Starting phenix.real_space_refine on Thu Jul 2 13:44:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cqi_30441/07_2026/7cqi_30441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cqi_30441/07_2026/7cqi_30441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cqi_30441/07_2026/7cqi_30441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cqi_30441/07_2026/7cqi_30441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cqi_30441/07_2026/7cqi_30441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cqi_30441/07_2026/7cqi_30441.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 51 5.16 5 C 5719 2.51 5 N 1486 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3926 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1028 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 182 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "T" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'GE0': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 1.48, per 1000 atoms: 0.17 Number of scatterers: 8881 At special positions: 0 Unit cell: (91.8, 85.32, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 4 15.00 O 1621 8.00 N 1486 7.00 C 5719 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 313.3 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 43.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'S' and resid 54 through 61 removed outlier: 3.518A pdb=" N GLU S 59 " --> pdb=" O LYS S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 77 through 81 removed outlier: 3.866A pdb=" N ASN S 81 " --> pdb=" O PRO S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 121 Processing helix chain 'S' and resid 144 through 156 removed outlier: 3.725A pdb=" N ARG S 151 " --> pdb=" O ASP S 147 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA S 153 " --> pdb=" O GLU S 149 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS S 154 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 173 removed outlier: 3.728A pdb=" N ALA S 172 " --> pdb=" O PHE S 168 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER S 173 " --> pdb=" O ALA S 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 168 through 173' Processing helix chain 'S' and resid 192 through 202 removed outlier: 3.554A pdb=" N ALA S 201 " --> pdb=" O LYS S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 230 removed outlier: 3.875A pdb=" N GLU S 223 " --> pdb=" O ARG S 219 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 257 through 262 removed outlier: 3.897A pdb=" N LYS S 262 " --> pdb=" O PRO S 258 " (cutoff:3.500A) Processing helix chain 'S' and resid 289 through 294 Processing helix chain 'S' and resid 296 through 300 removed outlier: 3.587A pdb=" N ASP S 299 " --> pdb=" O ASN S 296 " (cutoff:3.500A) Processing helix chain 'S' and resid 324 through 326 No H-bonds generated for 'chain 'S' and resid 324 through 326' Processing helix chain 'S' and resid 327 through 332 removed outlier: 3.594A pdb=" N SER S 331 " --> pdb=" O HIS S 327 " (cutoff:3.500A) Processing helix chain 'S' and resid 332 through 337 removed outlier: 3.557A pdb=" N CYS S 336 " --> pdb=" O GLY S 332 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE S 337 " --> pdb=" O GLN S 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 332 through 337' Processing helix chain 'S' and resid 347 through 359 removed outlier: 3.546A pdb=" N GLU S 351 " --> pdb=" O ALA S 347 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU S 357 " --> pdb=" O LEU S 353 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN S 359 " --> pdb=" O ILE S 355 " (cutoff:3.500A) Processing helix chain 'S' and resid 363 through 368 removed outlier: 3.594A pdb=" N LYS S 367 " --> pdb=" O PHE S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 376 removed outlier: 3.596A pdb=" N GLN S 372 " --> pdb=" O GLU S 368 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE S 373 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS S 374 " --> pdb=" O CYS S 370 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 375 " --> pdb=" O GLY S 371 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.559A pdb=" N LEU S 412 " --> pdb=" O ASP S 408 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU S 414 " --> pdb=" O ARG S 410 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET S 420 " --> pdb=" O VAL S 416 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN S 421 " --> pdb=" O ASP S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 453 through 469 removed outlier: 3.932A pdb=" N GLN S 469 " --> pdb=" O LYS S 465 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 91 removed outlier: 4.198A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU T 91 " --> pdb=" O LEU T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 134 removed outlier: 3.764A pdb=" N TRP T 134 " --> pdb=" O ARG T 131 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 181 removed outlier: 4.216A pdb=" N PHE T 181 " --> pdb=" O TYR T 178 " (cutoff:3.500A) Processing helix chain 'T' and resid 194 through 199 removed outlier: 4.343A pdb=" N GLU T 198 " --> pdb=" O LYS T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 228 removed outlier: 3.680A pdb=" N GLU T 218 " --> pdb=" O ASP T 214 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA T 224 " --> pdb=" O GLU T 220 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG T 225 " --> pdb=" O GLU T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 241 through 250 removed outlier: 3.529A pdb=" N ASN T 245 " --> pdb=" O THR T 