Starting phenix.real_space_refine on Mon Nov 18 15:38:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hat_34608/11_2024/8hat_34608.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hat_34608/11_2024/8hat_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hat_34608/11_2024/8hat_34608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hat_34608/11_2024/8hat_34608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hat_34608/11_2024/8hat_34608.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hat_34608/11_2024/8hat_34608.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 10.30, per 1000 atoms: 0.61 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: 4.14 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.85 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: 5.00 Time building geometry restraints manager: 4.80 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.870 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- 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= 0.603 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 : 39.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.075 0.003 TRP D 406 HIS 0.019 0.002 HIS E 233 PHE 0.053 0.003 PHE B 365 TYR 0.041 0.003 TYR F 241 ARG 0.011 0.001 ARG D 101 *********************** 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 : 1.919 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: 0.5223 (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: 0.4597 (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: 0.4895 (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: 0.3276 time to fit residues: 166.6845 Evaluate side-chains 312 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 184 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 chunk 56 optimal weight: 0.0770 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 92 ASN F 243 ASN F 244 GLN D 244 GLN A 68 ASN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 233 HIS C 244 GLN C 411 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17320 Z= 0.247 Angle : 0.913 12.063 23507 Z= 0.472 Chirality : 0.052 0.300 2661 Planarity : 0.008 0.139 3064 Dihedral : 11.143 79.671 2517 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 1.88 % Allowed : 16.09 % Favored : 82.03 % Rotamer: Outliers : 8.52 % Allowed : 30.44 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.15), residues: 2182 helix: -4.23 (0.25), residues: 152 sheet: -3.06 (0.24), residues: 353 loop : -3.33 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 406 HIS 0.010 0.002 HIS E 141 PHE 0.039 0.002 PHE A 135 TYR 0.032 0.002 TYR D 357 ARG 0.011 0.001 ARG D 101 *********************** 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 435 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 278 time to evaluate : 1.842 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 75 LYS cc_start: 0.4735 (OUTLIER) cc_final: 0.3046 (pttt) REVERT: F 77 LEU cc_start: 0.3902 (OUTLIER) cc_final: 0.3606 (mt) REVERT: F 142 LYS cc_start: 0.6984 (ptpp) cc_final: 0.5911 (tppt) REVERT: F 166 ASP cc_start: 0.6605 (t0) cc_final: 0.5911 (m-30) REVERT: F 241 TYR cc_start: -0.1641 (OUTLIER) cc_final: -0.2114 (m-10) REVERT: F 384 ASP cc_start: 0.7710 (m-30) cc_final: 0.7415 (m-30) REVERT: D 201 SER cc_start: 0.6802 (t) cc_final: 0.6580 (p) REVERT: D 211 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.5439 (p90) REVERT: D 331 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4678 (tp) REVERT: D 409 THR cc_start: 0.0939 (OUTLIER) cc_final: 0.0567 (p) REVERT: D 427 THR cc_start: 0.5336 (OUTLIER) cc_final: 0.4904 (p) REVERT: E 126 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6566 (pp) REVERT: E 245 LYS cc_start: 0.7151 (ttmm) cc_final: 0.5944 (pttm) REVERT: E 260 LEU cc_start: 0.4284 (OUTLIER) cc_final: 0.3704 (mp) REVERT: E 297 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4532 (m-80) REVERT: E 338 LYS cc_start: 0.5025 (OUTLIER) cc_final: 0.4623 (pttp) REVERT: A 59 GLN cc_start: 0.5498 (OUTLIER) cc_final: 0.5081 (mm-40) REVERT: A 69 TYR cc_start: 0.5284 (OUTLIER) cc_final: 0.4744 (p90) REVERT: A 80 ARG cc_start: 0.2778 (OUTLIER) cc_final: 0.0599 (mtt90) REVERT: A 142 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6116 (mmtm) REVERT: A 320 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.5936 (tptp) REVERT: A 353 TYR cc_start: 0.7973 (t80) cc_final: 0.7378 (t80) REVERT: B 265 ARG cc_start: 0.2592 (OUTLIER) cc_final: 0.1787 (ttp80) REVERT: B 397 GLU cc_start: 0.4585 (OUTLIER) cc_final: 0.3757 (pm20) REVERT: C 275 TRP cc_start: 0.1796 (OUTLIER) cc_final: 0.1140 (m-90) REVERT: C 297 PHE cc_start: 0.5033 (OUTLIER) cc_final: 0.4256 (m-80) outliers start: 157 outliers final: 59 residues processed: 401 average time/residue: 0.3043 time to fit residues: 182.8837 Evaluate side-chains 319 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 240 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 GLN 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 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 369 ILE 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 172 TYR 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 381 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 427 THR 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 80 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 100 ILE 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 197 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 397 GLU 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 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 355 LEU Chi-restraints excluded: chain C residue 437 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 196 optimal weight: 0.0270 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 HIS D 244 GLN ** E 226 