Starting phenix.real_space_refine on Sun Aug 24 20:12:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fth_50745/08_2025/9fth_50745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fth_50745/08_2025/9fth_50745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fth_50745/08_2025/9fth_50745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fth_50745/08_2025/9fth_50745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fth_50745/08_2025/9fth_50745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fth_50745/08_2025/9fth_50745.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 14675 2.51 5 N 3795 2.21 5 O 4265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22780 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4556 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 573} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 3, 'GLN:plan1': 4, 'ASP:plan': 5, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 134 Restraints were copied for chains: A, C, D, E Time building chain proxies: 3.60, per 1000 atoms: 0.16 Number of scatterers: 22780 At special positions: 0 Unit cell: (137.01, 133.563, 156.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 4265 8.00 N 3795 7.00 C 14675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS D 371 " - pdb=" SG CYS D 373 " distance=2.03 Simple disulfide: pdb=" SG CYS E 371 " - pdb=" SG CYS E 373 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 30 sheets defined 26.6% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 88 through 98 removed outlier: 3.575A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 118 removed outlier: 4.272A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 4.472A pdb=" N THR B 317 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.805A pdb=" N CYS B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.902A pdb=" N ALA B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 522 through 537 removed outlier: 3.615A pdb=" N PHE B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 565 removed outlier: 4.002A pdb=" N GLU B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.512A pdb=" N ALA B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 636 removed outlier: 3.893A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Proline residue: B 621 - end of helix removed outlier: 3.822A pdb=" N TYR B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.575A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 removed outlier: 4.272A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 4.472A pdb=" N THR A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.805A pdb=" N CYS A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.903A pdb=" N ALA A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.615A pdb=" N PHE A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 565 removed outlier: 4.003A pdb=" N GLU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.512A pdb=" N ALA A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 removed outlier: 3.893A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix removed outlier: 3.823A pdb=" N TYR A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 98 removed outlier: 3.575A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 118 removed outlier: 4.272A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 4.472A pdb=" N THR C 317 " --> pdb=" O SER C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.805A pdb=" N CYS C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 391 removed outlier: 3.902A pdb=" N ALA C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 522 Processing helix chain 'C' and resid 522 through 537 removed outlier: 3.615A pdb=" N PHE C 537 " --> pdb=" O SER C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 565 removed outlier: 4.003A pdb=" N GLU C 547 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.512A pdb=" N ALA C 588 " --> pdb=" O PHE C 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 636 removed outlier: 3.893A pdb=" N VAL C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 3.822A pdb=" N TYR C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.576A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 118 removed outlier: 4.272A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 removed outlier: 4.471A pdb=" N THR D 317 " --> pdb=" O SER D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.805A pdb=" N CYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 391 removed outlier: 3.901A pdb=" N ALA D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 522 through 537 removed outlier: 3.615A pdb=" N PHE D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 removed outlier: 4.002A pdb=" N GLU D 547 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.513A pdb=" N ALA D 588 " --> pdb=" O PHE D 584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 removed outlier: 3.892A pdb=" N VAL D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Proline residue: D 621 - end of helix removed outlier: 3.822A pdb=" N TYR D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 removed outlier: 3.576A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 118 removed outlier: 4.272A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 4.471A pdb=" N THR E 317 " --> pdb=" O SER E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.805A pdb=" N CYS E 371 " --> pdb=" O SER E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 391 removed outlier: 3.902A pdb=" N ALA E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 522 Processing helix chain 'E' and resid 522 through 537 removed outlier: 3.616A pdb=" N PHE E 537 " --> pdb=" O SER E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 565 removed outlier: 4.003A pdb=" N GLU E 547 " --> pdb=" O GLY E 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 564 " --> pdb=" O ASN E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.513A pdb=" N ALA E 588 " --> pdb=" O PHE E 584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 590 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 removed outlier: 