (m-80) cc_final: 0.6883 (m-80) REVERT: D 279 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5403 (t80) REVERT: D 369 ASP cc_start: 0.7207 (p0) cc_final: 0.6856 (t0) REVERT: D 376 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7173 (mtm) REVERT: E 356 GLN cc_start: 0.6735 (mp10) cc_final: 0.6476 (mp10) REVERT: G 140 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7286 (tp) outliers start: 53 outliers final: 46 residues processed: 312 average time/residue: 0.1426 time to fit residues: 66.9025 Evaluate side-chains 316 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 267 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 168 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 147 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 182 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 overall best weight: 0.5474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.178787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143604 restraints weight = 28380.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141708 restraints weight = 35011.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143248 restraints weight = 28870.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143512 restraints weight = 17862.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143750 restraints weight = 17799.413| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17948 Z= 0.110 Angle : 0.510 11.333 24239 Z= 0.270 Chirality : 0.037 0.154 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.799 25.931 2279 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.94 % Allowed : 17.87 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 2055 helix: 1.70 (0.15), residues: 1356 sheet: -0.23 (0.47), residues: 138 loop : -2.49 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.014 0.001 TYR B 279 PHE 0.032 0.001 PHE G 372 TRP 0.041 0.001 TRP C 145 HIS 0.011 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00247 (17934) covalent geometry : angle 0.51028 (24211) SS BOND : bond 0.00245 ( 14) SS BOND : angle 0.49033 ( 28) hydrogen bonds : bond 0.03499 ( 1021) hydrogen bonds : angle 3.57656 ( 3024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 281 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6963 (tmm) cc_final: 0.6719 (tmm) REVERT: B 239 LYS cc_start: 0.6617 (mptt) cc_final: 0.6221 (mtmm) REVERT: C 48 MET cc_start: 0.7087 (ttp) cc_final: 0.6681 (ttt) REVERT: D 279 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.5510 (t80) REVERT: D 373 MET cc_start: 0.5409 (ptt) cc_final: 0.5202 (ptt) REVERT: E 49 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7972 (tp40) REVERT: G 383 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.5889 (mt) outliers start: 57 outliers final: 46 residues processed: 313 average time/residue: 0.1412 time to fit residues: 66.8308 Evaluate side-chains 312 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 187 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.178015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142329 restraints weight = 28363.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139349 restraints weight = 39913.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141312 restraints weight = 33873.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141605 restraints weight = 21628.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141837 restraints weight = 18686.424| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17948 Z= 0.121 Angle : 0.537 14.631 24239 Z= 0.279 Chirality : 0.038 0.156 2643 Planarity : 0.003 0.074 2948 Dihedral : 3.828 26.107 2279 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.25 % Allowed : 18.18 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 2055 helix: 1.68 (0.15), residues: 1358 sheet: -0.29 (0.46), residues: 138 loop : -2.52 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.014 0.001 TYR B 279 PHE 0.035 0.001 PHE G 372 TRP 0.039 0.001 TRP C 145 HIS 0.010 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00274 (17934) covalent geometry : angle 0.53719 (24211) SS BOND : bond 0.00268 ( 14) SS BOND : angle 0.53161 ( 28) hydrogen bonds : bond 0.03587 ( 1021) hydrogen bonds : angle 3.60051 ( 3024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 MET cc_start: 0.7639 (ptm) cc_final: 0.7356 (ppp) REVERT: B 239 LYS cc_start: 0.6718 (mptt) cc_final: 0.6248 (mtmm) REVERT: C 48 MET cc_start: 0.7185 (ttp) cc_final: 0.6751 (ttt) REVERT: D 279 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5494 (t80) REVERT: G 383 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.5886 (mt) outliers start: 63 outliers final: 48 residues processed: 316 average time/residue: 0.1170 time to fit residues: 55.9864 Evaluate side-chains 322 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS C 143 ASN E 112 ASN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.178879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140643 restraints weight = 28456.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138298 restraints weight = 22084.