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** C 183 GLN C 233 HIS C 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.2447 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= 0.225 Angle : 0.844 11.005 23507 Z= 0.435 Chirality : 0.051 0.322 2661 Planarity : 0.007 0.137 3064 Dihedral : 9.126 79.169 2430 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 1.42 % Allowed : 16.18 % Favored : 82.40 % Rotamer: Outliers : 8.41 % Allowed : 31.20 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.15), residues: 2182 helix: -3.99 (0.28), residues: 148 sheet: -2.90 (0.24), residues: 358 loop : -3.06 (0.13), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 53 HIS 0.011 0.002 HIS E 141 PHE 0.022 0.002 PHE F 170 TYR 0.030 0.002 TYR D 357 ARG 0.007 0.000 ARG B 101 *********************** 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 414 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 259 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 TYR cc_start: 0.3462 (OUTLIER) cc_final: 0.2771 (t80) REVERT: F 78 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.3945 (pp) REVERT: F 81 HIS cc_start: 0.1213 (OUTLIER) cc_final: -0.0025 (t-90) REVERT: F 142 LYS cc_start: 0.7070 (ptpp) cc_final: 0.5828 (tppt) REVERT: F 164 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7056 (t0) REVERT: F 166 ASP cc_start: 0.6565 (t0) cc_final: 0.5786 (m-30) REVERT: F 315 ASP cc_start: 0.7693 (p0) cc_final: 0.7404 (t70) REVERT: D 213 THR cc_start: 0.5236 (OUTLIER) cc_final: 0.4559 (t) REVERT: D 409 THR cc_start: 0.1207 (OUTLIER) cc_final: 0.0844 (p) REVERT: D 427 THR cc_start: 0.5296 (OUTLIER) cc_final: 0.4874 (p) REVERT: D 428 SER cc_start: 0.3899 (OUTLIER) cc_final: 0.3507 (m) REVERT: E 126 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6625 (pp) REVERT: E 245 LYS cc_start: 0.6926 (ttmm) cc_final: 0.6060 (pttm) REVERT: E 297 PHE cc_start: 0.5289 (OUTLIER) cc_final: 0.4638 (m-80) REVERT: A 59 GLN cc_start: 0.5924 (OUTLIER) cc_final: 0.5568 (mm-40) REVERT: A 66 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.5875 (tpp-160) REVERT: A 69 TYR cc_start: 0.5625 (OUTLIER) cc_final: 0.4885 (p90) REVERT: A 90 GLN cc_start: 0.5112 (OUTLIER) cc_final: 0.4889 (tt0) REVERT: A 142 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6066 (mmtm) REVERT: A 320 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.5620 (tptp) REVERT: A 324 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 328 LEU cc_start: 0.5255 (OUTLIER) cc_final: 0.5021 (tt) REVERT: A 353 TYR cc_start: 0.8108 (t80) cc_final: 0.7305 (t80) REVERT: B 301 PHE cc_start: 0.4157 (t80) cc_final: 0.3897 (t80) REVERT: B 397 GLU cc_start: 0.4564 (OUTLIER) cc_final: 0.3782 (pm20) REVERT: B 404 ILE cc_start: 0.3759 (OUTLIER) cc_final: 0.3539 (mt) REVERT: C 275 TRP cc_start: 0.2067 (OUTLIER) cc_final: 0.1184 (m-90) REVERT: C 297 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3996 (m-80) outliers start: 155 outliers final: 74 residues processed: 380 average time/residue: 0.3044 time to fit residues: 176.0570 Evaluate side-chains 322 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 226 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 349 THR 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 D residue 95 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 199 ILE 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 381 LEU Chi-restraints excluded: chain D residue 409 THR 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 126 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS 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 338 LYS 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 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 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 205 VAL 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 328 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 140 VAL 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 300 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 404 ILE 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 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 419 SER Chi-restraints excluded: chain C residue 437 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 0.0010 chunk 133 optimal weight: 0.2980 chunk 199 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 188 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 GLN D 425 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 233 HIS C 244 GLN C 335 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17320 Z= 0.189 Angle : 0.797 11.175 23507 Z= 0.408 Chirality : 0.050 0.322 2661 Planarity : 0.006 0.135 3064 Dihedral : 8.561 80.251 2409 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 1.15 % Allowed : 14.99 % Favored : 83.87 % Rotamer: Outliers : 7.49 % Allowed : 32.23 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.15), residues: 2182 helix: -3.76 (0.30), residues: 152 sheet: -2.86 (0.25), residues: 334 loop : -2.98 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 53 HIS 0.005 0.001 HIS D 141 PHE 0.025 0.002 PHE B 294 TYR 0.035 0.002 TYR D 357 ARG 0.010 0.000 ARG B 221 *********************** 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 387 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 249 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.3902 (pp) REVERT: F 85 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.3803 (mp) REVERT: F 142 LYS cc_start: 0.6913 (ptpp) cc_final: 0.5792 (tppt) REVERT: F 196 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5657 (t0) REVERT: D 213 THR cc_start: 0.5089 (OUTLIER) cc_final: 0.4455 (t) REVERT: D 427 THR cc_start: 0.5256 (OUTLIER) cc_final: 0.4826 (p) REVERT: D 428 SER cc_start: 0.3921 (OUTLIER) cc_final: 0.3574 (m) REVERT: E 126 