Starting phenix.real_space_refine on Thu Aug 6 02:40:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24ve_69837/08_2026/24ve_69837.cif Found real_map, /net/cci-nas-00/data/ceres_data/24ve_69837/08_2026/24ve_69837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24ve_69837/08_2026/24ve_69837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24ve_69837/08_2026/24ve_69837.map" model { file = "/net/cci-nas-00/data/ceres_data/24ve_69837/08_2026/24ve_69837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24ve_69837/08_2026/24ve_69837.cif" } resolution = 2.98 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 59 5.16 5 C 8278 2.51 5 N 2098 2.21 5 O 2257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12696 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3538 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 420} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12696 At special positions: 0 Unit cell: (132.84, 89.298, 135.792, 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 59 16.00 P 4 15.00 O 2257 8.00 N 2098 7.00 C 8278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 475 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 481.7 milliseconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 74.5% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 removed outlier: 3.521A pdb=" N GLN A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 removed outlier: 3.507A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.969A pdb=" N GLY A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 125 removed outlier: 3.595A pdb=" N ARG A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 removed outlier: 4.061A pdb=" N ASN A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 148 through 183 removed outlier: 4.960A pdb=" N SER A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LYS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Proline residue: A 168 - end of helix removed outlier: 3.637A pdb=" N TYR A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 232 removed outlier: 3.636A pdb=" N VAL A 188 " --> pdb=" O TRP A 184 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix removed outlier: 3.604A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 241 through 267 removed outlier: 3.645A pdb=" N ARG A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 296 removed outlier: 3.793A pdb=" N PHE A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 302 through 355 removed outlier: 3.973A pdb=" N THR A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.544A pdb=" N LEU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.825A pdb=" N ASP A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.610A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 removed outlier: 3.897A pdb=" N GLN A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.748A pdb=" N LEU A 582 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.917A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 62 removed outlier: 3.606A pdb=" N MET B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.023A pdb=" N GLY B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.531A pdb=" N PHE B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 148 through 183 removed outlier: 4.850A pdb=" N SER B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 3.717A pdb=" N TYR B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 232 removed outlier: 3.745A pdb=" N VAL B 188 " --> pdb=" O TRP B 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix removed outlier: 4.099A pdb=" N VAL B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.524A pdb=" N TYR B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 267 Processing helix chain 'B' and resid 267 through 296 removed outlier: 4.155A pdb=" N PHE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 302 through 354 removed outlier: 4.059A pdb=" N THR B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.864A pdb=" N LEU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.617A pdb=" N VAL B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 501 removed outlier: 3.569A pdb=" N ASP B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 509 removed outlier: 3.529A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.694A pdb=" N GLU B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 3.986A pdb=" N LEU B 582 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 37 removed outlier: 3.539A pdb=" N TYR C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 73 removed outlier: 4.500A pdb=" N LEU C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 91 through 114 Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.616A pdb=" N TYR C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 161 removed outlier: 3.577A pdb=" N TYR C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 147 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 225 removed outlier: 3.593A pdb=" N SER C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Proline residue: C 220 - end of helix Processing helix chain 'C' and resid 233 through 253 Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.549A pdb=" N ASP C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 292 removed outlier: 3.640A pdb=" N ALA C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.081A pdb=" N LYS C 296 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 