3.892A pdb=" N VAL E 618 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR E 620 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Proline residue: E 621 - end of helix removed outlier: 3.822A pdb=" N TYR E 624 " --> pdb=" O TYR E 620 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 135 removed outlier: 6.501A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 168 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 43 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 58 removed outlier: 4.231A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 212 removed outlier: 3.746A pdb=" N ILE B 210 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 303 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.362A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 379 removed outlier: 5.691A pdb=" N SER B 408 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR B 428 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP B 359 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN B 348 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY B 341 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER B 350 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE B 339 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS B 360 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU B 329 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL B 332 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE B 466 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LEU B 334 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.430A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 486 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 135 removed outlier: 6.502A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 168 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 43 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 51 through 58 removed outlier: 4.232A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 212 removed outlier: 3.745A pdb=" N ILE A 210 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 303 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.361A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 376 through 379 removed outlier: 5.692A pdb=" N SER A 408 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR A 428 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 359 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN A 348 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY A 341 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 350 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE A 339 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS A 360 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU A 329 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 332 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 466 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N LEU A 334 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.430A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 486 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 135 removed outlier: 6.502A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 168 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY C 43 " --> pdb=" O PHE C 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 51 through 58 removed outlier: 4.231A pdb=" N ASP C 57 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY C 141 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY C 120 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 205 through 212 removed outlier: 3.745A pdb=" N ILE C 210 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA C 298 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 303 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.362A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 5.692A pdb=" N SER C 408 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR C 428 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP C 359 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL C 332 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE C 466 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N LEU C 334 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.431A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 486 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 132 through 135 removed outlier: 6.502A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 168 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY D 43 " --> pdb=" O PHE D 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 51 through 58 removed outlier: 4.231A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 205 through 212 removed outlier: 3.746A pdb=" N ILE D 210 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 303 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 218 through 222 removed outlier: 7.362A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 376 through 379 removed outlier: 5.691A pdb=" N SER D 408 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR D 428 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP D 359 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN D 348 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY D 341 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER D 350 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE D 339 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS D 360 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU D 329 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL D 332 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE D 466 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N LEU D 334 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.431A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 486 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.502A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 168 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY E 43 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 51 through 58 removed outlier: 