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6579 (pp) REVERT: E 297 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: A 59 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5433 (mm-40) REVERT: A 66 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6194 (tpp-160) REVERT: A 69 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.4894 (p90) REVERT: A 74 GLN cc_start: 0.4568 (OUTLIER) cc_final: 0.4199 (pp30) REVERT: A 142 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.5869 (mmtm) REVERT: A 320 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5741 (tptp) REVERT: A 328 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4879 (tt) REVERT: A 353 TYR cc_start: 0.7905 (t80) cc_final: 0.7253 (t80) REVERT: B 95 LEU cc_start: 0.7138 (pp) cc_final: 0.6646 (tt) REVERT: B 254 LEU cc_start: 0.5325 (pt) cc_final: 0.4143 (tp) REVERT: B 397 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.3822 (pm20) REVERT: B 404 ILE cc_start: 0.3680 (OUTLIER) cc_final: 0.3423 (mt) REVERT: C 245 LYS cc_start: 0.5938 (tptm) cc_final: 0.5294 (tppt) REVERT: C 275 TRP cc_start: 0.1988 (OUTLIER) cc_final: 0.1069 (m-90) REVERT: C 297 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.3964 (m-80) outliers start: 138 outliers final: 74 residues processed: 356 average time/residue: 0.2906 time to fit residues: 155.5373 Evaluate side-chains 323 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 230 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 172 TYR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS 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 336 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 368 ASP 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 98 MET Chi-restraints excluded: chain A residue 103 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 205 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 THR 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 328 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 213 THR 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 397 GLU Chi-restraints excluded: chain B residue 404 ILE 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 119 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 258 VAL 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 368 ASP Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 394 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 179 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 189 optimal weight: 0.0670 chunk 53 optimal weight: 7.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 244 GLN E 226 GLN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17320 Z= 0.216 Angle : 0.795 11.311 23507 Z= 0.406 Chirality : 0.050 0.287 2661 Planarity : 0.007 0.135 3064 Dihedral : 8.384 83.279 2406 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 1.01 % Allowed : 15.77 % Favored : 83.23 % Rotamer: Outliers : 8.57 % Allowed : 31.31 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 5.10 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.16), residues: 2182 helix: -3.62 (0.31), residues: 153 sheet: -2.68 (0.26), residues: 333 loop : -2.87 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 53 HIS 0.015 0.001 HIS D 233 PHE 0.023 0.002 PHE F 170 TYR 0.031 0.002 TYR D 357 ARG 0.009 0.000 ARG B 221 *********************** 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 401 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 243 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.3894 (pp) REVERT: F 81 HIS cc_start: 0.1240 (OUTLIER) cc_final: -0.0045 (t70) REVERT: F 85 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.3793 (mp) REVERT: F 142 LYS cc_start: 0.7085 (ptpp) cc_final: 0.5820 (tppt) REVERT: F 196 ASP cc_start: 0.6087 (OUTLIER) cc_final: 0.5776 (t70) REVERT: F 315 ASP cc_start: 0.7655 (p0) cc_final: 0.7379 (t70) REVERT: F 382 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7382 (tm-30) REVERT: F 445 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5874 (pt) REVERT: D 331 LEU cc_start: 0.4609 (OUTLIER) cc_final: 0.4273 (tp) REVERT: D 363 ILE cc_start: 0.3185 (OUTLIER) cc_final: 0.2894 (tt) REVERT: D 427 THR cc_start: 0.5396 (OUTLIER) cc_final: 0.4960 (p) REVERT: E 126 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6641 (pp) REVERT: E 184 MET cc_start: 0.5374 (mtp) cc_final: 0.2282 (ptp) REVERT: E 245 LYS cc_start: 0.6381 (tttm) cc_final: 0.5421 (pttm) REVERT: E 297 PHE cc_start: 0.5291 (OUTLIER) cc_final: 0.4690 (m-80) REVERT: A 59 GLN cc_start: 0.6128 (OUTLIER) cc_final: 0.5879 (mm-40) REVERT: A 66 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6134 (tpp-160) REVERT: A 69 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.5119 (p90) REVERT: A 106 LYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5458 (pptt) REVERT: A 142 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.5930 (mmtm) REVERT: A 318 ASP cc_start: 0.6723 (t0) cc_final: 0.6367 (m-30) REVERT: A 320 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5395 (tptp) REVERT: A 324 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7324 (mp) REVERT: A 328 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.5042 (tt) REVERT: A 353 TYR cc_start: 0.7995 (t80) cc_final: 0.7295 (t80) REVERT: A 400 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5936 (mtp85) REVERT: B 95 LEU cc_start: 0.7117 (pp) cc_final: 0.6542 (tt) REVERT: B 220 ARG cc_start: 0.3635 (ptt-90) cc_final: 0.2245 (mtm-85) REVERT: B 254 LEU cc_start: 0.5361 (pt) cc_final: 0.4418 (tt) REVERT: B 375 ASN cc_start: 0.6539 (t0) cc_final: 0.6188 (t0) REVERT: B 397 GLU cc_start: 0.4504 (OUTLIER) cc_final: 0.3881 (pm20) REVERT: B 404 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3314 (mt) REVERT: B 416 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5292 (pttm) REVERT: B 444 ILE cc_start: 0.5582 (OUTLIER) cc_final: 0.5367 (mt) REVERT: C 151 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5297 (pp) REVERT: C 245 LYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5559 (tppt) REVERT: C 275 TRP cc_start: 0.2005 (OUTLIER) cc_final: 0.1167 (m-90) REVERT: C 297 PHE cc_start: 0.4788 (OUTLIER) cc_final: 0.3950 (m-80) outliers start: 158 outliers final: 83 residues processed: 368 average time/residue: 0.2964 time to fit residues: 163.1007 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 : 1.911 ------------------------------------------------------------------------------- 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 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 134 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 172 TYR 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 265 ARG 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 363 ILE 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 134 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS 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 338 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 427 THR 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 85 LEU Chi-restraints excluded: chain A residue 98 MET 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 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 205 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 235 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 328 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 VAL 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 349 THR Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 ILE 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 247 PHE Chi-restraints excluded: chain C residue 258 VAL 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 369 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 435 LEU 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 70 optimal weight: 0.8980 chunk 189 optimal weight: 0.0050 chunk 41 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 210 optimal weight: 0.0370 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN D 244 GLN D 375 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17320 Z= 0.185 Angle : 0.746 9.594 23507 Z= 0.381 Chirality : 0.048 0.235 2661 Planarity : 0.006 0.133 3064 Dihedral : 7.970 82.914 2401 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.92 % Allowed : 14.25 % Favored : 84.83 % Rotamer: Outliers : 7.54 % Allowed : 31.96 % Favored : 60.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.16), residues: 2182 helix: -3.30 (0.35), residues: 139 sheet: -2.50 (0.27), residues: 333 loop : -2.72 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 53 HIS 0.007 0.001 HIS D 233 PHE 0.021 0.002 PHE F 170 TYR 0.030 0.001 TYR D 357 ARG 0.012 0.000 ARG D 434 *********************** 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 374 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 235 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.3871 (pp) REVERT: F 85 LEU cc_start: 0.4379 (OUTLIER) cc_final: 0.3874 (mm) REVERT: F 196 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5691 (t70) REVERT: F 315 ASP cc_start: 0.7707 (p0) cc_final: 0.7464 (t70) REVERT: F 353 TYR cc_start: 0.8236 (t80) cc_final: 0.7939 (t80) REVERT: F 382 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 331 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.4250 (tp) REVERT: D 414 ARG cc_start: 0.5260 (mmt180) cc_final: 0.4599 (mmm160) REVERT: D 427 THR cc_start: 0.5437 (OUTLIER) cc_final: 0.5024 (p) REVERT: E 126 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6622 (pp) REVERT: E 184 MET cc_start: 0.5067 (mtp) cc_final: 0.2360 (ptp) REVERT: E 245 LYS cc_start: 0.6209 (tttm) cc_final: 0.5605 (pttm) REVERT: E 259 TYR cc_start: 0.5180 (t80) cc_final: 0.4870 (t80) REVERT: E 297 PHE cc_start: 0.5225 (OUTLIER) cc_final: 0.4693 (m-80) REVERT: A 66 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6085 (tpp-160) REVERT: A 69 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5053 (p90) REVERT: A 106 LYS cc_start: 0.6038 (OUTLIER) cc_final: 0.5746 (pptt) REVERT: A 142 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.5857 (mmtm) REVERT: A 225 LYS cc_start: 0.6817 (mtmt) cc_final: 0.6116 (pttt) REVERT: A 318 ASP cc_start: 0.6760 (t0) cc_final: 0.6196 (m-30) REVERT: A 320 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5507 (tptp) REVERT: A 324 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 353 TYR cc_start: 0.7613 (t80) cc_final: 0.7040 (t80) REVERT: A 400 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5871 (mtp85) REVERT: B 95 LEU cc_start: 0.7193 (pp) cc_final: 0.6613 (tt) REVERT: B 209 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.5725 (tm-30) REVERT: B 220 ARG cc_start: 0.3813 (ptt-90) cc_final: 0.2500 (mtm-85) REVERT: B 254 LEU cc_start: 0.5328 (pt) cc_final: 0.4586 (tt) REVERT: B 300 ASP cc_start: 0.4026 (OUTLIER) cc_final: 0.3536 (t0) REVERT: B 375 ASN cc_start: 0.6606 (t0) cc_final: 0.6286 (t0) REVERT: B 397 GLU cc_start: 0.4549 (OUTLIER) cc_final: 0.3962 (pm20) REVERT: B 432 LEU cc_start: 0.3664 (OUTLIER) cc_final: 0.3196 (mp) REVERT: B 444 ILE cc_start: 0.5386 (OUTLIER) cc_final: 0.5174 (mt) REVERT: C 151 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.4988 (pp) REVERT: C 156 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6455 (tm-30) REVERT: C 245 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5473 (tppt) REVERT: C 267 THR cc_start: 0.1405 (OUTLIER) cc_final: 0.0968 (p) REVERT: C 275 TRP cc_start: 0.1971 (OUTLIER) cc_final: 0.0806 (m-90) REVERT: C 297 PHE cc_start: 0.4817 (OUTLIER) cc_final: 0.3906 (m-80) outliers start: 139 outliers final: 76 residues processed: 342 average time/residue: 