333 removed outlier: 4.431A pdb=" N VAL C 307 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 360 Proline residue: C 357 - end of helix Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 406 through 432 removed outlier: 4.213A pdb=" N SER C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C 427 " --> pdb=" O HIS C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.537A pdb=" N LEU C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 513 removed outlier: 3.874A pdb=" N ASN C 498 " --> pdb=" O TYR C 494 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TRP C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 402 through 411 removed outlier: 6.541A pdb=" N LEU A 403 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER A 395 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 405 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 393 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 407 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 387 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 546 through 548 removed outlier: 6.123A pdb=" N LEU A 418 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 592 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 420 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 387 through 395 removed outlier: 5.935A pdb=" N LEU B 388 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE B 411 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU B 390 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 409 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE B 394 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LYS B 405 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 575 through 576 removed outlier: 3.549A pdb=" N CYS B 593 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 597 " --> pdb=" O CYS B 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 390 through 391 842 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3940 1.34 - 1.46: 3205 1.46 - 1.58: 5746 1.58 - 1.70: 6 1.70 - 1.82: 94 Bond restraints: 12991 Sorted by residual: bond pdb=" N LEU C 318 " pdb=" CA LEU C 318 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.59e+00 bond pdb=" N LEU C 317 " pdb=" CA LEU C 317 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.17e-02 7.31e+03 4.69e+00 bond pdb=" N ASP B 100 " pdb=" CA ASP B 100 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.20e-02 6.94e+03 4.45e+00 bond pdb=" C ILE B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.29e+00 bond pdb=" CA LEU C 318 " pdb=" C LEU C 318 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.35e-02 5.49e+03 1.86e+00 ... (remaining 12986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 17400 2.33 - 4.66: 165 4.66 - 6.99: 36 6.99 - 9.32: 11 9.32 - 11.65: 3 Bond angle restraints: 17615 Sorted by residual: angle pdb=" N ASP B 100 " pdb=" CA ASP B 100 " pdb=" C ASP B 100 " ideal model delta sigma weight residual 111.14 107.24 3.90 1.08e+00 8.57e-01 1.30e+01 angle pdb=" C LEU A 478 " pdb=" N LYS A 479 " pdb=" CA LYS A 479 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA LEU C 145 " pdb=" CB LEU C 145 " pdb=" CG LEU C 145 " ideal model delta sigma weight residual 116.30 127.95 -11.65 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.70e+00 3.46e-01 1.09e+01 angle pdb=" CA LEU C 20 " pdb=" CB LEU C 20 " pdb=" CG LEU C 20 " ideal model delta sigma weight residual 116.30 127.78 -11.48 3.50e+00 8.16e-02 1.08e+01 ... (remaining 17610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6627 17.67 - 35.35: 776 35.35 - 53.02: 215 53.02 - 70.70: 28 70.70 - 88.37: 15 Dihedral angle restraints: 7661 sinusoidal: 3100 harmonic: 4561 Sorted by residual: dihedral pdb=" CA ILE A 475 " pdb=" C ILE A 475 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 37 " pdb=" C SER A 37 " pdb=" N GLN A 38 " pdb=" CA GLN A 38 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE A 573 " pdb=" C PHE A 573 " pdb=" N ILE A 574 " pdb=" CA ILE A 574 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 7658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1807 0.062 - 0.124: 200 0.124 - 0.185: 7 0.185 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CG LEU C 20 " pdb=" CB LEU C 20 " pdb=" CD1 LEU C 20 " pdb=" CD2 LEU C 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CG LEU C 26 " pdb=" CB LEU C 26 " pdb=" CD1 LEU C 26 " pdb=" CD2 LEU C 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE C 372 " pdb=" CA ILE C 372 " pdb=" CG1 ILE C 372 " pdb=" CG2 ILE C 372 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 2013 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 363 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO C 364 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 364 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 364 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 316 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ALA C 316 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA C 316 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU C 317 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 393 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C PHE C 393 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE C 393 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP C 394 " -0.009 2.00e-02 2.50e+03 