Starting phenix.real_space_refine on Sun Aug 24 03:55:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hat_34608/08_2025/8hat_34608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hat_34608/08_2025/8hat_34608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hat_34608/08_2025/8hat_34608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hat_34608/08_2025/8hat_34608.map" model { file = "/net/cci-nas-00/data/ceres_data/8hat_34608/08_2025/8hat_34608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hat_34608/08_2025/8hat_34608.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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 68 5.16 5 C 10754 2.51 5 N 2947 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 16967 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3051 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2714 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 15, 'TRANS': 337} Chain breaks: 1 Chain: "E" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2714 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 15, 'TRANS': 337} Chain breaks: 1 Chain: "A" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3072 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 379} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2714 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 15, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 2702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2702 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain breaks: 1 Time building chain proxies: 4.20, per 1000 atoms: 0.25 Number of scatterers: 16967 At special positions: 0 Unit cell: (135.299, 151.406, 111.675, 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 68 16.00 O 3198 8.00 N 2947 7.00 C 10754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 989.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 35 sheets defined 11.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'F' and resid 53 through 57 removed outlier: 3.850A pdb=" N SER F 56 " --> pdb=" O TRP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 111 removed outlier: 3.780A pdb=" N PHE F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 236 removed outlier: 4.126A pdb=" N VAL F 235 " --> pdb=" O ASN F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 331 removed outlier: 3.701A pdb=" N LEU F 331 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 435 Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.976A pdb=" N THR D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 193 removed outlier: 4.162A pdb=" N ASP D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.779A pdb=" N VAL D 235 " --> pdb=" O ASN D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 removed outlier: 4.275A pdb=" N TRP D 275 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 276' Processing helix chain 'D' and resid 328 through 333 removed outlier: 3.609A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 333' Processing helix chain 'D' and resid 373 through 377 removed outlier: 3.521A pdb=" N GLN D 377 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 438 removed outlier: 3.936A pdb=" N ARG D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 removed outlier: 3.545A pdb=" N ASP D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 109 removed outlier: 3.546A pdb=" N LEU E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA E 102 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE E 107 " --> pdb=" O PHE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.969A pdb=" N ASP E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 327 through 331 removed outlier: 3.620A pdb=" N SER E 330 " --> pdb=" O PRO E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 439 Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.761A pdb=" N THR A 305 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.800A pdb=" N LEU A 331 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.734A pdb=" N LEU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 454' Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.480A pdb=" N THR B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 removed outlier: 3.590A pdb=" N ASP B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.913A pdb=" N ALA B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 409 through 412 removed outlier: 3.738A pdb=" N ARG B 412 " --> pdb=" O THR B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 412' Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.516A pdb=" N LEU C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 186 through 191 removed outlier: 4.130A pdb=" N ASP C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 432 through 439 removed outlier: 4.098A pdb=" N ASP C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 115 through 122 removed outlier: 3.575A pdb=" N ALA F 131 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE F 129 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG F 122 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR F 127 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP F 166 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 204 through 206 removed outlier: 3.650A pdb=" N VAL F 205 " --> pdb=" O GLY F 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'F' and resid 247 through 249 Processing sheet with id=AA5, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.758A pdb=" N SER F 268 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 290 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE F 287 " --> pdb=" O PHE F 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 401 through 404 removed outlier: 6.929A pdb=" N ILE F 389 " --> pdb=" O ILE F 402 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 388 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 339 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR F 346 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU F 370 " --> pdb=" O MET F 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.836A pdb=" N LEU D 155 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP D 166 " --> pdb=" O PRO D 130 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE D 132 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 119 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N MET D 351 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR D 349 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 370 " --> pdb=" O MET D 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.836A pdb=" N LEU D 155 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP D 166 " --> pdb=" O PRO D 130 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE D 132 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 119 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N MET D 351 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY D 348 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D 336 " --> pdb=" O GLY D 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AB1, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AB2, first strand: chain 'D' and resid 247 through 248 Processing sheet with id=AB3, first strand: chain 'D' and resid 404 through 405 Processing sheet with id=AB4, first strand: chain 'D' and resid 414 through 415 Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 122 removed outlier: 4.292A pdb=" N ARG E 120 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 122 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 216 through 218 removed outlier: 3.906A pdb=" N ALA E 216 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 230 