0.2879 time to fit residues: 147.5973 Evaluate side-chains 320 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 220 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 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 134 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 172 TYR 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 265 ARG 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 430 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 121 ILE 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 172 TYR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 381 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 126 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 249 PRO Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 427 THR 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 134 VAL 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 214 LEU Chi-restraints excluded: chain A residue 222 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 265 ARG Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 400 ARG 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 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 397 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 444 ILE 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 247 PHE Chi-restraints excluded: chain C residue 258 VAL 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 369 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 GLN 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 203 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 120 optimal weight: 0.0470 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS F 234 HIS D 244 GLN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17320 Z= 0.258 Angle : 0.809 11.799 23507 Z= 0.414 Chirality : 0.051 0.362 2661 Planarity : 0.007 0.136 3064 Dihedral : 7.791 67.933 2397 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.96 % Allowed : 15.44 % Favored : 83.59 % Rotamer: Outliers : 7.43 % Allowed : 32.39 % Favored : 60.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 3.06 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.16), residues: 2182 helix: -3.38 (0.32), residues: 148 sheet: -2.67 (0.26), residues: 340 loop : -2.69 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 53 HIS 0.007 0.001 HIS D 248 PHE 0.025 0.002 PHE F 170 TYR 0.030 0.002 TYR D 357 ARG 0.009 0.000 ARG A 109 *********************** 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 356 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 219 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 TYR cc_start: 0.3632 (OUTLIER) cc_final: 0.2672 (t80) REVERT: F 78 LEU cc_start: 0.4678 (OUTLIER) cc_final: 0.3922 (pp) REVERT: F 142 LYS cc_start: 0.7092 (ptpp) cc_final: 0.5937 (tppt) REVERT: F 196 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.5986 (t70) REVERT: F 315 ASP cc_start: 0.7689 (p0) cc_final: 0.7388 (t70) REVERT: F 353 TYR cc_start: 0.8367 (t80) cc_final: 0.8111 (t80) REVERT: F 382 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7257 (tm-30) REVERT: F 445 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5963 (pt) REVERT: D 390 ILE cc_start: 0.5299 (OUTLIER) cc_final: 0.4508 (pt) REVERT: D 427 THR cc_start: 0.5641 (OUTLIER) cc_final: 0.5234 (p) REVERT: E 126 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6610 (pp) REVERT: E 259 TYR cc_start: 0.5465 (t80) cc_final: 0.5168 (t80) REVERT: E 297 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.4721 (m-80) REVERT: A 66 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6073 (tpp-160) REVERT: A 69 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5018 (p90) REVERT: A 106 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5700 (pptt) REVERT: A 142 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6151 (mmtm) REVERT: A 318 ASP cc_start: 0.6742 (t0) cc_final: 0.6239 (m-30) REVERT: A 320 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5604 (tptp) REVERT: A 324 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 328 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4849 (tt) REVERT: A 353 TYR cc_start: 0.8105 (t80) cc_final: 0.7708 (t80) REVERT: A 400 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5914 (mtp85) REVERT: B 95 LEU cc_start: 0.7289 (pp) cc_final: 0.6704 (tt) REVERT: B 209 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.5729 (tm-30) REVERT: B 220 ARG cc_start: 0.3760 (ptt-90) cc_final: 0.2443 (mtm-85) REVERT: B 300 ASP cc_start: 0.4770 (OUTLIER) cc_final: 0.4335 (t0) REVERT: B 375 ASN cc_start: 0.6651 (t0) cc_final: 0.6334 (t0) REVERT: B 397 GLU cc_start: 0.4535 (OUTLIER) cc_final: 0.4000 (pm20) REVERT: B 432 LEU cc_start: 0.3630 (OUTLIER) cc_final: 0.3204 (mp) REVERT: B 444 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.5495 (mt) REVERT: C 151 LEU cc_start: 0.5430 (OUTLIER) cc_final: 0.4941 (pp) REVERT: C 245 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5588 (tppt) REVERT: C 275 TRP cc_start: 0.2132 (OUTLIER) cc_final: 0.1345 (m-90) REVERT: C 297 PHE cc_start: 0.4637 (OUTLIER) cc_final: 0.3786 (m-80) REVERT: C 439 LEU cc_start: 0.4351 (mt) cc_final: 0.4106 (mp) outliers start: 137 outliers final: 90 residues processed: 327 average time/residue: 0.2968 time to fit residues: 144.3946 Evaluate side-chains 327 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 212 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 170 PHE Chi-restraints excluded: chain F residue 172 TYR 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 265 ARG 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 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 121 ILE 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 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 244 