241 " (cutoff:3.500A) Proline residue: T 247 - end of helix Processing helix chain 'T' and resid 263 through 272 Processing helix chain 'T' and resid 284 through 298 removed outlier: 4.056A pdb=" N ALA T 295 " --> pdb=" O LEU T 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE T 296 " --> pdb=" O LEU T 292 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL T 297 " --> pdb=" O LYS T 293 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR T 298 " --> pdb=" O ASP T 294 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 338 removed outlier: 3.595A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS T 336 " --> pdb=" O ALA T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 364 removed outlier: 3.655A pdb=" N PHE T 363 " --> pdb=" O VAL T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 391 through 402 removed outlier: 4.456A pdb=" N TYR T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER T 402 " --> pdb=" O LEU T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 402 through 408 removed outlier: 3.952A pdb=" N VAL T 406 " --> pdb=" O SER T 402 " (cutoff:3.500A) Processing helix chain 'T' and resid 412 through 424 removed outlier: 3.636A pdb=" N GLN T 418 " --> pdb=" O PRO T 414 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE T 420 " --> pdb=" O VAL T 416 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR T 421 " --> pdb=" O GLU T 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 437 through 455 removed outlier: 3.682A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 489 removed outlier: 3.573A pdb=" N GLY T 483 " --> pdb=" O ILE T 479 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET T 486 " --> pdb=" O PHE T 482 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 535 removed outlier: 3.544A pdb=" N GLU T 527 " --> pdb=" O THR T 523 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU T 530 " --> pdb=" O LYS T 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.642A pdb=" N TRP A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 66 removed outlier: 3.594A pdb=" N HIS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.830A pdb=" N TYR A 91 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 116 Proline residue: A 106 - end of helix removed outlier: 3.590A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 128 through 136 removed outlier: 4.099A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.722A pdb=" N PHE E 16 " --> pdb=" O GLN E 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR E 18 " --> pdb=" O SER E 14 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 21 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 22 " --> pdb=" O TYR E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 52 removed outlier: 3.523A pdb=" N ASN E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 4.100A pdb=" N ILE C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 85 through 86 removed outlier: 4.261A pdb=" N VAL S 94 " --> pdb=" O SER S 86 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA S 425 " --> pdb=" O GLU S 99 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE S 101 " --> pdb=" O ALA S 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 160 through 164 Processing sheet with id=AA3, first strand: chain 'S' and resid 206 through 208 removed outlier: 6.094A pdb=" N VAL S 185 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE S 184 " --> pdb=" O PHE S 241 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL S 243 " --> pdb=" O ILE S 184 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE S 186 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU S 245 " --> pdb=" O PHE S 186 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE S 272 " --> pdb=" O ARG S 240 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE S 242 " --> pdb=" O PHE S 272 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU S 274 " --> pdb=" O ILE S 242 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL S 244 " --> pdb=" O GLU S 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'S' and resid 383 through 385 removed outlier: 4.390A pdb=" N THR S 427 " --> pdb=" O ARG S 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 47 through 48 Processing sheet with id=AA6, first strand: chain 'T' and resid 61 through 62 Processing sheet with id=AA7, first strand: chain 'T' and resid 148 through 149 removed outlier: 3.528A pdb=" N ILE T 148 " --> pdb=" O ILE T 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 171 through 172 removed outlier: 6.695A pdb=" N ILE T 171 " --> pdb=" O GLY T 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'T' and resid 231 through 234 removed outlier: 3.736A pdb=" N GLY T 390 " --> pdb=" O ALA T 231 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE T 310 " --> pdb=" O TYR T 340 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR T 342 " --> pdb=" O ILE T 310 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE T 312 " --> pdb=" O TYR T 342 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP T 344 " --> pdb=" O ILE T 312 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP T 259 " --> pdb=" O LEU T 313 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 470 through 472 removed outlier: 3.519A pdb=" N ARG T 507 " --> pdb=" O VAL T 496 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL T 494 " --> pdb=" O ARG T 509 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 729 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: 0.85 