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 218 " --> pdb=" O GLY E 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 245 through 246 Processing sheet with id=AB9, first strand: chain 'E' and resid 348 through 352 removed outlier: 6.948A pdb=" N LEU E 370 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY E 373 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN E 425 " --> pdb=" O GLY E 373 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 348 through 352 removed outlier: 6.948A pdb=" N LEU E 370 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY E 373 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN E 425 " --> pdb=" O GLY E 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 89 through 90 removed outlier: 7.167A pdb=" N GLN A 89 " --> pdb=" O TRP A 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.705A pdb=" N LYS A 219 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 245 through 249 removed outlier: 6.856A pdb=" N MET A 246 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 260 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 267 through 271 removed outlier: 4.154A pdb=" N SER A 268 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 366 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 289 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 371 through 373 removed outlier: 4.095A pdb=" N VAL A 339 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 388 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 389 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 154 through 155 removed outlier: 7.247A pdb=" N ASP B 166 " --> pdb=" O PRO B 130 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE B 132 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 116 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 119 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N MET B 351 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 370 " --> pdb=" O MET B 351 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 154 through 155 removed outlier: 7.247A pdb=" N ASP B 166 " --> pdb=" O PRO B 130 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE B 132 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 116 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 119 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N MET B 351 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD1, first strand: chain 'B' and resid 217 through 219 removed outlier: 3.668A pdb=" N PHE B 229 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 295 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 231 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AD3, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AD4, first strand: chain 'C' and resid 134 through 136 removed outlier: 5.753A pdb=" N VAL C 134 " --> pdb=" O VAL C 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 246 through 247 removed outlier: 7.034A pdb=" N MET C 246 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 335 through 339 removed outlier: 6.746A pdb=" N LEU C 370 " --> pdb=" O MET C 351 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 388 through 391 removed outlier: 6.306A pdb=" N ILE C 389 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 400 " --> pdb=" O LEU C 391 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 414 through 415 removed outlier: 3.676A pdb=" N GLU C 424 " --> pdb=" O LEU C 415 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 534 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: 1.81 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 2375 1.25 - 1.39: 4551 1.39 - 1.53: 9142 1.53 - 1.67: 1160 1.67 - 1.82: 92 Bond restraints: 17320 Sorted by residual: bond pdb=" C LEU A 52 " pdb=" O LEU A 52 " ideal model delta sigma weight residual 1.235 1.103 0.132 1.21e-02 6.83e+03 1.20e+02 bond pdb=" CG PRO B 152 " pdb=" CD PRO B 152 " ideal model delta sigma weight residual 1.503 1.163 0.340 3.40e-02 8.65e+02 9.99e+01 bond pdb=" CA THR A 55 " pdb=" CB THR A 55 " ideal model delta sigma weight residual 1.524 1.643 -0.118 1.27e-02 6.20e+03 8.70e+01 bond pdb=" CA ARG A 101 " pdb=" C ARG A 101 " ideal model delta sigma weight residual 1.523 1.401 0.123 1.34e-02 5.57e+03 8.36e+01 bond pdb=" CA ASN F 57 " pdb=" C ASN F 57 " ideal model delta sigma weight residual 1.531 1.432 0.099 1.12e-02 7.97e+03 7.83e+01 ... (remaining 17315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.90: 23271 5.90 - 11.79: 195 11.79 - 17.69: 30 17.69 - 23.58: 9 23.58 - 29.48: 2 Bond angle restraints: 23507 Sorted by residual: angle pdb=" C PRO E 251 " pdb=" N PRO E 252 " pdb=" CA PRO E 252 " ideal model delta sigma weight residual 119.84 93.24 26.60 1.25e+00 6.40e-01 4.53e+02 angle pdb=" N ALA A 102 " pdb=" CA ALA A 102 " pdb=" C ALA A 102 " ideal model delta sigma weight residual 111.28 89.32 21.96 1.09e+00 8.42e-01 4.06e+02 angle pdb=" N GLU F 64 " pdb=" CA GLU F 64 " pdb=" C GLU F 64 " ideal model delta sigma weight residual 114.56 92.39 22.17 1.27e+00 6.20e-01 3.05e+02 angle pdb=" C ILE B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta sigma weight residual 119.78 103.49 16.29 1.03e+00 9.43e-01 2.50e+02 angle pdb=" N PRO B 152 " pdb=" CD PRO B 152 " pdb=" CG PRO B 152 " ideal model delta sigma weight residual 103.20 81.81 21.39 1.50e+00 4.44e-01 2.03e+02 ... (remaining 23502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8337 17.97 - 35.93: 1368 35.93 - 53.90: 379 53.90 - 71.87: 78 71.87 - 89.83: 27 Dihedral angle restraints: 10189 sinusoidal: 4014 harmonic: 6175 Sorted by residual: dihedral pdb=" C GLN F 59 " pdb=" N GLN F 59 " pdb=" CA GLN F 59 " pdb=" CB GLN F 59 " ideal model delta harmonic sigma weight residual -122.60 -149.56 26.96 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" CA HIS E 248 " pdb=" C HIS E 248 " pdb=" N PRO E 249 " pdb=" CA PRO E 249 " ideal model delta harmonic sigma weight residual -180.00 -130.71 -49.29 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" C ASN F 92 " pdb=" N ASN F 92 " pdb=" CA ASN F 92 " pdb=" CB ASN F 92 " ideal model delta harmonic sigma weight residual -122.60 -146.69 24.09 0 2.50e+00 1.60e-01 9.29e+01 ... (remaining 10186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 2607 0.219 - 0.437: 39 0.437 - 0.656: 8 0.656 - 0.875: 3 0.875 - 1.094: 4 Chirality restraints: 2661 Sorted by residual: chirality pdb=" CA TYR A 50 " pdb=" N TYR A 50 " pdb=" C TYR A 50 " pdb=" CB TYR A 50 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" CA GLN F 59 " pdb=" N GLN F 59 " pdb=" C GLN F 59 " pdb=" CB GLN F 59 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA ASN F 92 " pdb=" N ASN F 92 " pdb=" C ASN F 92 " pdb=" CB ASN F 92 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 2658 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 52 " -0.036 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C LEU A 52 " 0.132 2.00e-02 2.50e+03 pdb=" O LEU A 52 " -0.054 2.00e-02 2.50e+03 pdb=" N TRP A 53 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 248 " -0.120 5.00e-02 4.00e+02 1.88e-01 5.64e+01 pdb=" N PRO B 249 " 0.325 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " -0.114 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 256 " -0.036 2.00e-02 2.50e+03 7.07e-02 5.00e+01 pdb=" C PRO E 256 " 0.122 2.00e-02 2.50e+03 pdb=" O PRO E 256 " -0.046 2.00e-02 2.50e+03 pdb=" N GLY E 257 " -0.040 2.00e-02 2.50e+03 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 14 1.92 - 2.66: 793 2.66 - 3.41: 23016 3.41 - 4.15: 39806 4.15 - 4.90: 68509 Nonbonded interactions: 132138 Sorted by model distance: nonbonded