GLN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 427 THR 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 106 LYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 134 VAL 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 205 VAL Chi-restraints excluded: chain A residue 214 LEU 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 328 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain B residue 113 LEU 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 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 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 ILE 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 229 PHE Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 247 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 TYR Chi-restraints excluded: chain C residue 267 THR 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 419 SER Chi-restraints excluded: chain C residue 435 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 129 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS D 183 GLN ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17320 Z= 0.280 Angle : 0.823 10.591 23507 Z= 0.418 Chirality : 0.051 0.332 2661 Planarity : 0.007 0.134 3064 Dihedral : 7.770 63.876 2393 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.82 % Allowed : 15.17 % Favored : 84.01 % Rotamer: Outliers : 7.33 % Allowed : 33.32 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.16), residues: 2182 helix: -3.55 (0.30), residues: 164 sheet: -2.64 (0.26), residues: 350 loop : -2.64 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 144 HIS 0.010 0.001 HIS B 248 PHE 0.025 0.002 PHE F 170 TYR 0.033 0.002 TYR D 357 ARG 0.010 0.001 ARG A 109 *********************** 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 355 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 220 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5553 (OUTLIER) cc_final: 0.3107 (mp-120) REVERT: F 69 TYR cc_start: 0.3641 (OUTLIER) cc_final: 0.2678 (t80) REVERT: F 78 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.3941 (pp) REVERT: F 142 LYS cc_start: 0.7171 (ptpp) cc_final: 0.5850 (tppt) REVERT: F 196 ASP cc_start: 0.6382 (OUTLIER) cc_final: 0.6026 (t70) REVERT: F 315 ASP cc_start: 0.7634 (p0) cc_final: 0.7398 (t70) REVERT: F 353 TYR cc_start: 0.8370 (t80) cc_final: 0.8127 (t80) REVERT: F 382 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7246 (tm-30) REVERT: F 445 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6065 (pt) REVERT: D 427 THR cc_start: 0.5468 (OUTLIER) cc_final: 0.5098 (p) REVERT: E 126 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6589 (pp) REVERT: E 133 LEU cc_start: 0.5292 (mt) cc_final: 0.4574 (pt) REVERT: E 297 PHE cc_start: 0.5229 (OUTLIER) cc_final: 0.4769 (m-80) REVERT: A 66 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.5962 (tpp-160) REVERT: A 69 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5055 (p90) REVERT: A 106 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5719 (pptt) REVERT: A 142 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6114 (mmtm) REVERT: A 318 ASP cc_start: 0.6823 (t0) cc_final: 0.6381 (m-30) REVERT: A 320 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.5365 (tptp) REVERT: A 324 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 328 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.4975 (tt) REVERT: A 353 TYR cc_start: 0.8173 (t80) cc_final: 0.7897 (t80) REVERT: A 400 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5907 (mtp85) REVERT: B 95 LEU cc_start: 0.7228 (pp) cc_final: 0.6617 (tt) REVERT: B 209 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.5748 (tm-30) REVERT: B 220 ARG cc_start: 0.3563 (ptt-90) cc_final: 0.2231 (mtm-85) REVERT: B 300 ASP cc_start: 0.4784 (OUTLIER) cc_final: 0.4367 (t0) REVERT: B 375 ASN cc_start: 0.6568 (t0) cc_final: 0.6275 (t0) REVERT: B 397 GLU cc_start: 0.4582 (OUTLIER) cc_final: 0.4041 (pm20) REVERT: B 432 LEU cc_start: 0.3774 (OUTLIER) cc_final: 0.3351 (mp) REVERT: B 444 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5589 (mt) REVERT: C 151 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.4861 (pp) REVERT: C 245 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5671 (tppt) REVERT: C 275 TRP cc_start: 0.2131 (OUTLIER) cc_final: 0.1409 (m-90) REVERT: C 297 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.3817 (m-80) REVERT: C 439 LEU cc_start: 0.4305 (mt) cc_final: 0.3995 (mp) outliers start: 135 outliers final: 91 residues processed: 325 average time/residue: 0.3000 time to fit residues: 145.9950 Evaluate side-chains 325 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 209 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain F residue 164 ASP 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 265 ARG 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 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 121 ILE 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 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain A residue 51 PHE 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 106 LYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 134 VAL 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 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 328 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 GLU 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 397 GLU Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 117 VAL 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 203 SER 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 258 VAL Chi-restraints excluded: chain C residue 267 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 244 GLN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 HIS A 183 GLN ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17320 Z= 0.196 Angle : 0.772 11.216 23507 Z= 0.389 Chirality : 0.049 0.309 2661 Planarity : 0.006 0.132 3064 Dihedral : 7.400 59.435 2391 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.82 % Allowed : 14.44 % Favored : 84.74 % Rotamer: Outliers : 6.29 % Allowed : 34.94 % Favored : 58.