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139968 restraints weight = 21380.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140102 restraints weight = 14162.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140349 restraints weight = 12155.827| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17948 Z= 0.113 Angle : 0.544 14.322 24239 Z= 0.280 Chirality : 0.037 0.153 2643 Planarity : 0.003 0.043 2948 Dihedral : 3.796 26.038 2279 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.84 % Allowed : 18.60 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 2055 helix: 1.74 (0.15), residues: 1352 sheet: -0.21 (0.46), residues: 138 loop : -2.53 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.014 0.001 TYR B 279 PHE 0.054 0.001 PHE A 370 TRP 0.040 0.001 TRP C 145 HIS 0.011 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00252 (17934) covalent geometry : angle 0.54395 (24211) SS BOND : bond 0.00246 ( 14) SS BOND : angle 0.49494 ( 28) hydrogen bonds : bond 0.03446 ( 1021) hydrogen bonds : angle 3.54806 ( 3024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.7000 (mmm-85) REVERT: B 239 LYS cc_start: 0.6780 (mptt) cc_final: 0.6337 (mtmm) REVERT: C 373 MET cc_start: 0.8573 (mmm) cc_final: 0.8172 (mmm) REVERT: D 279 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.5762 (t80) REVERT: G 376 MET cc_start: 0.7425 (mpp) cc_final: 0.7205 (mpp) REVERT: G 383 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.5974 (mt) outliers start: 55 outliers final: 46 residues processed: 315 average time/residue: 0.1125 time to fit residues: 54.2010 Evaluate side-chains 324 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 54 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN G 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.180360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142282 restraints weight = 28450.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143189 restraints weight = 17176.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143544 restraints weight = 13385.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143901 restraints weight = 9953.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143950 restraints weight = 9100.080| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17948 Z= 0.160 Angle : 0.594 13.971 24239 Z= 0.309 Chirality : 0.040 0.158 2643 Planarity : 0.003 0.041 2948 Dihedral : 3.906 26.401 2279 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.53 % Allowed : 19.63 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.20), residues: 2055 helix: 1.61 (0.15), residues: 1356 sheet: -0.19 (0.46), residues: 136 loop : -2.56 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.027 0.001 TYR G 343 PHE 0.046 0.002 PHE A 370 TRP 0.052 0.002 TRP C 145 HIS 0.011 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00376 (17934) covalent geometry : angle 0.59374 (24211) SS BOND : bond 0.00384 ( 14) SS BOND : angle 0.66905 ( 28) hydrogen bonds : bond 0.04152 ( 1021) hydrogen bonds : angle 3.72535 ( 3024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 THR cc_start: 0.8184 (p) cc_final: 0.7964 (p) REVERT: B 139 MET cc_start: 0.7051 (mmp) cc_final: 0.6790 (mmp) REVERT: D 279 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5603 (t80) REVERT: E 347 ARG cc_start: 0.5869 (mmm160) cc_final: 0.5630 (tpp-160) outliers start: 49 outliers final: 43 residues processed: 307 average time/residue: 0.1218 time to fit residues: 56.4527 Evaluate side-chains 316 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 56 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.176582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139755 restraints weight = 28576.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137384 restraints weight = 28703.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138839 restraints weight = 27428.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139129 restraints weight = 17491.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139501 restraints weight = 16631.278| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17948 Z= 0.134 Angle : 0.564 13.862 24239 Z= 0.294 Chirality : 0.039 0.158 2643 Planarity : 0.003 0.050 2948 Dihedral : 3.903 26.283 2279 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.58 % Allowed : 19.68 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.20), residues: 2055 helix: 1.66 (0.15), residues: 1355 sheet: -0.23 (0.46), residues: 138 loop : -2.54 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 387 TYR 0.015 0.001 TYR A 330 PHE 0.046 0.001 PHE A 370 TRP 0.042 0.002 TRP C 145 HIS 0.013 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00307 (17934) covalent geometry : angle 0.56450 (24211) SS BOND : bond 0.00313 ( 14) SS BOND : angle 0.54831 ( 28) hydrogen bonds : bond 0.03863 ( 1021) hydrogen bonds : angle 3.67163 ( 3024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2588.64 seconds wall clock time: 45 minutes 51.76 seconds (2751.76 seconds total)