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4796 2.90 - 3.40: 13150 3.40 - 3.90: 20795 3.90 - 4.40: 22802 4.40 - 4.90: 39151 Nonbonded interactions: 100694 Sorted by model distance: nonbonded pdb=" OE2 GLU C 94 " pdb=" CG2 THR C 476 " model vdw 2.396 3.460 nonbonded pdb=" OD2 ASP C 240 " pdb=" CD1 LEU C 279 " model vdw 2.489 3.460 nonbonded pdb=" O2' ADP A 701 " pdb=" O3' ADP A 701 " model vdw 2.492 2.432 nonbonded pdb=" O2' ADP B 701 " pdb=" O3' ADP B 701 " model vdw 2.498 2.432 nonbonded pdb=" O VAL C 421 " pdb=" OG1 THR C 424 " model vdw 2.536 3.040 ... (remaining 100689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.002 0.038 12992 Z= 0.117 Angle : 0.620 11.654 17617 Z= 0.294 Chirality : 0.039 0.309 2016 Planarity : 0.003 0.057 2169 Dihedral : 16.485 88.374 4724 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.79 % Allowed : 24.19 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 0.63 (0.22), residues: 1546 helix: 1.06 (0.16), residues: 1113 sheet: -1.05 (0.78), residues: 58 loop : -1.11 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 391 TYR 0.016 0.001 TYR B 130 PHE 0.020 0.001 PHE B 55 TRP 0.013 0.001 TRP B 184 HIS 0.006 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (12991) covalent geometry : angle 0.62037 / 0.29 (17615) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 0.36742 / 0.20 ( 2) hydrogen bonds : bond 0.20448 / 13.41 ( 842) hydrogen bonds : angle 6.46575 / 4.55 ( 2490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8231 (tp30) cc_final: 0.7612 (mt-10) REVERT: A 353 ASP cc_start: 0.9094 (t0) cc_final: 0.8763 (t0) REVERT: A 391 ARG cc_start: 0.9073 (mmm-85) cc_final: 0.8333 (ttp-110) REVERT: A 491 GLU cc_start: 0.8437 (tt0) cc_final: 0.8195 (tp30) REVERT: A 518 TRP cc_start: 0.7598 (m-10) cc_final: 0.7327 (m-10) REVERT: B 117 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7217 (tm-30) REVERT: B 210 MET cc_start: 0.8919 (tpp) cc_final: 0.8641 (tpt) REVERT: B 216 GLU cc_start: 0.8530 (tp30) cc_final: 0.8297 (tp30) REVERT: B 226 HIS cc_start: 0.9348 (OUTLIER) cc_final: 0.8279 (m-70) REVERT: B 255 ARG cc_start: 0.7694 (tpp-160) cc_final: 0.7393 (mtm110) REVERT: B 353 ASP cc_start: 0.8867 (t0) cc_final: 0.8624 (t0) REVERT: B 447 MET cc_start: 0.5860 (tpp) cc_final: 0.5204 (tpp) REVERT: B 571 MET cc_start: 0.4315 (OUTLIER) cc_final: 0.2955 (ptm) REVERT: C 15 TRP cc_start: 0.6103 (m-10) cc_final: 0.5230 (m100) REVERT: C 34 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7459 (mtp-110) REVERT: C 101 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: C 114 PHE cc_start: 0.8142 (t80) cc_final: 0.7312 (m-10) REVERT: C 277 ARG cc_start: 0.8898 (tmm160) cc_final: 0.8517 (ptp-110) REVERT: C 366 ASP cc_start: 0.8196 (p0) cc_final: 0.7620 (p0) REVERT: C 375 MET cc_start: 0.8054 (mmm) cc_final: 0.7669 (mmm) REVERT: C 426 TYR cc_start: 0.7234 (t80) cc_final: 0.6863 (t80) outliers start: 11 outliers final: 4 residues processed: 130 average time/residue: 0.4649 time to fit residues: 67.5696 Evaluate side-chains 112 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 101 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A 342 HIS ** C 350 ASN ** 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 = 0.4219 r_free = 0.4219 target = 0.175472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099644 restraints weight = 17204.510| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.68 r_work: 0.3172 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12992 Z= 0.281 Angle : 0.699 11.512 17617 Z= 0.346 Chirality : 0.046 0.342 2016 Planarity : 0.004 0.047 2169 Dihedral : 5.567 53.185 1757 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 5.89 % Allowed : 20.60 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.21 (0.22), residues: 1546 helix: 1.60 (0.16), residues: 1113 sheet: -0.88 (0.77), residues: 58 loop : -1.32 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.017 0.002 TYR A 123 PHE 0.015 0.002 PHE A 55 TRP 0.010 0.001 TRP B 520 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.28 (12991) covalent geometry : angle 0.69852 / 0.35 (17615) SS BOND : bond 0.00227 / 0.12 ( 1) SS BOND : angle 0.45019 / 0.25 ( 2) hydrogen bonds : bond 0.06475 / 4.25 ( 842) hydrogen bonds : angle 4.46487 / 3.12 ( 2490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 114 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6716 (mtp85) REVERT: A 349 GLU cc_start: 0.8206 (tp30) cc_final: 0.8001 (tp30) REVERT: A 353 ASP cc_start: 0.9115 (t0) cc_final: 0.8758 (t0) REVERT: A 472 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 491 GLU cc_start: 0.8467 (tt0) cc_final: 0.8208 (tp30) REVERT: A 530 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7679 (mm-40) REVERT: B 48 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7221 (m) REVERT: B 112 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6550 (ttm170) REVERT: B 117 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 216 GLU cc_start: 0.8367 (tp30) cc_final: 0.8031 (tm-30) REVERT: B 229 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8076 (mt) REVERT: B 255 ARG cc_start: 0.7768 (tpp-160) cc_final: 0.7387 (mtm110) REVERT: B 280 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 353 ASP cc_start: 0.8925 (t0) cc_final: 0.8682 (t0) REVERT: B 403 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7303 (mp) REVERT: B 447 MET cc_start: 0.5978 (tpp) cc_final: 0.5371 (tpp) REVERT: B 571 MET cc_start: 0.4400 (OUTLIER) cc_final: 0.3044 (ptm) REVERT: C 15 TRP cc_start: 0.6093 (m-10) cc_final: 0.5254 (m100) REVERT: C 101 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: C 228 ARG cc_start: 0.2364 (OUTLIER) cc_final: 0.2130 (tpm170) REVERT: C 240 ASP cc_start: 0.6027 (t0) cc_final: 0.5543 (t70) REVERT: C 277 ARG cc_start: 0.8948 (tmm160) cc_final: 0.8646 (tmm-80) REVERT: C 322 SER cc_start: 0.9293 (OUTLIER) cc_final: 0.9091 (t) REVERT: C 366 ASP cc_start: 0.8096 (p0) cc_final: 0.7453 (p0) REVERT: C 375 MET cc_start: 0.8037 (mmm) cc_final: 0.7681 (mmm) REVERT: C 426 TYR cc_start: 0.7395 (t80) cc_final: 0.7005 (t80) REVERT: C 427 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7029 (mpt) outliers start: 82 outliers final: 32 residues processed: 182 average time/residue: 0.3705 time to fit residues: 75.7791 Evaluate side-chains 146 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 506 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 350 ASN ** 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 = 0.4311 r_free = 0.4311 target = 0.179440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106018 restraints weight = 16981.453| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.69 r_work: 0.3274 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12992 Z= 0.125 Angle : 0.592 12.409 17617 Z= 0.282 Chirality : 0.040 0.312 2016 Planarity : 0.004 0.050 2169 Dihedral : 5.125 54.751 1751 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 4.16 % Allowed : 22.18 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.96 (0.22), residues: 1546 helix: 2.18 (0.16), residues: 1097 sheet: -0.84 (0.77), residues: 58 loop : -0.94 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.017 0.001 TYR B 130 PHE 0.013 0.001 PHE A 55 TRP 0.009 0.001 TRP C 30 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12991) covalent geometry : angle 0.59156 / 0.28 (17615) SS BOND : bond 0.00172 / 0.09 ( 1) SS BOND : angle 0.43949 / 0.24 ( 2) hydrogen bonds : bond 0.04864 / 3.19 ( 842) hydrogen bonds : angle 3.98501 / 2.77 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6068 (ttm170) REVERT: A 266 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6924 (mptt) REVERT: A 349 GLU cc_start: 0.7710 (tp30) cc_final: 0.7499 (tp30) REVERT: A 353 ASP cc_start: 0.8894 (t0) cc_final: 0.8537 (t0) REVERT: A 472 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7004 (mm-30) REVERT: A 491 GLU cc_start: 0.8296 (tt0) cc_final: 0.8049 (tp30) REVERT: A 518 TRP cc_start: 0.7456 (m-10) cc_final: 0.7205 (m-10) REVERT: B 117 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 184 TRP cc_start: 0.8099 (p-90) cc_final: 0.7842 (p-90) REVERT: B 216 GLU cc_start: 0.8037 (tp30) cc_final: 0.7611 (tm-30) REVERT: B 229 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7622 (mt) REVERT: B 250 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 255 ARG cc_start: 0.7220 (tpp-160) cc_final: 0.6928 (mtm110) REVERT: B 447 MET cc_start: 0.6006 (tpp) cc_final: 0.5292 (tpp) REVERT: B 571 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.3001 (ptm) REVERT: C 15 TRP cc_start: 0.6112 (m-10) cc_final: 0.5250 (m100) REVERT: C 101 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: C 228 ARG cc_start: 0.2265 (OUTLIER) cc_final: 0.2005 (tpm170) REVERT: C 277 ARG cc_start: 0.8928 (tmm160) cc_final: 0.8626 (tmm-80) REVERT: C 366 ASP cc_start: 0.8067 (p0) cc_final: 0.7230 (p0) REVERT: C 375 MET cc_start: 0.7856 (mmm) cc_final: 0.7471 (mmm) REVERT: C 426 TYR cc_start: 0.6944 (t80) cc_final: 0.6575 (t80) outliers start: 58 outliers final: 15 residues processed: 163 average time/residue: 0.3974 time to fit residues: 71.8595 Evaluate side-chains 121 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 243 HIS C 222 ASN ** C 350 ASN ** 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 = 0.4308 r_free = 0.4308 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105797 restraints weight = 16951.624| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.59 r_work: 0.3265 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12992 Z= 0.134 Angle : 0.595 12.885 17617 Z= 0.281 Chirality : 0.040 0.316 2016 Planarity : 0.003 0.044 2169 Dihedral : 5.029 55.959 1748 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 4.24 % Allowed : 22.54 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.13 (0.22), residues: 1546 helix: 2.31 (0.16), residues: 1097 sheet: -0.75 (0.77), residues: 58 loop : -0.92 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 391 TYR 0.018 0.001 TYR B 130 PHE 0.014 0.001 PHE A 55 TRP 0.008 0.001 TRP C 30 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (12991) covalent geometry : angle 0.59536 / 0.28 (17615) SS BOND : bond 0.00197 / 0.10 ( 1) SS BOND : angle 0.73591 / 0.41 ( 2) hydrogen bonds : bond 0.04618 / 3.03 ( 842) hydrogen bonds : angle 3.84497 / 2.68 ( 2490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 111 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 GLU cc_start: 0.8054 (tp30) cc_final: 0.7842 (tp30) REVERT: A 353 ASP cc_start: 0.8961 (t0) cc_final: 0.8650 (t0) REVERT: A 391 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8399 (ttm-80) REVERT: A 472 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7401 (mm-30) REVERT: A 491 GLU cc_start: 0.8458 (tt0) cc_final: 0.8195 (tp30) REVERT: A 518 TRP cc_start: 0.7581 (m-10) cc_final: 0.7303 (m-10) REVERT: A 601 MET cc_start: 0.8832 (mmm) cc_final: 0.8626 (mmm) REVERT: B 48 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7333 (m) REVERT: B 117 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7043 (tm-30) REVERT: B 184 TRP cc_start: 0.8164 (p-90) cc_final: 0.7901 (p-90) REVERT: B 216 GLU cc_start: 0.8159 (tp30) cc_final: 0.7715 (tm-30) REVERT: B 250 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: B 255 ARG cc_start: 0.7533 (tpp-160) cc_final: 0.7182 (mtm110) REVERT: B 280 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 447 MET cc_start: 0.6089 (tpp) cc_final: 0.5372 (tpp) REVERT: B 520 TRP cc_start: 0.6746 (m-90) cc_final: 0.6096 (m-90) REVERT: B 571 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.3126 (ptm) REVERT: C 15 TRP cc_start: 0.6098 (m-10) cc_final: 0.5253 (m100) REVERT: C 101 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: C 277 ARG cc_start: 0.8940 (tmm160) cc_final: 0.8607 (ptp-110) REVERT: C 366 ASP cc_start: 0.8001 (p0) cc_final: 0.7237 (p0) REVERT: C 375 MET cc_start: 0.7952 (mmm) cc_final: 0.7590 (mmm) REVERT: C 426 TYR cc_start: 0.7235 (t80) cc_final: 0.6831 (t80) REVERT: C 427 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6959 (mpt) outliers start: 59 outliers final: 26 residues processed: 158 average time/residue: 0.3994 time to fit residues: 70.7506 Evaluate side-chains 129 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 260 GLN A 461 GLN ** C 350 ASN ** 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 = 0.4247 r_free = 0.4247 target = 0.171848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097932 restraints weight = 17068.129| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.56 r_work: 0.3154 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 12992 Z= 0.359 Angle : 0.746 11.340 17617 Z= 0.368 Chirality : 0.049 0.327 2016 Planarity : 0.004 0.049 2169 Dihedral : 5.526 56.862 1748 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 5.81 % Allowed : 22.04 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.32 (0.22), residues: 1546 helix: 1.68 (0.15), residues: 1119 sheet: -0.83 (0.76), residues: 58 loop : -1.32 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 248 TYR 0.023 0.002 TYR A 108 PHE 0.022 0.002 PHE A 277 TRP 0.010 0.001 TRP C 394 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.36 (12991) covalent geometry : angle 0.74616 / 0.37 (17615) SS BOND : bond 0.00354 / 0.19 ( 1) SS BOND : angle 0.87871 / 0.49 ( 2) hydrogen bonds : bond 0.06198 / 4.07 ( 842) hydrogen bonds : angle 4.27574 / 3.01 ( 2490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 111 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.6628 (ttm170) REVERT: A 251 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6748 (mtp85) REVERT: A 353 ASP cc_start: 0.9065 (t0) cc_final: 0.8792 (t0) REVERT: A 391 ARG cc_start: 0.8941 (mmm-85) cc_final: 0.8492 (ttm-80) REVERT: A 472 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 482 TYR cc_start: 0.7809 (t80) cc_final: 0.7472 (t80) REVERT: A 491 GLU cc_start: 0.8500 (tt0) cc_final: 0.8234 (tp30) REVERT: A 530 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: B 35 TRP cc_start: 0.8619 (m100) cc_final: 0.8249 (t-100) REVERT: B 48 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7457 (m) REVERT: B 117 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 216 GLU cc_start: 0.8416 (tp30) cc_final: 0.7895 (tm-30) REVERT: B 229 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8236 (mt) REVERT: B 255 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7538 (mtm110) REVERT: B 447 MET cc_start: 0.6297 (tpp) cc_final: 0.5750 (tpp) REVERT: B 571 MET cc_start: 0.4664 (OUTLIER) cc_final: 0.3243 (ptm) REVERT: C 15 TRP cc_start: 0.6091 (m-10) cc_final: 0.5225 (m100) REVERT: C 34 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7443 (mtp-110) REVERT: C 101 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: C 277 ARG cc_start: 0.8955 (tmm160) cc_final: 0.8655 (tmm-80) REVERT: C 322 SER cc_start: 0.9381 (m) cc_final: 0.9159 (t) REVERT: C 366 ASP cc_start: 0.7972 (p0) cc_final: 0.7254 (p0) REVERT: C 375 MET cc_start: 0.8088 (mmm) cc_final: 0.7772 (mmm) REVERT: C 426 TYR cc_start: 0.7535 (t80) cc_final: 0.7244 (t80) REVERT: C 427 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7150 (mpt) outliers start: 81 outliers final: 33 residues processed: 178 average time/residue: 0.3762 time to fit residues: 75.4383 Evaluate side-chains 146 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 513 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 54 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 HIS ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.179575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106180 restraints weight = 16754.202| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.67 r_work: 0.3271 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12992 Z= 0.119 Angle : 0.603 14.279 17617 Z= 0.282 Chirality : 0.040 0.323 2016 Planarity : 0.003 0.046 2169 Dihedral : 5.183 58.804 1748 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.18 % Rotamer: Outliers : 3.73 % Allowed : 24.26 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.11 (0.22), residues: 1546 helix: 2.30 (0.16), residues: 1097 sheet: -0.66 (0.76), residues: 58 loop : -0.94 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.014 0.001 TYR B 130 PHE 0.015 0.001 PHE A 55 TRP 0.019 0.001 TRP B 184 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (12991) covalent geometry : angle 0.60338 / 0.28 (17615) SS BOND : bond 0.00204 / 0.11 ( 1) SS BOND : angle 0.61936 / 0.34 ( 2) hydrogen bonds : bond 0.04451 / 2.91 ( 842) hydrogen bonds : angle 3.80233 / 2.66 ( 2490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6303 (ttm170) REVERT: A 353 ASP cc_start: 0.8943 (t0) cc_final: 0.8633 (t0) REVERT: A 391 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8482 (ttm-80) REVERT: A 472 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 479 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7398 (ptmt) REVERT: A 491 GLU cc_start: 0.8464 (tt0) cc_final: 0.8146 (tp30) REVERT: A 518 TRP cc_start: 0.7665 (m-10) cc_final: 0.7418 (m-10) REVERT: B 35 TRP cc_start: 0.8517 (m100) cc_final: 0.8135 (t-100) REVERT: B 117 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6896 (tm-30) REVERT: B 216 GLU cc_start: 0.8152 (tp30) cc_final: 0.7688 (tm-30) REVERT: B 229 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7645 (mt) REVERT: B 250 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: B 255 ARG cc_start: 0.7360 (tpp-160) cc_final: 0.7001 (mtm110) REVERT: B 447 MET cc_start: 0.6323 (tpp) cc_final: 0.5651 (tpp) REVERT: B 571 MET cc_start: 0.4594 (OUTLIER) cc_final: 0.2750 (ptm) REVERT: C 15 TRP cc_start: 0.6068 (m-10) cc_final: 0.5228 (m100) REVERT: C 34 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7347 (mtp-110) REVERT: C 101 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: C 277 ARG cc_start: 0.8941 (tmm160) cc_final: 0.8647 (tmm-80) REVERT: C 366 ASP cc_start: 0.8026 (p0) cc_final: 0.7275 (p0) REVERT: C 375 MET cc_start: 0.7836 (mmm) cc_final: 0.7462 (mmm) REVERT: C 426 TYR cc_start: 0.7093 (t80) cc_final: 0.6653 (t80) REVERT: C 427 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6852 (mpt) outliers start: 52 outliers final: 22 residues processed: 145 average time/residue: 0.3931 time to fit residues: 63.8167 Evaluate side-chains 128 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 513 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 232 ASN ** C 350 ASN ** 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 = 0.4282 r_free = 0.4282 target = 0.176491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102499 restraints weight = 16934.866| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.66 r_work: 0.3223 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12992 Z= 0.193 Angle : 0.643 13.056 17617 Z= 0.306 Chirality : 0.043 0.374 2016 Planarity : 0.004 0.047 2169 Dihedral : 5.280 59.379 1748 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 4.02 % Allowed : 24.55 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.91 (0.22), residues: 1546 helix: 2.19 (0.16), residues: 1105 sheet: -0.72 (0.75), residues: 58 loop : -1.23 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.016 0.001 TYR A 123 PHE 0.028 0.001 PHE B 573 TRP 0.022 0.001 TRP B 184 HIS 0.004 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (12991) covalent geometry : angle 0.64271 / 0.31 (17615) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 0.59378 / 0.33 ( 2) hydrogen bonds : bond 0.04990 / 3.28 ( 842) hydrogen bonds : angle 3.95434 / 2.78 ( 2490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 353 ASP cc_start: 0.8894 (t0) cc_final: 0.8639 (t0) REVERT: A 391 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8486 (ttm-80) REVERT: A 472 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 482 TYR cc_start: 0.7649 (t80) cc_final: 0.7320 (t80) REVERT: A 491 GLU cc_start: 0.8487 (tt0) cc_final: 0.8164 (tp30) REVERT: A 530 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: B 35 TRP cc_start: 0.8525 (m100) cc_final: 0.8149 (t-100) REVERT: B 117 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6926 (tm-30) REVERT: B 216 GLU cc_start: 0.8147 (tp30) cc_final: 0.7648 (tm-30) REVERT: B 229 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7718 (mt) REVERT: B 247 MET cc_start: 0.7450 (mmt) cc_final: 0.6726 (ttt) REVERT: B 255 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7053 (mtm110) REVERT: B 447 MET cc_start: 0.6428 (tpp) cc_final: 0.5747 (tpp) REVERT: B 571 MET cc_start: 0.4344 (OUTLIER) cc_final: 0.2897 (ptm) REVERT: C 15 TRP cc_start: 0.6060 (m-10) cc_final: 0.5214 (m100) REVERT: C 34 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7371 (mtp-110) REVERT: C 101 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: C 277 ARG cc_start: 0.8937 (tmm160) cc_final: 0.8611 (ptp-110) REVERT: C 322 SER cc_start: 0.9280 (m) cc_final: 0.9036 (t) REVERT: C 366 ASP cc_start: 0.8020 (p0) cc_final: 0.7287 (p0) REVERT: C 375 MET cc_start: 0.7823 (mmm) cc_final: 0.7442 (mmm) REVERT: C 426 TYR cc_start: 0.7200 (t80) cc_final: 0.6766 (t80) REVERT: C 427 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6846 (mpt) outliers start: 56 outliers final: 29 residues processed: 152 average time/residue: 0.4106 time to fit residues: 69.6463 Evaluate side-chains 136 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 513 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN ** C 350 ASN ** 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 = 0.4300 r_free = 