4.231A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 205 through 212 removed outlier: 3.745A pdb=" N ILE E 210 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 303 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.362A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 376 through 379 removed outlier: 5.691A pdb=" N SER E 408 " --> pdb=" O THR E 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR E 428 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP E 359 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN E 348 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY E 341 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER E 350 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE E 339 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N HIS E 360 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU E 329 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL E 332 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE E 466 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N LEU E 334 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.431A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E 486 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 3060 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: 3.78 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7480 1.35 - 1.46: 5551 1.46 - 1.58: 10209 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 23300 Sorted by residual: bond pdb=" CB GLN A 370 " pdb=" CG GLN A 370 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CB GLN C 370 " pdb=" CG GLN C 370 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.22e+00 bond pdb=" CB GLN E 370 " pdb=" CG GLN E 370 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CB GLN D 370 " pdb=" CG GLN D 370 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLN B 370 " pdb=" CG GLN B 370 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 ... (remaining 23295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 31545 2.06 - 4.12: 225 4.12 - 6.18: 25 6.18 - 8.23: 5 8.23 - 10.29: 10 Bond angle restraints: 31810 Sorted by residual: angle pdb=" CA GLN D 370 " pdb=" CB GLN D 370 " pdb=" CG GLN D 370 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA GLN B 370 " pdb=" CB GLN B 370 " pdb=" CG GLN B 370 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA GLN A 370 " pdb=" CB GLN A 370 " pdb=" CG GLN A 370 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CA GLN C 370 " pdb=" CB GLN C 370 " pdb=" CG GLN C 370 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CA GLN E 370 " pdb=" CB GLN E 370 " pdb=" CG GLN E 370 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 ... (remaining 31805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 11947 17.63 - 35.26: 1288 35.26 - 52.89: 345 52.89 - 70.52: 55 70.52 - 88.14: 20 Dihedral angle restraints: 13655 sinusoidal: 5020 harmonic: 8635 Sorted by residual: dihedral pdb=" CB CYS E 371 " pdb=" SG CYS E 371 " pdb=" SG CYS E 373 " pdb=" CB CYS E 373 " ideal model delta sinusoidal sigma weight residual 93.00 124.46 -31.46 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CB CYS D 371 " pdb=" SG CYS D 371 " pdb=" SG CYS D 373 " pdb=" CB CYS D 373 " ideal model delta sinusoidal sigma weight residual 93.00 124.45 -31.45 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CB CYS B 371 " pdb=" SG CYS B 371 " pdb=" SG CYS B 373 " pdb=" CB CYS B 373 " ideal model delta sinusoidal sigma weight residual 93.00 124.44 -31.44 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 13652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2287 0.026 - 0.052: 743 0.052 - 0.077: 345 0.077 - 0.103: 178 0.103 - 0.129: 132 Chirality restraints: 3685 Sorted by residual: chirality pdb=" CA PRO C 417 " pdb=" N PRO C 417 " pdb=" C PRO C 417 " pdb=" CB PRO C 417 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE C 279 " pdb=" N ILE C 279 " pdb=" C ILE C 279 " pdb=" CB ILE C 279 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA PRO B 417 " pdb=" N PRO B 417 " pdb=" C PRO B 417 " pdb=" CB PRO B 417 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 3682 not shown) Planarity restraints: 4135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 281 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" CD GLU B 281 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU B 281 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 281 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 281 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" CD GLU E 281 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU E 281 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU E 281 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 281 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU C 281 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU C 281 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU C 281 " 0.010 2.00e-02 2.50e+03 ... (remaining 4132 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5985 2.80 - 3.33: 18744 3.33 - 3.85: 34774 3.85 - 4.38: 37929 4.38 - 4.90: 70538 Nonbonded interactions: 167970 Sorted by model distance: nonbonded pdb=" O PRO A 243 " pdb=" OH TYR A 300 " model vdw 2.280 3.040 nonbonded pdb=" O PRO C 243 " pdb=" OH TYR C 300 " model vdw 2.281 3.040 nonbonded pdb=" O PRO D 243 " pdb=" OH TYR D 300 " model vdw 2.281 3.040 nonbonded pdb=" O PRO B 243 " pdb=" OH TYR B 300 " model vdw 2.281 3.040 nonbonded pdb=" O PRO E 243 " pdb=" OH TYR E 300 " model vdw 2.281 3.040 ... (remaining 167965 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.800 Find NCS groups from input model: 0.260 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 0.045 23310 Z= 0.083 Angle : 0.462 10.294 31830 Z= 0.228 Chirality : 0.040 0.129 3685 Planarity : 0.003 0.036 4135 Dihedral : 15.685 88.144 8095 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 26.27 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 3000 helix: 1.62 (0.19), residues: 710 sheet: 1.02 (0.17), residues: 995 loop : -0.82 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 521 TYR 0.006 