pdb=" CE2 PHE C 247 " pdb=" CD PRO C 252 " model vdw 1.173 3.740 nonbonded pdb=" OD1 ASN F 92 " pdb=" C CYS F 326 " model vdw 1.208 3.270 nonbonded pdb=" OD1 ASN F 92 " pdb=" O CYS F 326 " model vdw 1.439 3.040 nonbonded pdb=" O ALA F 236 " pdb=" CB ASN F 243 " model vdw 1.548 3.440 nonbonded pdb=" CA LYS D 245 " pdb=" OH TYR D 259 " model vdw 1.635 3.470 ... (remaining 132133 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 90 through 171 or resid 183 through 452)) selection = (chain 'B' and (resid 90 through 171 or resid 183 through 452)) selection = chain 'C' selection = (chain 'D' and (resid 90 through 171 or resid 183 through 452)) selection = (chain 'E' and (resid 90 through 171 or resid 183 through 452)) selection = (chain 'F' and (resid 90 through 171 or resid 183 through 452)) } 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 individual isotropic 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.880 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 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 : 0.009 0.340 17320 Z= 0.568 Angle : 1.513 29.476 23507 Z= 0.910 Chirality : 0.082 1.094 2661 Planarity : 0.010 0.188 3064 Dihedral : 19.558 89.834 6253 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 39.62 Ramachandran Plot: Outliers : 4.26 % Allowed : 16.54 % Favored : 79.19 % Rotamer: Outliers : 5.43 % Allowed : 34.18 % Favored : 60.39 % Cbeta Deviations : 1.07 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 3.06 % Twisted General : 0.14 % 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: -4.89 (0.15), residues: 2182 helix: -4.51 (0.22), residues: 156 sheet: -3.31 (0.25), residues: 301 loop : -3.42 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 101 TYR 0.041 0.003 TYR F 241 PHE 0.053 0.003 PHE B 365 TRP 0.075 0.003 TRP D 406 HIS 0.019 0.002 HIS E 233 Details of bonding type rmsd covalent geometry : bond 0.00896 (17320) covalent geometry : angle 1.51328 (23507) hydrogen bonds : bond 0.31775 ( 202) hydrogen bonds : angle 10.65083 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 265 time to evaluate : 0.764 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: F 59 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5224 (mp10) REVERT: F 64 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5783 (tp30) REVERT: F 78 LEU cc_start: 0.5372 (OUTLIER) cc_final: 0.4178 (pp) REVERT: F 81 HIS cc_start: 0.1396 (OUTLIER) cc_final: 0.0886 (p-80) REVERT: F 142 LYS cc_start: 0.6998 (ptpp) cc_final: 0.5940 (tppt) REVERT: F 208 HIS cc_start: 0.7229 (p90) cc_final: 0.6980 (p90) REVERT: F 241 TYR cc_start: -0.0795 (OUTLIER) cc_final: -0.1642 (m-80) REVERT: F 243 ASN cc_start: 0.3973 (OUTLIER) cc_final: 0.3715 (t0) REVERT: F 384 ASP cc_start: 0.7718 (m-30) cc_final: 0.7378 (m-30) REVERT: F 394 GLN cc_start: 0.7707 (tp40) cc_final: 0.7359 (tt0) REVERT: D 320 LYS cc_start: 0.5425 (tmtt) cc_final: 0.4595 (tptp) REVERT: A 59 GLN cc_start: 0.5103 (OUTLIER) cc_final: 0.4539 (mp10) REVERT: A 69 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4393 (p90) REVERT: A 80 ARG cc_start: 0.2195 (OUTLIER) cc_final: -0.0448 (mtt90) REVERT: A 84 ARG cc_start: 0.4259 (OUTLIER) cc_final: 0.3097 (ttt90) REVERT: A 125 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6926 (p0) REVERT: A 142 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6544 (mmtm) REVERT: B 151 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.4270 (pp) REVERT: C 214 LEU cc_start: 0.5134 (tp) cc_final: 0.4894 (tp) REVERT: C 297 PHE cc_start: 0.5419 (OUTLIER) cc_final: 0.4583 (m-80) outliers start: 100 outliers final: 54 residues processed: 350 average time/residue: 0.1527 time to fit residues: 78.1597 Evaluate side-chains 311 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 243 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 243 ASN Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 249 PRO Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 447 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN F 81 HIS F 90 GLN F 92 ASN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN F 425 ASN D 104 HIS D 244 GLN A 57 ASN A 60 HIS A 92 ASN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN C 149 GLN C 183 GLN C 233 HIS C 244 GLN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.250278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.184615 restraints weight = 22400.610| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.87 r_work: 0.3977 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.101 17320 Z= 0.465 Angle : 1.285 17.665 23507 Z= 0.668 Chirality : 0.067 0.319 2661 Planarity : 0.010 0.145 3064 Dihedral : 12.112 76.377 2517 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 2.15 % Allowed : 20.26 % Favored : 77.59 % Rotamer: Outliers : 13.51 % Allowed : 29.57 % Favored : 56.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 3.06 % Twisted General : 0.52 % 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: -5.06 (0.15), residues: 2182 helix: -4.46 (0.19), residues: 194 sheet: -3.30 (0.23), residues: 372 loop : -3.52 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 101 TYR 0.032 0.004 TYR A 353 PHE 0.048 0.005 PHE A 170 TRP 0.048 0.005 TRP A 53 HIS 0.014 0.003 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.01091 (17320) covalent geometry : angle 1.28460 (23507) hydrogen bonds : bond 0.07264 ( 202) hydrogen bonds : angle 8.70441 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 244 time to evaluate : 0.650 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: symmetry clash REVERT: F 69 TYR cc_start: 0.3740 (OUTLIER) cc_final: 0.2548 (t80) REVERT: F 98 MET cc_start: 0.7063 (ptm) cc_final: 0.6811 (ptm) REVERT: F 110 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6661 (ttp-170) REVERT: F 241 TYR cc_start: -0.0406 (OUTLIER) cc_final: -0.2512 (m-80) REVERT: F 315 ASP cc_start: 0.8080 (p0) cc_final: 0.7436 (t70) REVERT: F 331 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7068 (tp) REVERT: F 382 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7662 (tm-30) REVERT: F 438 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7519 (mmt-90) REVERT: F 445 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.6089 (pt) REVERT: D 369 ILE cc_start: 0.1500 (mp) cc_final: 0.1285 (mm) REVERT: D 415 LEU cc_start: 0.3932 (OUTLIER) cc_final: 0.3530 (tt) REVERT: D 427 THR cc_start: 0.6325 (OUTLIER) cc_final: 0.6051 (p) REVERT: D 428 SER cc_start: 0.4358 (OUTLIER) cc_final: 0.3882 (m) REVERT: E 113 LEU cc_start: 0.4230 (OUTLIER) cc_final: 0.3771 (pt) REVERT: E 119 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: E 192 LEU cc_start: 0.4818 (OUTLIER) cc_final: 0.4554 (mt) REVERT: E 233 HIS cc_start: 0.5786 (t-90) cc_final: 0.4922 (t-170) REVERT: E 245 LYS cc_start: 0.6577 (ttmm) cc_final: 0.5384 (pttm) REVERT: E 264 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: E 297 PHE cc_start: 0.5028 (OUTLIER) cc_final: 0.4301 (m-80) REVERT: E 374 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7741 (mt-10) REVERT: E 412 ARG cc_start: 0.4711 (mtt180) cc_final: 0.4059 (mmt180) REVERT: A 59 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5633 (mm-40) REVERT: A 69 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5037 (p90) REVERT: A 80 ARG cc_start: 0.1397 (OUTLIER) cc_final: -0.0447 (mtt90) REVERT: A 94 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7066 (tt) REVERT: A 142 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6404 (mmtm) REVERT: A 225 LYS cc_start: 0.7068 (mtmm) cc_final: 0.6459 (mtpp) REVERT: A 318 ASP cc_start: 0.6956 (p0) cc_final: 0.6716 (p0) REVERT: A 320 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.5443 (tptp) REVERT: A 324 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7546 (mp) REVERT: A 328 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.5136 (tt) REVERT: A 353 TYR cc_start: 0.8761 (t80) cc_final: 0.7934 (t80) REVERT: A 400 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6662 (mtt90) REVERT: A 442 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: A 448 GLU cc_start: 0.6640 (tp30) cc_final: 0.5773 (tp30) REVERT: B 211 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.6066 (p90) REVERT: B 397 GLU cc_start: 0.3747 (OUTLIER) cc_final: 0.3079 (pm20) REVERT: C 123 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6025 (tppt) REVERT: C 248 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6605 (t-90) REVERT: C 297 PHE cc_start: 0.5057 (OUTLIER) cc_final: 0.4334 (m-80) REVERT: C 374 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 415 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7497 (pt) REVERT: C 450 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6658 (mp) outliers start: 249 outliers final: 129 residues processed: 445 average time/residue: 0.1401 time to fit residues: 92.9076 Evaluate side-chains 364 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 205 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 364 CYS Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 249 PRO Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 205 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS E 421 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS C 183 GLN C 233 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.259720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.199483 restraints weight = 22729.738| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 3.99 r_work: 0.4082 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17320 Z= 0.185 Angle : 0.933 12.385 23507 Z= 0.481 Chirality : 0.053 0.323 2661 Planarity : 0.008 0.139 3064 Dihedral : 10.280 77.031 2455 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 1.47 % Allowed : 17.74 % Favored : 80.80 % Rotamer: Outliers : 9.22 % Allowed : 32.61 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.14 % 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: -4.73 (0.15), residues: 2182 helix: -4.20 (0.23), residues: 182 sheet: -3.04 (0.23), residues: 409 loop : -3.29 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 101 TYR 0.032 0.002 TYR D 357 PHE 0.030 0.002 PHE A 135 TRP 0.029 0.002 TRP A 53 HIS 0.010 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00416 (17320) covalent geometry : angle 0.93341 (23507) hydrogen bonds : bond 0.04879 ( 202) hydrogen bonds : angle 7.44963 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 251 time to evaluate : 0.506 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: symmetry clash REVERT: F 59 GLN cc_start: 0.5404 (OUTLIER) cc_final: 0.2149 (mp-120) REVERT: F 69 TYR cc_start: 0.3424 (OUTLIER) cc_final: 0.2278 (t80) REVERT: F 81 HIS cc_start: -0.0954 (OUTLIER) cc_final: -0.1952 (t-170) REVERT: F 89 GLN cc_start: 0.5785 (tm-30) cc_final: 0.5522 (tm-30) REVERT: F 110 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6669 (ttp-170) REVERT: F 145 LEU cc_start: 0.3943 (OUTLIER) cc_final: 0.3705 (mt) REVERT: F 156 GLU cc_start: 0.3993 (OUTLIER) cc_final: 0.3760 (mp0) REVERT: F 244 GLN cc_start: 0.7094 (pm20) cc_final: 0.6704 (pm20) REVERT: F 315 ASP cc_start: 0.7930 (p0) cc_final: 0.7384 (t70) REVERT: F 382 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 191 LYS cc_start: 0.5575 (mmtm) cc_final: 0.5217 (ttpt) REVERT: D 201 SER cc_start: 0.7110 (t) cc_final: 0.6740 (m) REVERT: D 214 LEU cc_start: 0.4113 (tt) cc_final: 0.3866 (tt) REVERT: D 331 LEU cc_start: 0.3742 (OUTLIER) cc_final: 0.3343 (tp) REVERT: D 369 ILE cc_start: 0.1229 (OUTLIER) cc_final: 0.1029 (mm) REVERT: D 381 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4122 (mp) REVERT: D 415 LEU cc_start: 0.3533 (OUTLIER) cc_final: 0.3238 (tt) REVERT: E 136 VAL cc_start: 0.6170 (OUTLIER) cc_final: 0.5964 (t) REVERT: E 211 PHE cc_start: 0.5234 (m-80) cc_final: 0.4951 (m-80) REVERT: E 245 LYS cc_start: 0.6249 (ttmm) cc_final: 0.5569 (pttm) REVERT: E 247 PHE cc_start: 0.5019 (OUTLIER) cc_final: 0.4708 (p90) REVERT: E 264 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: E 297 PHE cc_start: 0.4877 (OUTLIER) cc_final: 0.4093 (m-80) REVERT: E 374 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7603 (mt-10) REVERT: E 412 ARG cc_start: 0.4642 (mtt180) cc_final: 0.4159 (mmt180) REVERT: A 59 GLN cc_start: 0.6069 (OUTLIER) cc_final: 0.5336 (mm-40) REVERT: A 66 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.5889 (tpp-160) REVERT: A 69 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5081 (p90) REVERT: A 98 MET cc_start: 0.7341 (tpt) cc_final: 0.6991 (tpt) REVERT: A 132 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6333 (mt) REVERT: A 142 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.5947 (mmtm) REVERT: A 208 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6985 (t-90) REVERT: A 225 LYS cc_start: 0.6996 (mtmm) cc_final: 0.6333 (mtpp) REVERT: A 320 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.5730 (tptp) REVERT: A 353 TYR cc_start: 0.8580 (t80) cc_final: 0.7861 (t80) REVERT: A 432 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7923 (tp) REVERT: B 101 ARG cc_start: 0.6041 (ttt90) cc_final: 0.5768 (tpt-90) REVERT: B 211 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5909 (p90) REVERT: B 311 ARG cc_start: 0.5477 (mtm-85) cc_final: 0.5142 (mtt90) REVERT: B 397 GLU cc_start: 0.3835 (OUTLIER) cc_final: 0.3145 (pm20) REVERT: C 275 TRP cc_start: 0.3228 (OUTLIER) cc_final: 0.2450 (m-90) REVERT: C 297 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.4048 (m-80) REVERT: C 374 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7850 (mt-10) outliers start: 170 outliers final: 87 residues processed: 392 average time/residue: 0.1299 time to fit residues: 76.3809 Evaluate side-chains 337 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 224 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 447 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 214 optimal weight: 8.9990 chunk 204 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN C 149 GLN C 183 GLN C 233 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.265048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.229503 restraints weight = 22918.806| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 4.43 r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17320 Z= 0.142 Angle : 0.835 11.348 23507 Z= 0.430 Chirality : 0.051 0.317 2661 Planarity : 0.007 0.137 3064 Dihedral : 9.085 77.533 2428 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 1.19 % Allowed : 15.95 % Favored : 82.86 % Rotamer: Outliers : 8.30 % Allowed : 33.15 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.44 (0.15), residues: 2182 helix: -4.07 (0.26), residues: 166 sheet: -2.90 (0.24), residues: 387 loop : -3.08 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 109 TYR 0.033 0.002 TYR D 357 PHE 0.024 0.002 PHE A 103 TRP 0.025 0.002 TRP A 53 HIS 0.009 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00310 (17320) covalent geometry : angle 0.83491 (23507) hydrogen bonds : bond 0.04002 ( 202) hydrogen bonds : angle 6.84046 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 255 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 GLN cc_start: 0.4792 (OUTLIER) cc_final: 0.1767 (mp-120) REVERT: F 69 TYR cc_start: 0.4059 (OUTLIER) cc_final: 