0.4300 target = 0.178225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107159 restraints weight = 16741.522| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.26 r_work: 0.3229 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12992 Z= 0.129 Angle : 0.631 12.697 17617 Z= 0.293 Chirality : 0.041 0.410 2016 Planarity : 0.004 0.045 2169 Dihedral : 5.199 59.899 1748 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 3.30 % Allowed : 25.48 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.25 (0.22), residues: 1546 helix: 2.43 (0.15), residues: 1093 sheet: -0.70 (0.76), residues: 58 loop : -0.92 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 136 TYR 0.018 0.001 TYR B 130 PHE 0.018 0.001 PHE A 55 TRP 0.028 0.001 TRP B 184 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12991) covalent geometry : angle 0.63052 / 0.29 (17615) SS BOND : bond 0.00199 / 0.10 ( 1) SS BOND : angle 0.53599 / 0.29 ( 2) hydrogen bonds : bond 0.04442 / 2.92 ( 842) hydrogen bonds : angle 3.82017 / 2.68 ( 2490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.5983 (ttm170) REVERT: A 353 ASP cc_start: 0.8837 (t0) cc_final: 0.8558 (t0) REVERT: A 391 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8434 (ttm-80) REVERT: A 472 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 491 GLU cc_start: 0.8378 (tt0) cc_final: 0.8064 (tp30) REVERT: A 518 TRP cc_start: 0.7610 (m-10) cc_final: 0.7332 (m-10) REVERT: A 530 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6815 (mm-40) REVERT: A 601 MET cc_start: 0.8817 (mmm) cc_final: 0.8454 (tpp) REVERT: B 35 TRP cc_start: 0.8430 (m100) cc_final: 0.8097 (t-100) REVERT: B 117 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6625 (tm-30) REVERT: B 216 GLU cc_start: 0.8066 (tp30) cc_final: 0.7552 (tm-30) REVERT: B 229 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7550 (mt) REVERT: B 247 MET cc_start: 0.7176 (mmt) cc_final: 0.6551 (ttt) REVERT: B 255 ARG cc_start: 0.7199 (tpp-160) cc_final: 0.6883 (mtm110) REVERT: B 447 MET cc_start: 0.6419 (tpp) cc_final: 0.5739 (tpp) REVERT: C 15 TRP cc_start: 0.6074 (m-10) cc_final: 0.5236 (m100) REVERT: C 34 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7318 (mtp-110) REVERT: C 101 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: C 277 ARG cc_start: 0.8939 (tmm160) cc_final: 0.8618 (ptp-110) REVERT: C 314 LEU cc_start: 0.8670 (mm) cc_final: 0.8396 (tm) REVERT: C 322 SER cc_start: 0.9280 (m) cc_final: 0.8995 (t) REVERT: C 366 ASP cc_start: 0.8018 (p0) cc_final: 0.7279 (p0) REVERT: C 375 MET cc_start: 0.7721 (mmm) cc_final: 0.7321 (mmm) REVERT: C 426 TYR cc_start: 0.6945 (t80) cc_final: 0.6493 (t80) REVERT: C 427 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6583 (mpt) outliers start: 46 outliers final: 27 residues processed: 149 average time/residue: 0.4521 time to fit residues: 74.9749 Evaluate side-chains 136 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 422 ASN ** C 350 ASN ** 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 = 0.4308 r_free = 0.4308 target = 0.179167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.105547 restraints weight = 16891.099| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.67 r_work: 0.3266 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12992 Z= 0.131 Angle : 0.629 13.403 17617 Z= 0.292 Chirality : 0.042 0.441 2016 Planarity : 0.003 0.042 2169 Dihedral : 5.025 58.548 1745 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 3.02 % Allowed : 26.06 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.35 (0.22), residues: 1546 helix: 2.50 (0.15), residues: 1092 sheet: 0.76 (0.88), residues: 38 loop : -1.04 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.018 0.001 TYR B 271 PHE 0.019 0.001 PHE A 55 TRP 0.031 0.001 TRP B 184 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (12991) covalent geometry : angle 0.62939 / 0.29 (17615) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 0.48779 / 0.27 ( 2) hydrogen bonds : bond 0.04371 / 2.87 ( 842) hydrogen bonds : angle 3.79161 / 2.65 ( 2490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6163 (ttm170) REVERT: A 353 ASP cc_start: 0.8851 (t0) cc_final: 0.8592 (t0) REVERT: A 391 ARG cc_start: 0.8906 (mmm-85) cc_final: 0.8446 (ttm-80) REVERT: A 472 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 491 GLU cc_start: 0.8479 (tt0) cc_final: 0.8152 (tp30) REVERT: A 518 TRP cc_start: 0.7656 (m-10) cc_final: 0.7321 (m-10) REVERT: A 530 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: A 601 MET cc_start: 0.8842 (mmm) cc_final: 0.8486 (tpp) REVERT: B 35 TRP cc_start: 0.8489 (m100) cc_final: 0.8150 (t-100) REVERT: B 117 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6870 (tm-30) REVERT: B 216 GLU cc_start: 0.8163 (tp30) cc_final: 0.7633 (tm-30) REVERT: B 226 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.7739 (m-70) REVERT: B 229 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7653 (mt) REVERT: B 247 MET cc_start: 0.7461 (mmt) cc_final: 0.6764 (ttt) REVERT: B 255 ARG cc_start: 0.7430 (tpp-160) cc_final: 0.7072 (mtm110) REVERT: B 447 MET cc_start: 0.6390 (tpp) cc_final: 0.5700 (tpp) REVERT: B 571 MET cc_start: 0.4276 (pp-130) cc_final: 0.2635 (ptm) REVERT: C 15 TRP cc_start: 0.6068 (m-10) cc_final: 0.5218 (m100) REVERT: C 34 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7339 (mtp-110) REVERT: C 101 