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.16), residues: 2182 helix: -3.44 (0.31), residues: 169 sheet: -2.52 (0.26), residues: 360 loop : -2.55 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 144 HIS 0.012 0.001 HIS B 248 PHE 0.021 0.002 PHE E 247 TYR 0.033 0.001 TYR D 357 ARG 0.007 0.000 ARG B 221 *********************** 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 337 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 221 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5029 (OUTLIER) cc_final: 0.2504 (mp10) REVERT: F 78 LEU cc_start: 0.4705 (OUTLIER) cc_final: 0.3982 (pp) REVERT: F 142 LYS cc_start: 0.7226 (ptpp) cc_final: 0.5909 (tppt) REVERT: F 164 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7182 (t0) REVERT: F 196 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5865 (t70) REVERT: F 225 LYS cc_start: 0.6398 (mptp) cc_final: 0.6022 (mmtm) REVERT: F 353 TYR cc_start: 0.8338 (t80) cc_final: 0.8023 (t80) REVERT: F 382 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7250 (tm-30) REVERT: F 445 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6149 (pt) REVERT: D 427 THR cc_start: 0.5525 (OUTLIER) cc_final: 0.5141 (p) REVERT: E 113 LEU cc_start: 0.3324 (pt) cc_final: 0.2801 (pt) REVERT: E 126 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6477 (pp) REVERT: E 133 LEU cc_start: 0.5151 (mt) cc_final: 0.4533 (pt) REVERT: E 297 PHE cc_start: 0.5170 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: A 66 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6057 (tpp-160) REVERT: A 69 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.5076 (p90) REVERT: A 74 GLN cc_start: 0.4318 (OUTLIER) cc_final: 0.3503 (pm20) REVERT: A 106 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5881 (pptt) REVERT: A 142 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.5708 (mmtm) REVERT: A 320 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5282 (tptp) REVERT: A 324 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7342 (mp) REVERT: A 353 TYR cc_start: 0.7956 (t80) cc_final: 0.7686 (t80) REVERT: A 400 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5892 (mtp85) REVERT: B 95 LEU cc_start: 0.7231 (pp) cc_final: 0.6629 (tt) REVERT: B 209 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.5714 (tm-30) REVERT: B 220 ARG cc_start: 0.3735 (ptt-90) cc_final: 0.2477 (mtm-85) REVERT: B 300 ASP cc_start: 0.4840 (OUTLIER) cc_final: 0.4460 (t0) REVERT: B 375 ASN cc_start: 0.6656 (t0) cc_final: 0.6383 (t0) REVERT: B 397 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.4030 (pm20) REVERT: B 432 LEU cc_start: 0.3038 (OUTLIER) cc_final: 0.2715 (mp) REVERT: B 444 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5684 (mt) REVERT: C 151 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4737 (pp) REVERT: C 245 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5641 (tptt) REVERT: C 267 THR cc_start: 0.0984 (OUTLIER) cc_final: 0.0445 (p) REVERT: C 275 TRP cc_start: 0.2230 (OUTLIER) cc_final: 0.1576 (t-100) REVERT: C 297 PHE cc_start: 0.4813 (OUTLIER) cc_final: 0.3806 (m-80) outliers start: 116 outliers final: 80 residues processed: 313 average time/residue: 0.2875 time to fit residues: 136.2245 Evaluate side-chains 321 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 215 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 164 ASP 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 265 ARG 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 430 VAL Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 121 ILE 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 199 ILE Chi-restraints excluded: chain D residue 201 SER 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 331 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 249 PRO Chi-restraints excluded: chain E residue 254 LEU 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 371 VAL Chi-restraints excluded: chain E residue 427 THR 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 98 MET 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 134 VAL 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 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 400 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 GLN 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 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 444 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 117 VAL 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 247 PHE Chi-restraints excluded: chain C residue 258 VAL 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 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 437 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.0082 ------------------------------------------------------------------------------- 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 244 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** B 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17320 Z= 0.195 Angle : 0.766 10.142 23507 Z= 0.388 Chirality : 0.049 0.294 2661 Planarity : 0.006 0.133 3064 Dihedral : 7.223 61.446 2387 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.78 % Allowed : 14.80 % Favored : 84.42 % Rotamer: Outliers : 5.91 % Allowed : 35.05 % Favored : 59.