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1649 1.32 - 1.45: 2352 1.45 - 1.58: 4978 1.58 - 1.70: 12 1.70 - 1.83: 84 Bond restraints: 9075 Sorted by residual: bond pdb=" OBQ GE0 T 602 " pdb=" PAS GE0 T 602 " ideal model delta sigma weight residual 1.495 1.611 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O3' GE0 T 602 " pdb=" PAY GE0 T 602 " ideal model delta sigma weight residual 1.728 1.612 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O4P PLS T 601 " pdb=" P PLS T 601 " ideal model delta sigma weight residual 1.712 1.610 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" OBS GE0 T 602 " pdb=" PAQ GE0 T 602 " ideal model delta sigma weight residual 1.501 1.599 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" OBA GE0 T 602 " pdb=" PAY GE0 T 602 " ideal model delta sigma weight residual 1.521 1.610 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 9070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 11862 3.54 - 7.08: 341 7.08 - 10.61: 70 10.61 - 14.15: 9 14.15 - 17.69: 7 Bond angle restraints: 12289 Sorted by residual: angle pdb=" N VAL S 144 " pdb=" CA VAL S 144 " pdb=" C VAL S 144 " ideal model delta sigma weight residual 113.42 97.86 15.56 1.17e+00 7.31e-01 1.77e+02 angle pdb=" N LEU T 69 " pdb=" CA LEU T 69 " pdb=" C LEU T 69 " ideal model delta sigma weight residual 113.55 100.90 12.65 1.26e+00 6.30e-01 1.01e+02 angle pdb=" C HIS S 77 " pdb=" N PRO S 78 " pdb=" CA PRO S 78 " ideal model delta sigma weight residual 119.24 128.77 -9.53 1.04e+00 9.25e-01 8.40e+01 angle pdb=" C GLN T 300 " pdb=" N PRO T 301 " pdb=" CA PRO T 301 " ideal model delta sigma weight residual 119.84 130.56 -10.72 1.25e+00 6.40e-01 7.36e+01 angle pdb=" N TYR T 199 " pdb=" CA TYR T 199 " pdb=" C TYR T 199 " ideal model delta sigma weight residual 111.36 120.39 -9.03 1.09e+00 8.42e-01 6.87e+01 ... (remaining 12284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4753 17.14 - 34.29: 388 34.29 - 51.43: 202 51.43 - 68.57: 59 68.57 - 85.71: 4 Dihedral angle restraints: 5406 sinusoidal: 2173 harmonic: 3233 Sorted by residual: dihedral pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" N SER A 39 " pdb=" CA SER A 39 " ideal model delta harmonic sigma weight residual -180.00 -138.52 -41.48 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA LEU A 142 " pdb=" C LEU A 142 " pdb=" N HIS A 143 " pdb=" CA HIS A 143 " ideal model delta harmonic sigma weight residual -180.00 -139.84 -40.16 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" C PHE S 394 " pdb=" N PHE S 394 " pdb=" CA PHE S 394 " pdb=" CB PHE S 394 " ideal model delta harmonic sigma weight residual -122.60 -139.75 17.15 0 2.50e+00 1.60e-01 4.70e+01 ... (remaining 5403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1237 0.138 - 0.277: 118 0.277 - 0.415: 17 0.415 - 0.553: 2 0.553 - 0.692: 1 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA PHE S 394 " pdb=" N PHE S 394 " pdb=" C PHE S 394 " pdb=" CB PHE S 394 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN T 120 " pdb=" N ASN T 120 " pdb=" C ASN T 120 " pdb=" CB ASN T 120 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA TYR T 235 " pdb=" N TYR T 235 " pdb=" C TYR T 235 " pdb=" CB TYR T 235 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1372 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG T 305 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO T 306 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO T 306 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO T 306 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 45 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO A 46 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE S 61 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ILE S 61 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE S 61 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU S 62 " -0.016 2.00e-02 2.50e+03 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.78: 8 1.78 - 2.56: 84 2.56 - 3.34: 10214 3.34 - 4.12: 19920 4.12 - 4.90: 38149 Warning: very small nonbonded interaction distances. Nonbonded interactions: 68375 Sorted by model distance: nonbonded pdb=" OD1 ASP T 344 " pdb=" CE MET T 374 " model vdw 0.997 3.460 nonbonded pdb=" OD2 ASP S 188 " pdb=" OH TYR S 248 " model vdw 1.295 3.040 nonbonded pdb=" CG1 VAL T 195 " pdb=" OE1 GLU T 417 " model vdw 1.387 3.460 nonbonded pdb=" OE1 GLU T 119 " pdb=" O PHE A 72 " model vdw 1.491 3.040 nonbonded pdb=" O LYS T 194 " pdb=" OE2 GLU T 197 " model vdw 1.636 3.040 ... (remaining 68370 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.80 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.600 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.013 0.603 9076 Z= 0.836 Angle : 1.533 17.689 12289 Z= 0.887 Chirality : 0.090 0.692 1375 Planarity : 0.008 0.072 1550 Dihedral : 16.788 85.712 3336 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.68 % Favored : 88.60 % Rotamer: Outliers : 13.06 % Allowed : 9.98 % Favored : 76.96 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.50 (0.19), residues: 1105 helix: -4.40 (0.13), residues: 474 sheet: -2.54 (0.52), residues: 92 loop : -3.07 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 543 TYR 0.039 0.003 TYR S 166 PHE 0.036 0.004 PHE T 377 TRP 0.031 0.004 TRP T 134 HIS 0.029 0.003 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.55 ( 9075) covalent geometry : angle 1.53295 / 0.89 (12289) hydrogen bonds : bond 0.34757 / 23.61 ( 257) hydrogen bonds : angle 10.68310 / 7.62 ( 729) Misc. bond : bond 0.60308 / 31.74 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 179 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 249 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7779 (ttm) REVERT: S 266 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: S 391 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8351 (p) REVERT: S 395 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7216 (p-80) REVERT: S 459 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7646 (ttp80) REVERT: T 82 THR cc_start: 0.8570 (m) cc_final: 0.8166 (p) REVERT: T 88 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7863 (mmm-85) REVERT: T 106 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6200 (mt-10) REVERT: T 119 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4954 (mm-30) REVERT: T 262 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8827 (m110) REVERT: T 278 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8486 (mtt-85) REVERT: T 304 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7828 (mmm-85) REVERT: T 369 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7642 (t0) REVERT: T 418 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.7938 (tm130) REVERT: T 423 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8722 (ttp) REVERT: T 427 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7501 (mpt) REVERT: A 17 MET cc_start: 0.5378 (pp-130) cc_final: 0.3133 (mmm) REVERT: A 73 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.5045 (pp20) outliers start: 123 outliers final: 65 residues processed: 275 average time/residue: 0.0948 time to fit residues: 34.4441 Evaluate side-chains 186 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 106 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 197 LYS Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 214 MET Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 240 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 266 LYS Chi-restraints excluded: chain S residue 325 ILE Chi-restraints excluded: chain S residue 326 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 391 SER Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 405 ARG Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 459 ARG Chi-restraints excluded: chain S residue 467 VAL Chi-restraints excluded: chain S residue 472 LEU Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 68 MET Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 TYR Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 106 GLU Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 145 ARG Chi-restraints excluded: chain T residue 165 ASN Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain T residue 173 MET Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 209 GLU Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 262 ASN Chi-restraints excluded: chain T residue 277 ILE Chi-restraints excluded: chain T residue 278 ARG Chi-restraints excluded: chain T residue 285 MET Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 345 GLU Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 379 LYS Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 418 GLN Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 423 MET Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 427 MET Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 475 MET Chi-restraints excluded: chain T residue 494 VAL Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 542 HIS Chi-restraints excluded: chain A residue 73 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS S 83 ASN S 114 ASN S 211 HIS S 224 GLN S 327 HIS S 395 HIS T 120 ASN T 242 ASN T 262 ASN T 263 HIS T 284 ASN T 418 GLN A 53 ASN A 57 ASN E 38 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109088 restraints weight = 12301.790| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.91 r_work: 0.3080 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9076 Z= 0.151 Angle : 0.732 10.388 12289 Z= 0.374 Chirality : 0.048 0.199 1375 Planarity : 0.006 0.062 1550 Dihedral : 13.071 59.234 1430 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.90 % Allowed : 13.48 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.21), residues: 1105 helix: -2.80 (0.19), residues: 461 sheet: -2.36 (0.55), residues: 89 loop : -2.64 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 410 TYR 0.022 0.002 TYR T 342 PHE 0.019 0.002 PHE A 101 TRP 0.013 0.001 TRP T 134 HIS 0.005 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9075) covalent geometry : angle 0.73207 / 0.37 (12289) hydrogen bonds : bond 0.05226 / 3.40 ( 257) hydrogen bonds : angle 5.51839 / 3.87 ( 729) Misc. bond : bond 0.00206 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8691 (tt) cc_final: 0.8342 (mp) REVERT: S 77 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7611 (t-170) REVERT: S 395 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7103 (p90) REVERT: S 458 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8093 (pp20) REVERT: T 88 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7945 (mmm-85) REVERT: T 106 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6275 (mt-10) REVERT: T 304 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8393 (mmm-85) REVERT: T 418 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: T 423 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8850 (mtm) REVERT: T 475 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7950 (mpt) REVERT: T 541 ARG cc_start: 0.8009 (mmp-170) cc_final: 0.7755 (mtp-110) REVERT: A 17 MET cc_start: 0.5274 (pp-130) cc_final: 0.3120 (mtp) REVERT: C 24 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.5240 (t-170) outliers start: 65 outliers final: 32 residues processed: 171 average time/residue: 0.0877 time to fit residues: 20.7968 Evaluate side-chains 136 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 326 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 83 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 98 LYS Chi-restraints excluded: chain T residue 106 GLU Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 209 GLU Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 418 GLN Chi-restraints excluded: chain T residue 423 MET Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 475 MET Chi-restraints excluded: chain T residue 501 THR Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 77 HIS S 107 ASN S 327 HIS A 18 ASN A 123 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105763 restraints weight = 12193.740| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.89 r_work: 0.3045 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9076 Z= 0.200 Angle : 0.700 9.386 12289 Z= 0.358 Chirality : 0.048 0.184 1375 Planarity : 0.005 0.058 1550 Dihedral : 10.619 59.752 1311 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.33 % Favored : 92.58 % Rotamer: Outliers : 6.69 % Allowed : 14.01 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.23), residues: 1105 helix: -2.08 (0.21), residues: 470 sheet: -2.16 (0.56), residues: 89 loop : -2.54 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 410 TYR 0.018 0.002 TYR E 50 PHE 0.017 0.002 PHE T 280 TRP 0.014 0.002 TRP T 94 HIS 0.014 0.001 HIS S 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 9075) covalent geometry : angle 0.70028 / 0.36 (12289) hydrogen bonds : bond 0.05011 / 3.37 ( 257) hydrogen bonds : angle 4.92893 / 3.44 ( 729) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 99 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8789 (tt) cc_final: 0.8440 (mp) REVERT: S 321 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8321 (ttp80) REVERT: S 326 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8239 (t0) REVERT: S 395 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7267 (p90) REVERT: S 458 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8224 (pp20) REVERT: S 469 GLN cc_start: 0.7431 (mt0) cc_final: 0.7172 (mp10) REVERT: T 88 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7935 (mmm-85) REVERT: T 423 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8910 (mtt) REVERT: T 441 GLN cc_start: 0.8634 (tp40) cc_final: 0.8373 (tp40) REVERT: T 475 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (mpt) REVERT: T 491 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8788 (mt) REVERT: T 541 ARG cc_start: 0.7997 (mmp-170) cc_final: 0.7714 (mtp-110) REVERT: A 17 MET cc_start: 0.5454 (pp-130) cc_final: 0.2874 (mtp) REVERT: C 24 HIS cc_start: 0.5496 (OUTLIER) cc_final: 0.5205 (t-170) outliers start: 63 outliers final: 34 residues processed: 153 average time/residue: 0.0909 time to fit residues: 19.2605 Evaluate side-chains 134 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 321 ARG Chi-restraints excluded: chain S residue 326 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 393 GLU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 423 MET Chi-restraints excluded: chain T residue 475 MET Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 501 THR Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 327 HIS S 407 GLN E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106416 restraints weight = 12375.082| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.94 r_work: 0.3080 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9076 Z= 0.153 Angle : 0.630 8.980 12289 Z= 0.322 Chirality : 0.047 0.179 1375 Planarity : 0.005 0.057 1550 Dihedral : 9.597 59.397 1294 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 4.99 % Allowed : 16.88 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.23), residues: 1105 helix: -1.54 (0.23), residues: 478 sheet: -1.95 (0.57), residues: 88 loop : -2.39 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 410 TYR 0.014 0.001 TYR E 50 PHE 0.017 0.001 PHE S 394 TRP 0.013 0.001 TRP T 94 HIS 0.005 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 9075) covalent geometry : angle 0.63000 / 0.32 (12289) hydrogen bonds : bond 0.04058 / 2.71 ( 257) hydrogen bonds : angle 4.58916 / 3.21 ( 729) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8819 (tt) cc_final: 0.8475 (mp) REVERT: S 391 SER cc_start: 0.8616 (t) cc_final: 0.8122 (p) REVERT: S 395 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7418 (p90) REVERT: S 407 GLN cc_start: 0.8232 (mm110) cc_final: 0.7760 (mt0) REVERT: S 408 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: S 410 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.8198 (mtm-85) REVERT: S 458 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: T 61 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: T 88 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7992 (mmm-85) REVERT: T 423 MET cc_start: 0.9126 (mtt) cc_final: 0.8884 (mtm) REVERT: T 441 GLN cc_start: 0.8539 (tp40) cc_final: 0.8248 (tp40) REVERT: T 491 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8611 (mt) REVERT: T 541 ARG cc_start: 0.7977 (mmp-170) cc_final: 0.7701 (mtp-110) REVERT: A 17 MET cc_start: 0.5206 (pp-130) cc_final: 0.2732 (mtp) REVERT: C 24 HIS cc_start: 0.5319 (OUTLIER) cc_final: 0.5103 (t-170) outliers start: 47 outliers final: 28 residues processed: 133 average time/residue: 0.0884 time to fit residues: 16.7667 Evaluate side-chains 125 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 501 THR Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain C residue 24 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105394 restraints weight = 12301.255| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.89 r_work: 0.3037 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9076 Z= 0.166 Angle : 0.631 9.995 12289 Z= 0.322 Chirality : 0.047 0.180 1375 Planarity : 0.005 0.055 1550 Dihedral : 8.885 59.785 1279 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer: Outliers : 5.20 % Allowed : 17.30 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.24), residues: 1105 helix: -1.18 (0.23), residues: 490 sheet: -1.55 (0.55), residues: 94 loop : -2.37 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 410 TYR 0.013 0.001 TYR T 342 PHE 0.018 0.001 PHE S 394 TRP 0.015 0.001 TRP T 94 HIS 0.006 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 9075) covalent geometry : angle 0.63115 / 0.32 (12289) hydrogen bonds : bond 0.03982 / 2.68 ( 257) hydrogen bonds : angle 4.49561 / 3.13 ( 729) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8858 (tt) cc_final: 0.8534 (mp) REVERT: S 80 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8159 (mm) REVERT: S 236 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7246 (ttp-110) REVERT: S 321 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8316 (ttp80) REVERT: S 326 ASP cc_start: 0.9059 (t70) cc_final: 0.8299 (t0) REVERT: S 369 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8938 (mmtp) REVERT: S 391 SER cc_start: 0.8664 (t) cc_final: 0.8174 (p) REVERT: S 395 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.7490 (p90) REVERT: S 408 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: S 458 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: S 469 GLN cc_start: 0.7494 (mt0) cc_final: 0.7227 (mp10) REVERT: T 88 ARG cc_start: 0.8299 (tpp80) cc_final: 0.8018 (mmm-85) REVERT: T 423 MET cc_start: 0.9128 (mtt) cc_final: 0.8899 (mtm) REVERT: T 441 GLN cc_start: 0.8531 (tp40) cc_final: 0.8256 (tp40) REVERT: T 491 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8587 (mt) REVERT: T 541 ARG cc_start: 0.7903 (mmp-170) cc_final: 0.7626 (mtp-110) REVERT: A 17 MET cc_start: 0.5242 (pp-130) cc_final: 0.2785 (mtp) outliers start: 49 outliers final: 33 residues processed: 139 average time/residue: 0.0850 time to fit residues: 16.6837 Evaluate side-chains 131 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 254 ILE Chi-restraints excluded: chain S residue 321 ARG Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106612 restraints weight = 12185.238| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.88 r_work: 0.3064 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9076 Z= 0.137 Angle : 0.612 15.163 12289 Z= 0.308 Chirality : 0.045 0.178 1375 Planarity : 0.004 0.053 1550 Dihedral : 8.540 59.895 1277 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 5.10 % Allowed : 17.94 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.24), residues: 1105 helix: -0.92 (0.24), residues: 484 sheet: -1.56 (0.53), residues: 100 loop : -2.20 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 410 TYR 0.013 0.001 TYR A 119 PHE 0.016 0.001 PHE S 394 TRP 0.015 0.001 TRP T 94 HIS 0.007 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9075) covalent geometry : angle 0.61187 / 0.31 (12289) hydrogen bonds : bond 0.03604 / 2.42 ( 257) hydrogen bonds : angle 4.41940 / 3.01 ( 729) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 60 LEU cc_start: 0.8909 (tt) cc_final: 0.8576 (mp) REVERT: S 80 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8281 (mm) REVERT: S 321 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8310 (ttp80) REVERT: S 326 ASP cc_start: 0.9069 (t70) cc_final: 0.8319 (t0) REVERT: S 369 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8916 (mmtp) REVERT: S 391 SER cc_start: 0.8601 (t) cc_final: 0.8153 (p) REVERT: S 395 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7842 (p90) REVERT: S 407 GLN cc_start: 0.8361 (mm110) cc_final: 0.7866 (mt0) REVERT: S 408 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: S 458 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: T 88 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7912 (mmm-85) REVERT: T 94 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7013 (p90) REVERT: T 423 MET cc_start: 0.9096 (mtt) cc_final: 0.8874 (mtm) REVERT: T 441 GLN cc_start: 0.8475 (tp40) cc_final: 0.8189 (tp40) REVERT: T 491 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8556 (mt) REVERT: T 541 ARG cc_start: 0.7950 (mmp-170) cc_final: 0.7644 (mtp-110) REVERT: A 17 MET cc_start: 0.5105 (pp-130) cc_final: 0.2650 (mtm) outliers start: 48 outliers final: 30 residues processed: 145 average time/residue: 0.0870 time to fit residues: 17.5021 Evaluate side-chains 132 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 321 ARG Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 107 ASN T 212 ASN T 542 HIS ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105457 restraints weight = 12310.569| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.90 r_work: 0.2928 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9076 Z= 0.198 Angle : 0.671 12.105 12289 Z= 0.343 Chirality : 0.048 0.182 1375 Planarity : 0.005 0.053 