0.000 TYR A 441 PHE 0.003 0.000 PHE D 443 TRP 0.004 0.000 TRP E 359 HIS 0.002 0.000 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00194 (23300) covalent geometry : angle 0.46193 (31810) SS BOND : bond 0.00148 ( 10) SS BOND : angle 0.36216 ( 20) hydrogen bonds : bond 0.29889 ( 1085) hydrogen bonds : angle 8.12127 ( 3060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.814 Fit side-chains REVERT: B 160 GLN cc_start: 0.8891 (tt0) cc_final: 0.8664 (tp40) REVERT: D 390 ILE cc_start: 0.7436 (pt) cc_final: 0.7162 (pt) REVERT: D 460 MET cc_start: 0.8825 (mtm) cc_final: 0.8590 (mtm) outliers start: 0 outliers final: 3 residues processed: 152 average time/residue: 0.3656 time to fit residues: 67.9299 Evaluate side-chains 137 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain E residue 370 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 69 GLN B 307 ASN B 391 ASN B 471 GLN A 40 HIS A 69 GLN A 307 ASN A 471 GLN C 40 HIS C 69 GLN C 307 ASN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 69 GLN D 307 ASN ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN E 40 HIS E 69 GLN E 160 GLN E 307 ASN E 391 ASN E 471 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.133111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083960 restraints weight = 40038.915| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.63 r_work: 0.3034 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23310 Z= 0.179 Angle : 0.582 9.908 31830 Z= 0.305 Chirality : 0.043 0.149 3685 Planarity : 0.004 0.038 4135 Dihedral : 3.965 24.451 3239 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.92 % Allowed : 23.39 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.15), residues: 3000 helix: 2.18 (0.19), residues: 740 sheet: 0.89 (0.16), residues: 1020 loop : -0.95 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 301 TYR 0.015 0.001 TYR E 441 PHE 0.012 0.001 PHE E 584 TRP 0.009 0.001 TRP C 359 HIS 0.003 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00420 (23300) covalent geometry : angle 0.58173 (31810) SS BOND : bond 0.00279 ( 10) SS BOND : angle 0.55937 ( 20) hydrogen bonds : bond 0.05529 ( 1085) hydrogen bonds : angle 5.20105 ( 3060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 301 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6842 (mmm160) REVERT: B 374 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8327 (t) REVERT: B 379 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 118 PHE cc_start: 0.7922 (m-10) cc_final: 0.7459 (m-80) REVERT: A 281 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 374 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8408 (t) REVERT: C 374 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8313 (t) REVERT: C 379 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: D 379 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: E 118 PHE cc_start: 0.7762 (m-10) cc_final: 0.7259 (m-80) REVERT: E 281 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6817 (tm-30) REVERT: E 301 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7228 (ttt-90) REVERT: E 357 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8869 (mp) REVERT: E 379 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: E 431 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9054 (mt) outliers start: 69 outliers final: 17 residues processed: 187 average time/residue: 0.3876 time to fit residues: 87.8364 Evaluate side-chains 148 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 171 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 298 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 40.0000 chunk 237 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 391 ASN A 160 GLN C 40 HIS C 160 GLN C 370 GLN D 370 GLN E 40 HIS E 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085491 restraints weight = 39649.434| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.64 r_work: 0.3050 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23310 Z= 0.125 Angle : 0.519 9.205 31830 Z= 0.268 Chirality : 0.042 0.136 3685 Planarity : 0.003 0.039 4135 Dihedral : 3.729 13.637 3230 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.37 % Allowed : 24.28 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.15), residues: 3000 helix: 2.39 (0.19), residues: 740 sheet: 0.85 (0.16), residues: 1010 loop : -1.04 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 498 TYR 0.012 0.001 TYR C 441 PHE 0.025 0.001 PHE C 146 TRP 0.009 0.001 TRP D 359 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00292 (23300) covalent geometry : angle 0.51886 (31810) SS BOND : bond 0.00191 ( 10) SS BOND : angle 0.41385 ( 20) hydrogen bonds : bond 0.04683 ( 1085) hydrogen bonds : angle 4.64104 ( 3060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: B 118 PHE cc_start: 0.7907 (m-10) cc_final: 0.7463 (m-80) REVERT: B 281 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6788 (tm-30) REVERT: B 301 ARG cc_start: 0.7194 (ttp-110) cc_final: 0.6979 (ptm160) REVERT: B 374 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8389 (t) REVERT: B 379 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: B 390 ILE cc_start: 0.7581 (pt) cc_final: 0.7380 (pt) REVERT: A 118 PHE cc_start: 0.7888 (m-10) cc_final: 0.7446 (m-80) REVERT: A 281 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6942 (tm-30) REVERT: C 118 PHE cc_start: 0.7946 (m-10) cc_final: 0.7426 (m-80) REVERT: C 301 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7163 (tpp80) REVERT: C 374 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8393 (t) REVERT: C 379 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: D 301 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6815 (ttt-90) REVERT: D 379 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: E 118 PHE cc_start: 0.7810 (m-10) cc_final: 0.7402 (m-80) REVERT: E 301 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6890 (ptp-110) REVERT: E 431 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9041 (mt) outliers start: 56 outliers final: 16 residues processed: 195 average time/residue: 0.3932 