0.3027 (t80) REVERT: F 78 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.3533 (pp) REVERT: F 81 HIS cc_start: 0.0613 (OUTLIER) cc_final: -0.0761 (t-90) REVERT: F 94 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4505 (mp) REVERT: F 382 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6843 (tm-30) REVERT: D 201 SER cc_start: 0.6964 (t) cc_final: 0.6597 (m) REVERT: D 331 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.4609 (tp) REVERT: D 415 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4212 (tt) REVERT: E 119 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.6021 (m-10) REVERT: E 188 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6628 (mm) REVERT: E 297 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4543 (m-80) REVERT: A 59 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.4281 (mp10) REVERT: A 66 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6345 (tpp-160) REVERT: A 69 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.5939 (p90) REVERT: A 142 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6058 (mmtm) REVERT: A 208 HIS cc_start: 0.6121 (OUTLIER) cc_final: 0.5913 (t-90) REVERT: A 320 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5569 (tptp) REVERT: A 324 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 341 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7300 (ppt170) REVERT: A 353 TYR cc_start: 0.7649 (t80) cc_final: 0.7095 (t80) REVERT: B 95 LEU cc_start: 0.6404 (pp) cc_final: 0.5964 (tt) REVERT: B 211 PHE cc_start: 0.6042 (OUTLIER) cc_final: 0.5638 (p90) REVERT: B 220 ARG cc_start: 0.3939 (ptt-90) cc_final: 0.3578 (ptt-90) REVERT: B 311 ARG cc_start: 0.5427 (mtm-85) cc_final: 0.5184 (mtt90) REVERT: B 376 ARG cc_start: 0.5292 (mtp180) cc_final: 0.3769 (tpt170) REVERT: B 381 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.4625 (mp) REVERT: B 393 SER cc_start: 0.5955 (OUTLIER) cc_final: 0.5611 (t) REVERT: B 397 GLU cc_start: 0.4366 (OUTLIER) cc_final: 0.3510 (pm20) REVERT: C 151 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.4971 (pp) REVERT: C 275 TRP cc_start: 0.2087 (OUTLIER) cc_final: 0.1385 (m-90) REVERT: C 297 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4087 (m-80) outliers start: 153 outliers final: 71 residues processed: 377 average time/residue: 0.1217 time to fit residues: 68.5124 Evaluate side-chains 320 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 224 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 265 ARG Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 249 PRO Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 437 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 202 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 205 optimal weight: 0.0770 chunk 59 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS E 226 GLN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 141 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 244 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.262180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.207331 restraints weight = 22730.288| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 3.16 r_work: 0.4140 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17320 Z= 0.151 Angle : 0.825 11.551 23507 Z= 0.423 Chirality : 0.051 0.332 2661 Planarity : 0.007 0.137 3064 Dihedral : 8.546 77.832 2407 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 1.15 % Allowed : 16.68 % Favored : 82.17 % Rotamer: Outliers : 8.25 % Allowed : 33.32 % Favored : 58.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (0.16), residues: 2182 helix: -3.68 (0.32), residues: 145 sheet: -2.80 (0.24), residues: 369 loop : -2.95 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 109 TYR 0.030 0.002 TYR D 357 PHE 0.023 0.002 PHE A 103 TRP 0.029 0.002 TRP A 53 HIS 0.009 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00339 (17320) covalent geometry : angle 0.82473 (23507) hydrogen bonds : bond 0.04022 ( 202) hydrogen bonds : angle 6.72784 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 238 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5912 (OUTLIER) cc_final: 0.2324 (mp10) REVERT: F 69 TYR cc_start: 0.3667 (OUTLIER) cc_final: 0.2538 (t80) REVERT: F 78 LEU cc_start: 0.4443 (OUTLIER) cc_final: 0.3257 (pp) REVERT: F 94 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4065 (mt) REVERT: F 196 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.6057 (t0) REVERT: F 382 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7391 (tm-30) REVERT: F 445 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6477 (pt) REVERT: D 201 SER cc_start: 0.7213 (t) cc_final: 0.6924 (m) REVERT: D 415 LEU cc_start: 0.4146 (OUTLIER) cc_final: 0.3655 (tt) REVERT: E 188 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6659 (mm) REVERT: E 297 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4470 (m-80) REVERT: A 59 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.6120 (mm-40) REVERT: A 66 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6272 (tpp-160) REVERT: A 69 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5609 (p90) REVERT: A 106 LYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5904 (pptt) REVERT: A 142 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6064 (mmtm) REVERT: A 208 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.6468 (t-90) REVERT: A 320 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5836 (tptp) REVERT: A 324 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7632 (mp) REVERT: A 328 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4882 (tt) REVERT: A 353 TYR cc_start: 0.8207 (t80) cc_final: 0.7653 (t80) REVERT: A 404 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 95 LEU cc_start: 0.7441 (pp) cc_final: 0.7011 (tp) REVERT: B 211 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5860 (p90) REVERT: B 220 ARG cc_start: 0.3073 (ptt-90) cc_final: 0.2682 (ptt-90) REVERT: B 311 ARG cc_start: 0.5344 (mtm-85) cc_final: 0.4992 (mtt90) REVERT: B 376 ARG cc_start: 0.5472 (mtp180) cc_final: 0.3482 (tpt170) REVERT: B 381 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4757 (mp) REVERT: B 397 GLU cc_start: 0.4045 (OUTLIER) cc_final: 0.3316 (pm20) REVERT: B 432 LEU cc_start: 0.2694 (OUTLIER) cc_final: 0.2312 (mp) REVERT: C 151 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4643 (pp) REVERT: C 275 TRP cc_start: 0.2961 (OUTLIER) cc_final: 0.2165 (m-90) REVERT: C 297 PHE cc_start: 0.4806 (OUTLIER) cc_final: 0.3917 (m-80) outliers start: 152 outliers final: 90 residues processed: 357 average time/residue: 0.1336 time to fit residues: 71.0675 Evaluate side-chains 339 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 223 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 437 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 215 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 192 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS D 375 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN C 335 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.260621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.202749 restraints weight = 22711.249| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.25 r_work: 0.4072 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17320 Z= 0.169 Angle : 0.841 12.296 23507 Z= 0.430 Chirality : 0.052 0.314 2661 Planarity : 0.007 0.138 3064 Dihedral : 8.438 77.041 2400 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 1.05 % Allowed : 16.96 % Favored : 81.99 % Rotamer: Outliers : 8.63 % Allowed : 33.37 % Favored : 58.