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: C 277 ARG cc_start: 0.8961 (tmm160) cc_final: 0.8628 (ptp-110) REVERT: C 322 SER cc_start: 0.9278 (m) cc_final: 0.8991 (t) REVERT: C 366 ASP cc_start: 0.8022 (p0) cc_final: 0.7289 (p0) REVERT: C 375 MET cc_start: 0.7799 (mmm) cc_final: 0.7435 (mmm) REVERT: C 426 TYR cc_start: 0.7200 (t80) cc_final: 0.6751 (t80) REVERT: C 427 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6897 (mpt) outliers start: 42 outliers final: 28 residues processed: 145 average time/residue: 0.4770 time to fit residues: 77.1040 Evaluate side-chains 139 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 513 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 114 optimal weight: 0.0370 chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 243 HIS A 422 ASN ** C 350 ASN ** 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 = 0.4320 r_free = 0.4320 target = 0.180270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109734 restraints weight = 16826.069| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.33 r_work: 0.3269 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12992 Z= 0.115 Angle : 0.638 14.257 17617 Z= 0.291 Chirality : 0.041 0.471 2016 Planarity : 0.003 0.041 2169 Dihedral : 4.885 57.391 1745 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 2.44 % Allowed : 26.78 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.51 (0.22), residues: 1546 helix: 2.62 (0.15), residues: 1093 sheet: 0.86 (0.89), residues: 38 loop : -1.00 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 136 TYR 0.019 0.001 TYR B 130 PHE 0.020 0.001 PHE A 55 TRP 0.038 0.001 TRP B 184 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12991) covalent geometry : angle 0.63756 / 0.29 (17615) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 0.39412 / 0.21 ( 2) hydrogen bonds : bond 0.04018 / 2.63 ( 842) hydrogen bonds : angle 3.69954 / 2.58 ( 2490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8040 (p0) cc_final: 0.7591 (p0) REVERT: A 112 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.5876 (ttm170) REVERT: A 278 ASP cc_start: 0.8482 (t0) cc_final: 0.8240 (t0) REVERT: A 353 ASP cc_start: 0.8748 (t0) cc_final: 0.8497 (t0) REVERT: A 391 ARG cc_start: 0.8847 (mmm-85) cc_final: 0.8403 (ttm-80) REVERT: A 472 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6757 (mt-10) REVERT: A 491 GLU cc_start: 0.8377 (tt0) cc_final: 0.8050 (tp30) REVERT: A 518 TRP cc_start: 0.7382 (m-10) cc_final: 0.6827 (m-10) REVERT: A 530 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6023 (mt0) REVERT: A 601 MET cc_start: 0.8772 (mmm) cc_final: 0.8421 (tpp) REVERT: B 35 TRP cc_start: 0.8396 (m100) cc_final: 0.8084 (t-100) REVERT: B 117 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6550 (tm-30) REVERT: B 216 GLU cc_start: 0.8088 (tp30) cc_final: 0.7563 (tm-30) REVERT: B 226 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.7572 (m-70) REVERT: B 229 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7434 (mt) REVERT: B 247 MET cc_start: 0.7223 (mmt) cc_final: 0.6577 (ttt) REVERT: B 255 ARG cc_start: 0.7171 (tpp-160) cc_final: 0.6852 (mtm110) REVERT: B 447 MET cc_start: 0.6318 (tpp) cc_final: 0.5603 (tpp) REVERT: B 571 MET cc_start: 0.4407 (pp-130) cc_final: 0.2785 (ptm) REVERT: C 15 TRP cc_start: 0.6078 (m-10) cc_final: 0.5240 (m100) REVERT: C 114 PHE cc_start: 0.8211 (t80) cc_final: 0.7332 (m-10) REVERT: C 277 ARG cc_start: 0.8932 (tmm160) cc_final: 0.8612 (ptp-110) REVERT: C 314 LEU cc_start: 0.8662 (mm) cc_final: 0.8446 (tp) REVERT: C 322 SER cc_start: 0.9258 (m) cc_final: 0.8987 (t) REVERT: C 366 ASP cc_start: 0.8016 (p0) cc_final: 0.7215 (p0) REVERT: C 375 MET cc_start: 0.7675 (mmm) cc_final: 0.7295 (mmm) REVERT: C 426 TYR cc_start: 0.6967 (t80) cc_final: 0.6519 (t80) REVERT: C 427 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6661 (mpt) outliers start: 34 outliers final: 23 residues processed: 138 average time/residue: 0.4487 time to fit residues: 69.1790 Evaluate side-chains 134 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 513 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 243 HIS A 260 GLN A 422 ASN A 446 GLN B 415 GLN ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.179913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108919 restraints weight = 16704.703| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.24 r_work: 0.3260 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12992 Z= 0.120 Angle : 0.636 15.599 17617 Z= 0.291 Chirality : 0.041 0.450 2016 Planarity : 0.003 0.040 2169 Dihedral : 4.856 57.276 1745 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 2.37 % Allowed : 26.78 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.53 (0.22), residues: 1546 helix: 2.63 (0.15), residues: 1093 sheet: 0.98 (0.90), residues: 38 loop : -1.00 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 597 TYR 0.020 0.001 TYR B 130 PHE 0.020 0.001 PHE A 55 TRP 0.040 0.001 TRP B 184 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12991) covalent geometry : angle 0.63614 / 0.29 (17615) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 0.40761 / 0.22 ( 2) hydrogen bonds : bond 0.04065 / 2.67 ( 842) hydrogen bonds : angle 3.69869 / 2.58 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.48 seconds wall clock time: 79 minutes 4.60 seconds (4744.60 seconds total)