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.16), residues: 2182 helix: -3.42 (0.31), residues: 165 sheet: -2.49 (0.27), residues: 358 loop : -2.51 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 144 HIS 0.012 0.001 HIS B 248 PHE 0.023 0.002 PHE E 247 TYR 0.032 0.001 TYR D 357 ARG 0.007 0.000 ARG B 221 ********************** 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 324 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 215 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 GLN cc_start: 0.5020 (OUTLIER) cc_final: 0.2584 (mp10) REVERT: F 78 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4031 (pp) REVERT: F 142 LYS cc_start: 0.7245 (ptpp) cc_final: 0.5986 (tppt) REVERT: F 164 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7097 (t0) REVERT: F 196 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5903 (t70) REVERT: F 353 TYR cc_start: 0.8308 (t80) cc_final: 0.8101 (t80) REVERT: F 382 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7253 (tm-30) REVERT: F 445 ILE cc_start: 0.6250 (OUTLIER) cc_final: 0.5928 (pt) REVERT: D 427 THR cc_start: 0.5507 (OUTLIER) cc_final: 0.5105 (p) REVERT: E 113 LEU cc_start: 0.3460 (pt) cc_final: 0.2986 (pt) REVERT: E 126 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6424 (pp) REVERT: E 133 LEU cc_start: 0.5129 (mt) cc_final: 0.4510 (pt) REVERT: E 297 PHE cc_start: 0.5183 (OUTLIER) cc_final: 0.4833 (m-80) REVERT: A 66 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6003 (tpp-160) REVERT: A 69 TYR cc_start: 0.5914 (OUTLIER) cc_final: 0.5065 (p90) REVERT: A 106 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.6086 (pptt) REVERT: A 142 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.5591 (mmtm) REVERT: A 320 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5290 (tptp) REVERT: A 324 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7301 (mp) REVERT: A 328 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4660 (tt) REVERT: A 353 TYR cc_start: 0.7989 (t80) cc_final: 0.7724 (t80) REVERT: A 400 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5723 (mtp85) REVERT: A 404 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8113 (pt) REVERT: B 95 LEU cc_start: 0.7157 (pp) cc_final: 0.6547 (tt) REVERT: B 209 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.5692 (tm-30) REVERT: B 220 ARG cc_start: 0.4011 (ptt-90) cc_final: 0.2738 (mtm-85) REVERT: B 254 LEU cc_start: 0.5733 (pt) cc_final: 0.4909 (tt) REVERT: B 300 ASP cc_start: 0.4846 (OUTLIER) cc_final: 0.4453 (t0) REVERT: B 319 VAL cc_start: 0.2128 (OUTLIER) cc_final: 0.1890 (p) REVERT: B 375 ASN cc_start: 0.6582 (t0) cc_final: 0.6345 (t0) REVERT: B 397 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.4061 (pm20) REVERT: B 432 LEU cc_start: 0.3041 (OUTLIER) cc_final: 0.2735 (mp) REVERT: B 444 ILE cc_start: 0.5795 (OUTLIER) cc_final: 0.5575 (mt) REVERT: C 151 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.4822 (pp) REVERT: C 156 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6305 (tm-30) REVERT: C 214 LEU cc_start: 0.5657 (tp) cc_final: 0.5369 (tp) REVERT: C 267 THR cc_start: 0.1040 (OUTLIER) cc_final: 0.0477 (p) REVERT: C 275 TRP cc_start: 0.2193 (OUTLIER) cc_final: 0.1561 (t-100) REVERT: C 297 PHE cc_start: 0.4790 (OUTLIER) cc_final: 0.3749 (m-80) outliers start: 109 outliers final: 78 residues processed: 301 average time/residue: 0.2913 time to fit residues: 133.0856 Evaluate side-chains 307 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 202 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 164 ASP 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 265 ARG 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 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 121 ILE 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 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 254 LEU 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 371 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 427 THR 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 106 LYS Chi-restraints excluded: chain A residue 134 VAL 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 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 328 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 GLN 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 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 444 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 117 VAL 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 247 PHE Chi-restraints excluded: chain C residue 258 VAL 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 369 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 419 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 25 optimal weight: 0.0060 chunk 48 optimal weight: 0.1980 chunk 173 optimal weight: 0.9990 chunk 72 optimal weight: 0.0050 chunk 177 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN F 89 GLN F 208 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 HIS ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.270140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.215405 restraints weight = 22815.380| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.21 r_work: 0.4219 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.4786 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= 0.173 Angle : 0.739 10.289 23507 Z= 0.372 Chirality : 0.048 0.286 2661 Planarity : 0.006 0.133 3064 Dihedral : 7.046 66.544 2387 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.64 % Allowed : 13.79 % Favored : 85.56 % Rotamer: Outliers : 5.53 % Allowed : 35.59 % Favored : 58.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.16), residues: 2182 helix: -3.30 (0.32), residues: 165 sheet: -2.34 (0.28), residues: 331 loop : -2.44 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 144 HIS 0.011 0.001 HIS B 248 PHE 0.024 0.001 PHE E 247 TYR 0.032 0.001 TYR D 357 ARG 0.009 0.000 ARG B 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.54 seconds wall clock time: 76 minutes 52.64 seconds (4612.64 seconds total)