1550 Dihedral : 8.489 57.747 1272 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.14 % Favored : 91.76 % Rotamer: Outliers : 5.10 % Allowed : 18.58 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.24), residues: 1105 helix: -0.95 (0.23), residues: 495 sheet: -1.39 (0.55), residues: 93 loop : -2.28 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 410 TYR 0.014 0.002 TYR E 50 PHE 0.018 0.002 PHE T 280 TRP 0.018 0.002 TRP T 94 HIS 0.006 0.001 HIS T 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 9075) covalent geometry : angle 0.67115 / 0.34 (12289) hydrogen bonds : bond 0.04131 / 2.80 ( 257) hydrogen bonds : angle 4.52256 / 3.16 ( 729) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: S 60 LEU cc_start: 0.9051 (tt) cc_final: 0.8668 (mp) REVERT: S 80 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8189 (mm) REVERT: S 326 ASP cc_start: 0.9051 (t70) cc_final: 0.8338 (t0) REVERT: S 369 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8921 (mmtp) REVERT: S 391 SER cc_start: 0.8713 (t) cc_final: 0.8262 (p) REVERT: S 395 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7610 (p90) REVERT: S 408 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: S 458 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: T 88 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8100 (mmm-85) REVERT: T 94 TRP cc_start: 0.8280 (OUTLIER) cc_final: 0.7174 (p90) REVERT: T 441 GLN cc_start: 0.8523 (tp40) cc_final: 0.8240 (tp40) REVERT: T 491 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8601 (mt) REVERT: T 541 ARG cc_start: 0.7969 (mmp-170) cc_final: 0.7668 (mtp-110) REVERT: A 17 MET cc_start: 0.5098 (pp-130) cc_final: 0.2522 (mtm) outliers start: 48 outliers final: 34 residues processed: 137 average time/residue: 0.0951 time to fit residues: 17.9728 Evaluate side-chains 130 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 426 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 542 HIS Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 107 ASN T 542 HIS ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106213 restraints weight = 12319.785| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.86 r_work: 0.2970 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9076 Z= 0.170 Angle : 0.647 11.868 12289 Z= 0.329 Chirality : 0.047 0.216 1375 Planarity : 0.005 0.053 1550 Dihedral : 8.447 58.328 1272 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.78 % Favored : 92.13 % Rotamer: Outliers : 5.52 % Allowed : 18.37 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.25), residues: 1105 helix: -0.79 (0.24), residues: 492 sheet: -1.42 (0.52), residues: 99 loop : -2.22 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 410 TYR 0.015 0.002 TYR T 539 PHE 0.017 0.001 PHE T 280 TRP 0.018 0.002 TRP T 94 HIS 0.013 0.001 HIS T 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 9075) covalent geometry : angle 0.64732 / 0.33 (12289) hydrogen bonds : bond 0.03880 / 2.62 ( 257) hydrogen bonds : angle 4.48576 / 3.09 ( 729) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 98 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 80 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8186 (mm) REVERT: S 236 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7358 (ttp-110) REVERT: S 326 ASP cc_start: 0.9039 (t70) cc_final: 0.8333 (t0) REVERT: S 369 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8924 (mmtp) REVERT: S 388 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: S 391 SER cc_start: 0.8762 (t) cc_final: 0.8333 (p) REVERT: S 395 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.7575 (p90) REVERT: S 407 GLN cc_start: 0.8431 (mm110) cc_final: 0.7942 (mt0) REVERT: S 408 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: S 458 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: T 88 ARG cc_start: 0.8462 (tpp80) cc_final: 0.8085 (mmm-85) REVERT: T 94 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7326 (p90) REVERT: T 441 GLN cc_start: 0.8508 (tp40) cc_final: 0.8232 (tp40) REVERT: T 491 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8606 (mt) REVERT: T 541 ARG cc_start: 0.7898 (mmp-170) cc_final: 0.7649 (mtp85) REVERT: A 17 MET cc_start: 0.5095 (pp-130) cc_final: 0.2440 (mtm) outliers start: 52 outliers final: 36 residues processed: 143 average time/residue: 0.0963 time to fit residues: 19.2361 Evaluate side-chains 137 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 545 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 74 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 107 ASN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108281 restraints weight = 12159.911| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.01 r_work: 0.3032 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9076 Z= 0.112 Angle : 0.598 11.753 12289 Z= 0.300 Chirality : 0.044 0.177 1375 Planarity : 0.004 0.053 1550 Dihedral : 8.146 59.066 1272 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 4.14 % Allowed : 19.32 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.25), residues: 1105 helix: -0.51 (0.25), residues: 487 sheet: -1.36 (0.53), residues: 100 loop : -2.08 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 410 TYR 0.013 0.001 TYR T 539 PHE 0.031 0.001 PHE S 108 TRP 0.016 0.001 TRP T 94 HIS 0.004 0.001 HIS T 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9075) covalent geometry : angle 0.59777 / 0.30 (12289) hydrogen bonds : bond 0.03157 / 2.09 ( 257) hydrogen bonds : angle 4.30892 / 2.99 ( 729) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 60 LEU cc_start: 0.9066 (tt) cc_final: 0.8759 (mp) REVERT: S 80 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8252 (mm) REVERT: S 236 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7345 (ttp-110) REVERT: S 326 ASP cc_start: 0.9043 (t70) cc_final: 0.8328 (t0) REVERT: S 369 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8923 (mmtp) REVERT: S 388 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: S 391 SER cc_start: 0.8646 (t) cc_final: 0.8211 (p) REVERT: S 395 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.7595 (p90) REVERT: S 407 GLN cc_start: 0.8428 (mm110) cc_final: 0.7899 (mt0) REVERT: S 408 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: S 458 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8309 (pp20) REVERT: T 88 ARG cc_start: 0.8429 (tpp80) cc_final: 0.8040 (mmm-85) REVERT: T 94 TRP cc_start: 0.8266 (OUTLIER) cc_final: 0.7521 (p90) REVERT: T 441 GLN cc_start: 0.8456 (tp40) cc_final: 0.8180 (tp40) REVERT: T 541 ARG cc_start: 0.7880 (mmp-170) cc_final: 0.7640 (mtp85) REVERT: A 17 MET cc_start: 0.5014 (pp-130) cc_final: 0.2778 (ttm) outliers start: 39 outliers final: 28 residues processed: 135 average time/residue: 0.1053 time to fit residues: 19.6564 Evaluate side-chains 128 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 545 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106439 restraints weight = 12285.742| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.29 r_work: 0.2994 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9076 Z= 0.153 Angle : 0.637 11.260 12289 Z= 0.321 Chirality : 0.046 0.178 1375 Planarity : 0.005 0.053 1550 Dihedral : 8.173 59.868 1272 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 4.14 % Allowed : 19.53 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.25), residues: 1105 helix: -0.48 (0.24), residues: 492 sheet: -1.32 (0.52), residues: 100 loop : -2.13 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 57 TYR 0.014 0.001 TYR T 539 PHE 0.016 0.001 PHE T 280 TRP 0.017 0.001 TRP T 94 HIS 0.005 0.001 HIS T 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 9075) covalent geometry : angle 0.63740 / 0.32 (12289) hydrogen bonds : bond 0.03573 / 2.41 ( 257) hydrogen bonds : angle 4.35377 / 3.02 ( 729) Misc. bond : bond 0.00041 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 60 LEU cc_start: 0.9067 (tt) cc_final: 0.8733 (mp) REVERT: S 80 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8258 (mm) REVERT: S 236 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7361 (ttp-110) REVERT: S 326 ASP cc_start: 0.9096 (t70) cc_final: 0.8382 (t0) REVERT: S 369 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8921 (mmtp) REVERT: S 388 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: S 391 SER cc_start: 0.8748 (t) cc_final: 0.8306 (p) REVERT: S 395 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7557 (p90) REVERT: S 407 GLN cc_start: 0.8456 (mm110) cc_final: 0.7888 (mt0) REVERT: S 408 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: S 458 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8299 (pp20) REVERT: T 94 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7629 (p90) REVERT: T 220 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8572 (mt-10) REVERT: T 441 GLN cc_start: 0.8505 (tp40) cc_final: 0.8212 (tp40) REVERT: T 491 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8515 (mt) REVERT: T 539 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7495 (p90) REVERT: T 541 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7637 (mtp85) REVERT: A 17 MET cc_start: 0.4797 (pp-130) cc_final: 0.2840 (ttp) outliers start: 39 outliers final: 30 residues processed: 130 average time/residue: 0.0873 time to fit residues: 15.8765 Evaluate side-chains 135 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 321 ARG Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 395 HIS Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 458 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 94 TRP Chi-restraints excluded: chain T residue 109 LYS Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 415 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 422 SER Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 545 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.0170 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 542 HIS ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106993 restraints weight = 12111.518| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.86 r_work: 0.3062 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9076 Z= 0.110 Angle : 0.585 11.232 12289 Z= 0.295 Chirality : 0.044 0.179 1375 Planarity : 0.004 0.053 1550 Dihedral : 7.848 58.873 1272 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 3.93 % Allowed : 19.75 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.25), residues: 1105 helix: -0.27 (0.25), residues: 492 sheet: -1.13 (0.53), residues: 100 loop : -2.04 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 57 TYR 0.012 0.001 TYR A 119 PHE 0.012 0.001 PHE T 280 TRP 0.015 0.001 TRP T 94 HIS 0.004 0.001 HIS T 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9075) covalent geometry : angle 0.58488 / 0.30 (12289) hydrogen bonds : bond 0.02973 / 1.97 ( 257) hydrogen bonds : angle 4.20876 / 2.92 ( 729) Misc. bond : bond 0.00008 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.11 seconds wall clock time: 41 minutes 10.13 seconds (2470.13 seconds total)