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 5.10 % Twisted General : 0.10 % 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: -4.08 (0.16), residues: 2182 helix: -3.69 (0.31), residues: 152 sheet: -2.67 (0.25), residues: 367 loop : -2.86 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 221 TYR 0.031 0.002 TYR D 357 PHE 0.023 0.002 PHE A 103 TRP 0.040 0.002 TRP A 53 HIS 0.006 0.001 HIS D 248 Details of bonding type rmsd covalent geometry : bond 0.00385 (17320) covalent geometry : angle 0.84078 (23507) hydrogen bonds : bond 0.04093 ( 202) hydrogen bonds : angle 6.76675 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 231 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.4812 (mp10) REVERT: F 69 TYR cc_start: 0.3811 (OUTLIER) cc_final: 0.2579 (t80) REVERT: F 78 LEU cc_start: 0.4367 (OUTLIER) cc_final: 0.3213 (pp) REVERT: F 94 LEU cc_start: 0.4612 (OUTLIER) cc_final: 0.4131 (mt) REVERT: F 196 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6001 (t0) REVERT: F 225 LYS cc_start: 0.6546 (mptp) cc_final: 0.5827 (mmtm) REVERT: F 382 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7499 (tm-30) REVERT: F 445 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6135 (pt) REVERT: D 201 SER cc_start: 0.7195 (t) cc_final: 0.6675 (m) REVERT: D 246 MET cc_start: 0.3746 (tpt) cc_final: 0.3508 (tpt) REVERT: D 311 ARG cc_start: 0.5209 (ptp90) cc_final: 0.4970 (ptt-90) REVERT: D 415 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3573 (tt) REVERT: D 427 THR cc_start: 0.6182 (OUTLIER) cc_final: 0.5924 (p) REVERT: E 188 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6613 (mm) REVERT: E 196 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5366 (m-30) REVERT: E 297 PHE cc_start: 0.5163 (OUTLIER) cc_final: 0.4480 (m-80) REVERT: A 59 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.5985 (mm-40) REVERT: A 66 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6226 (tpp-160) REVERT: A 69 TYR cc_start: 0.6342 (OUTLIER) cc_final: 0.5254 (p90) REVERT: A 106 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5892 (pptt) REVERT: A 142 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6220 (mmtm) REVERT: A 208 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.6629 (t-90) REVERT: A 221 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.4388 (mtp180) REVERT: A 320 LYS cc_start: 0.6375 (OUTLIER) cc_final: 0.5752 (tptp) REVERT: A 324 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 328 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4874 (tt) REVERT: A 341 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8035 (ppt170) REVERT: A 353 TYR cc_start: 0.8349 (t80) cc_final: 0.7893 (t80) REVERT: A 404 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 95 LEU cc_start: 0.7444 (pp) cc_final: 0.7005 (tp) REVERT: B 211 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5782 (p90) REVERT: B 376 ARG cc_start: 0.5338 (mtp180) cc_final: 0.3379 (tpt170) REVERT: B 381 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4764 (mp) REVERT: B 397 GLU cc_start: 0.3851 (OUTLIER) cc_final: 0.3277 (pm20) REVERT: C 151 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4579 (pp) REVERT: C 245 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5245 (tppt) REVERT: C 275 TRP cc_start: 0.2872 (OUTLIER) cc_final: 0.2082 (m-90) REVERT: C 297 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.3791 (m-80) REVERT: C 436 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6330 (pp) outliers start: 159 outliers final: 98 residues processed: 357 average time/residue: 0.1080 time to fit residues: 58.6088 Evaluate side-chains 345 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 216 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 249 PRO Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 437 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 437 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 215 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS F 234 HIS ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 HIS A 60 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.261683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.207737 restraints weight = 22663.674| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.11 r_work: 0.4095 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17320 Z= 0.154 Angle : 0.814 11.451 23507 Z= 0.416 Chirality : 0.052 0.258 2661 Planarity : 0.007 0.137 3064 Dihedral : 8.241 78.163 2400 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.87 % Allowed : 16.27 % Favored : 82.86 % Rotamer: Outliers : 8.19 % Allowed : 33.80 % Favored : 58.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.16), residues: 2182 helix: -3.64 (0.32), residues: 150 sheet: -2.62 (0.25), residues: 365 loop : -2.77 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 289 TYR 0.034 0.002 TYR D 357 PHE 0.046 0.002 PHE B 103 TRP 0.045 0.002 TRP A 53 HIS 0.008 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00353 (17320) covalent geometry : angle 0.81374 (23507) hydrogen bonds : bond 0.03894 ( 202) hydrogen bonds : angle 6.76277 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 218 time to evaluate : 0.492 Fit side-chains REVERT: F 59 GLN cc_start: 0.5542 (OUTLIER) cc_final: 0.4789 (mp10) REVERT: F 69 TYR cc_start: 0.3673 (OUTLIER) cc_final: 0.2443 (t80) REVERT: F 78 LEU cc_start: 0.4348 (OUTLIER) cc_final: 0.3218 (pp) REVERT: F 81 HIS cc_start: -0.0560 (OUTLIER) cc_final: -0.1502 (t70) REVERT: F 87 LYS cc_start: 0.4171 (OUTLIER) cc_final: 0.3920 (mmtt) REVERT: F 94 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.4024 (mp) REVERT: F 196 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.5949 (t0) REVERT: F 225 LYS cc_start: 0.6498 (mptp) cc_final: 0.5842 (mmtm) REVERT: F 382 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7495 (tm-30) REVERT: F 445 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6192 (pt) REVERT: D 201 SER cc_start: 0.7184 (t) cc_final: 0.6716 (m) REVERT: D 311 ARG cc_start: 0.5310 (ptp90) cc_final: 0.5001 (ptt-90) REVERT: D 415 LEU cc_start: 0.4065 (OUTLIER) cc_final: 0.3633 (tt) REVERT: E 184 MET cc_start: 0.3458 (mtt) cc_final: 0.2479 (mtt) REVERT: E 188 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6625 (mm) REVERT: E 196 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.5368 (m-30) REVERT: E 297 PHE cc_start: 0.5258 (OUTLIER) cc_final: 0.4601 (m-80) REVERT: A 59 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6013 (mm-40) REVERT: A 66 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6203 (tpp-160) REVERT: A 69 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.5392 (p90) REVERT: A 142 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6048 (mmtm) REVERT: A 144 TRP cc_start: 0.4858 (m-10) cc_final: 0.4591 (m100) REVERT: A 320 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5800 (tptp) REVERT: A 324 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7572 (mp) REVERT: A 328 LEU cc_start: 0.5099 (OUTLIER) cc_final: 0.4813 (tt) REVERT: A 353 TYR cc_start: 0.8276 (t80) cc_final: 0.7918 (t80) REVERT: A 404 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 95 LEU cc_start: 0.7402 (pp) cc_final: 0.6934 (tp) REVERT: B 211 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5699 (p90) REVERT: B 220 ARG cc_start: 0.3357 (ptt-90) cc_final: 0.3068 (ptt-90) REVERT: B 376 ARG cc_start: 0.5221 (mtp180) cc_final: 0.3336 (tpt170) REVERT: B 381 LEU cc_start: 0.5160 (OUTLIER) cc_final: 0.4720 (mp) REVERT: B 397 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3354 (pm20) REVERT: B 432 LEU cc_start: 0.2629 (OUTLIER) cc_final: 0.2282 (mp) REVERT: C 151 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4513 (pp) REVERT: C 245 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5274 (tppt) REVERT: C 275 TRP cc_start: 0.2880 (OUTLIER) cc_final: 0.1961 (m-90) REVERT: C 297 PHE cc_start: 0.4664 (OUTLIER) cc_final: 0.3704 (m-80) REVERT: C 338 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4732 (tptp) REVERT: C 436 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6359 (pp) outliers start: 151 outliers final: 97 residues processed: 335 average time/residue: 0.1136 time to fit residues: 57.9505 Evaluate side-chains 341 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 214 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 351 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 437 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 102 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 211 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 80 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 HIS A 208 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN C 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.264564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.209069 restraints weight = 22786.150| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.20 r_work: 0.4123 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17320 Z= 0.131 Angle : 0.785 11.123 23507 Z= 0.400 Chirality : 0.050 0.208 2661 Planarity : 0.007 0.136 3064 Dihedral : 7.943 76.210 2398 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.82 % Allowed : 15.17 % Favored : 84.01 % Rotamer: Outliers : 7.60 % Allowed : 33.75 % Favored : 58.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (0.16), residues: 2182 helix: -3.45 (0.34), residues: 142 sheet: -2.58 (0.25), residues: 371 loop : -2.67 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 289 TYR 0.035 0.001 TYR D 357 PHE 0.042 0.002 PHE B 103 TRP 0.042 0.002 TRP A 53 HIS 0.028 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00294 (17320) covalent geometry : angle 0.78478 (23507) hydrogen bonds : bond 0.03638 ( 202) hydrogen bonds : angle 6.51969 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 232 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5474 (OUTLIER) cc_final: 0.2159 (mp10) REVERT: F 78 LEU cc_start: 0.4195 (OUTLIER) cc_final: 0.3149 (pp) REVERT: F 81 HIS cc_start: -0.0595 (OUTLIER) cc_final: -0.1451 (t70) REVERT: F 89 GLN cc_start: 0.5886 (tm-30) cc_final: 0.5433 (tt0) REVERT: F 142 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6001 (tppt) REVERT: F 196 ASP cc_start: 0.6525 (OUTLIER) cc_final: 0.5936 (t70) REVERT: F 382 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7516 (tm-30) REVERT: F 445 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6289 (pt) REVERT: D 201 SER cc_start: 0.7192 (t) cc_final: 0.6756 (m) REVERT: D 311 ARG cc_start: 0.5192 (ptp90) cc_final: 0.4877 (ptt-90) REVERT: D 415 LEU cc_start: 0.3950 (OUTLIER) cc_final: 0.3518 (tt) REVERT: D 427 THR cc_start: 0.5676 (OUTLIER) cc_final: 0.5445 (p) REVERT: E 184 MET cc_start: 0.3449 (mtt) cc_final: 0.2532 (mtt) REVERT: E 188 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6863 (mm) REVERT: E 297 PHE cc_start: 0.5213 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: A 59 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.4568 (mp10) REVERT: A 66 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6143 (tpp-160) REVERT: A 69 TYR cc_start: 0.6271 (OUTLIER) cc_final: 0.5335 (p90) REVERT: A 74 GLN cc_start: 0.3937 (OUTLIER) cc_final: 0.3394 (pm20) REVERT: A 142 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.5951 (mmtm) REVERT: A 221 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.4340 (mtp180) REVERT: A 320 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5764 (tptp) REVERT: A 324 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7507 (mp) REVERT: A 328 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4776 (tt) REVERT: A 353 TYR cc_start: 0.8321 (t80) cc_final: 0.7927 (t80) REVERT: A 404 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7974 (mp) REVERT: B 95 LEU cc_start: 0.7391 (pp) cc_final: 0.6928 (tp) REVERT: B 209 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5486 (tm-30) REVERT: B 211 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.5576 (p90) REVERT: B 246 MET cc_start: 0.4235 (tpt) cc_final: 0.3980 (tpt) REVERT: B 376 ARG cc_start: 0.5224 (mtp180) cc_final: 0.3470 (tpt170) REVERT: B 381 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.3648 (mp) REVERT: B 397 GLU cc_start: 0.3764 (OUTLIER) cc_final: 0.3258 (pm20) REVERT: B 432 LEU cc_start: 0.2529 (OUTLIER) cc_final: 0.2244 (mp) REVERT: C 151 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.4647 (pp) REVERT: C 245 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.4861 (tppt) REVERT: C 275 TRP cc_start: 0.2835 (OUTLIER) cc_final: 0.1991 (m-90) REVERT: C 297 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.3641 (m-80) outliers start: 140 outliers final: 89 residues processed: 339 average time/residue: 0.1161 time to fit residues: 59.8137 Evaluate side-chains 338 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 220 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 437 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 437 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 145 optimal weight: 0.1980 chunk 133 optimal weight: 0.0770 chunk 36 optimal weight: 0.0010 chunk 13 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.6548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 GLN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 ASN A 60 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.266261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.211725 restraints weight = 22715.110| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.06 r_work: 0.4159 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17320 Z= 0.126 Angle : 0.763 12.203 23507 Z= 0.386 Chirality : 0.049 0.202 2661 Planarity : 0.007 0.137 3064 Dihedral : 7.563 77.431 2392 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.82 % Allowed : 14.57 % Favored : 84.60 % Rotamer: Outliers : 6.73 % Allowed : 34.24 % Favored : 59.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.16), residues: 2182 helix: -3.64 (0.31), residues: 159 sheet: -2.65 (0.26), residues: 358 loop : -2.60 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 221 TYR 0.035 0.001 TYR D 357 PHE 0.037 0.002 PHE D 269 TRP 0.046 0.002 TRP A 53 HIS 0.013 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00283 (17320) covalent geometry : angle 0.76255 (23507) hydrogen bonds : bond 0.03467 ( 202) hydrogen bonds : angle 6.26884 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 239 time to evaluate : 0.609 Fit side-chains REVERT: F 59 GLN cc_start: 0.5454 (OUTLIER) cc_final: 0.2146 (mp10) REVERT: F 78 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3245 (pp) REVERT: F 142 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6081 (tppt) REVERT: F 196 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.5807 (t70) REVERT: F 382 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7474 (tm-30) REVERT: F 445 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6248 (pt) REVERT: D 201 SER cc_start: 0.7226 (t) cc_final: 0.6809 (m) REVERT: D 311 ARG cc_start: 0.5049 (ptp90) cc_final: 0.4720 (ptt-90) REVERT: D 384 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: D 415 LEU cc_start: 0.3901 (OUTLIER) cc_final: 0.3370 (tt) REVERT: D 427 THR cc_start: 0.5573 (OUTLIER) cc_final: 0.5332 (p) REVERT: E 184 MET cc_start: 0.3573 (mtt) cc_final: 0.2714 (mtt) REVERT: E 297 PHE cc_start: 0.5122 (OUTLIER) cc_final: 0.4542 (m-80) REVERT: A 60 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5429 (t-170) REVERT: A 66 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6117 (tpp-160) REVERT: A 69 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.5352 (p90) REVERT: A 142 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.5880 (mmtm) REVERT: A 221 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.4293 (mtp180) REVERT: A 225 LYS cc_start: 0.6812 (mtmt) cc_final: 0.6129 (pttt) REVERT: A 320 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5756 (tptp) REVERT: A 324 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 328 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4627 (tt) REVERT: A 353 TYR cc_start: 0.8268 (t80) cc_final: 0.7948 (t80) REVERT: A 404 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7841 (mp) REVERT: B 92 ASN cc_start: 0.6366 (t0) cc_final: 0.5490 (p0) REVERT: B 95 LEU cc_start: 0.7326 (pp) cc_final: 0.6889 (tp) REVERT: B 209 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5426 (tm-30) REVERT: B 211 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.5353 (p90) REVERT: B 376 ARG cc_start: 0.5266 (mtp180) cc_final: 0.3576 (tpt170) REVERT: B 397 GLU cc_start: 0.3885 (OUTLIER) cc_final: 0.3400 (pm20) REVERT: C 133 LEU cc_start: 0.5018 (mt) cc_final: 0.4673 (mt) REVERT: C 151 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4742 (pp) REVERT: C 214 LEU cc_start: 0.5203 (tp) cc_final: 0.4923 (tp) REVERT: C 245 LYS cc_start: 0.5375 (OUTLIER) cc_final: 0.5007 (tppt) REVERT: C 259 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.4439 (t80) REVERT: C 297 PHE cc_start: 0.4603 (OUTLIER) cc_final: 0.3657 (m-80) REVERT: C 338 LYS cc_start: 0.5186 (OUTLIER) cc_final: 0.4514 (tptp) outliers start: 124 outliers final: 81 residues processed: 329 average time/residue: 0.1074 time to fit residues: 54.2160 Evaluate side-chains 328 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 221 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 82 optimal weight: 0.0980 chunk 164 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 116 optimal weight: 0.3980 chunk 208 optimal weight: 0.0570 chunk 88 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 89 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.264288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.208663 restraints weight = 22640.650| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.03 r_work: 0.4130 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17320 Z= 0.140 Angle : 0.785 11.913 23507 Z= 0.398 Chirality : 0.050 0.214 2661 Planarity : 0.007 0.137 3064 Dihedral : 7.559 83.163 2390 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.17 % Favored : 84.10 % Rotamer: Outliers : 6.67 % Allowed : 34.13 % Favored : 59.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.16), residues: 2182 helix: -3.67 (0.30), residues: 165 sheet: -2.54 (0.26), residues: 358 loop : -2.56 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.031 0.001 TYR D 357 PHE 0.036 0.002 PHE B 103 TRP 0.044 0.002 TRP A 53 HIS 0.023 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00317 (17320) covalent geometry : angle 0.78519 (23507) hydrogen bonds : bond 0.03627 ( 202) hydrogen bonds : angle 6.25648 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 222 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5540 (OUTLIER) cc_final: 0.4858 (mp10) REVERT: F 78 LEU cc_start: 0.4211 (OUTLIER) cc_final: 0.3201 (pp) REVERT: F 142 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6147 (tppt) REVERT: F 196 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5926 (t70) REVERT: F 382 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7459 (tm-30) REVERT: F 445 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6245 (pt) REVERT: D 201 SER cc_start: 0.7264 (t) cc_final: 0.6824 (m) REVERT: D 305 THR cc_start: 0.6717 (p) cc_final: 0.6022 (t) REVERT: D 311 ARG cc_start: 0.4976 (ptp90) cc_final: 0.4594 (ptt-90) REVERT: D 415 LEU cc_start: 0.3867 (OUTLIER) cc_final: 0.3368 (tt) REVERT: E 184 MET cc_start: 0.3711 (mtt) cc_final: 0.2869 (mtt) REVERT: E 297 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: A 60 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5721 (t-170) REVERT: A 66 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6099 (tpp-160) REVERT: A 69 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5183 (p90) REVERT: A 142 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.5872 (mmtm) REVERT: A 221 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.4348 (mtp180) REVERT: A 260 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6636 (mt) REVERT: A 320 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5712 (tptp) REVERT: A 324 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7521 (mp) REVERT: A 328 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4779 (tt) REVERT: A 353 TYR cc_start: 0.8317 (t80) cc_final: 0.7953 (t80) REVERT: A 404 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8104 (mp) REVERT: B 92 ASN cc_start: 0.6332 (t0) cc_final: 0.5468 (p0) REVERT: B 95 LEU cc_start: 0.7330 (pp) cc_final: 0.6902 (tp) REVERT: B 209 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5277 (tm-30) REVERT: B 211 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5475 (p90) REVERT: B 300 ASP cc_start: 0.4729 (OUTLIER) cc_final: 0.4478 (t0) REVERT: B 376 ARG cc_start: 0.5289 (mtp180) cc_final: 0.3632 (tpt170) REVERT: B 381 LEU cc_start: 0.4774 (mp) cc_final: 0.3439 (mp) REVERT: B 397 GLU cc_start: 0.3871 (OUTLIER) cc_final: 0.3382 (pm20) REVERT: C 151 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4764 (pp) REVERT: C 214 LEU cc_start: 0.5228 (tp) cc_final: 0.4946 (tp) REVERT: C 245 LYS cc_start: 0.5473 (OUTLIER) cc_final: 0.5151 (tppt) REVERT: C 259 TYR cc_start: 0.4633 (OUTLIER) cc_final: 0.4332 (t80) REVERT: C 297 PHE cc_start: 0.4602 (OUTLIER) cc_final: 0.3655 (m-80) REVERT: C 338 LYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4387 (tptp) outliers start: 123 outliers final: 84 residues processed: 316 average time/residue: 0.1119 time to fit residues: 53.9619 Evaluate side-chains 329 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 219 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 394 GLN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 209 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.264368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.209847 restraints weight = 22739.410| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.12 r_work: 0.4117 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.260 17320 Z= 0.315 Angle : 1.087 59.200 23507 Z= 0.623 Chirality : 0.054 0.714 2661 Planarity : 0.008 0.183 3064 Dihedral : 7.566 82.795 2390 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.31 % Favored : 83.96 % Rotamer: Outliers : 6.46 % Allowed : 34.02 % Favored : 59.52 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.16), residues: 2182 helix: -3.67 (0.30), residues: 165 sheet: -2.54 (0.26), residues: 358 loop : -2.56 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 221 TYR 0.029 0.001 TYR D 357 PHE 0.032 0.002 PHE B 103 TRP 0.041 0.002 TRP A 53 HIS 0.289 0.005 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00591 (17320) covalent geometry : angle 1.08651 (23507) hydrogen bonds : bond 0.03623 ( 202) hydrogen bonds : angle 6.25544 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4791.14 seconds wall clock time: 82 minutes 27.94 seconds (4947.94 seconds total)