time to fit residues: 92.5674 Evaluate side-chains 141 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 587 THR Chi-restraints excluded: chain E residue 600 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 96 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 138 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 144 HIS B 285 HIS B 391 ASN A 144 HIS A 160 GLN C 144 HIS C 285 HIS D 144 HIS E 144 HIS E 160 GLN E 285 HIS E 391 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.128851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079950 restraints weight = 40261.454| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.62 r_work: 0.2959 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 23310 Z= 0.310 Angle : 0.674 10.129 31830 Z= 0.357 Chirality : 0.047 0.160 3685 Planarity : 0.004 0.048 4135 Dihedral : 4.564 15.994 3230 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.31 % Allowed : 24.32 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3000 helix: 1.88 (0.19), residues: 745 sheet: 0.66 (0.16), residues: 990 loop : -1.30 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 513 TYR 0.019 0.002 TYR E 441 PHE 0.019 0.002 PHE C 146 TRP 0.012 0.001 TRP B 359 HIS 0.005 0.002 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00764 (23300) covalent geometry : angle 0.67408 (31810) SS BOND : bond 0.00590 ( 10) SS BOND : angle 0.84330 ( 20) hydrogen bonds : bond 0.06480 ( 1085) hydrogen bonds : angle 5.03231 ( 3060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 108 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7208 (ttp-110) cc_final: 0.6974 (ptm160) REVERT: B 379 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: A 118 PHE cc_start: 0.8067 (m-10) cc_final: 0.7788 (m-80) REVERT: C 118 PHE cc_start: 0.8201 (m-10) cc_final: 0.7743 (m-80) REVERT: C 119 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8118 (tp) REVERT: C 301 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7221 (tpp80) REVERT: C 379 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: D 379 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: E 119 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8368 (tp) REVERT: E 301 ARG cc_start: 0.7426 (ttp-110) cc_final: 0.6825 (ptp-110) REVERT: E 329 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8794 (mt) REVERT: E 431 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9040 (mt) outliers start: 78 outliers final: 27 residues processed: 177 average time/residue: 0.3826 time to fit residues: 82.7923 Evaluate side-chains 132 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 587 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 282 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN C 40 HIS C 285 HIS E 40 HIS E 160 GLN E 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.130844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082036 restraints weight = 39792.692| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.62 r_work: 0.2995 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23310 Z= 0.178 Angle : 0.577 9.753 31830 Z= 0.302 Chirality : 0.043 0.137 3685 Planarity : 0.004 0.047 4135 Dihedral : 4.265 13.488 3230 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.29 % Allowed : 25.42 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3000 helix: 2.10 (0.19), residues: 740 sheet: 0.59 (0.16), residues: 1000 loop : -1.17 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 301 TYR 0.015 0.001 TYR C 441 PHE 0.017 0.001 PHE C 146 TRP 0.011 0.001 TRP C 359 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00429 (23300) covalent geometry : angle 0.57695 (31810) SS BOND : bond 0.00326 ( 10) SS BOND : angle 0.57830 ( 20) hydrogen bonds : bond 0.05014 ( 1085) hydrogen bonds : angle 4.70807 ( 3060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 PHE cc_start: 0.6413 (m-80) cc_final: 0.6191 (m-10) REVERT: B 301 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.7016 (ptm160) REVERT: B 379 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: A 118 PHE cc_start: 0.8130 (m-10) cc_final: 0.7837 (m-80) REVERT: A 329 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 118 PHE cc_start: 0.8069 (m-10) cc_final: 0.7636 (m-80) REVERT: C 301 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7175 (tpp80) REVERT: C 379 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: D 379 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: E 119 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8379 (tp) REVERT: E 301 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.6983 (tpp80) REVERT: E 329 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8729 (mt) REVERT: E 431 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9028 (mt) REVERT: E 592 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9033 (tt) outliers start: 54 outliers final: 30 residues processed: 166 average time/residue: 0.3430 time to fit residues: 69.4446 Evaluate side-chains 144 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 600 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 266 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 391 ASN A 160 GLN C 285 HIS E 160 GLN E 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080580 restraints weight = 39999.356| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.61 r_work: 0.2975 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 23310 Z= 0.239 Angle : 0.623 9.927 31830 Z= 0.326 Chirality : 0.045 0.182 3685 Planarity : 0.004 0.046 4135 Dihedral : 4.507 16.187 3230 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.35 % Allowed : 24.70 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3000 helix: 1.96 (0.19), residues: 740 sheet: 0.56 (0.16), residues: 1000 loop : -1.26 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.017 0.002 TYR D 441 PHE 0.016 0.002 PHE C 146 TRP 0.011 0.001 TRP B 359 HIS 0.005 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00584 (23300) covalent geometry : angle 0.62314 (31810) SS BOND : bond 0.00419 ( 10) SS BOND : angle 0.76387 ( 20) hydrogen bonds : bond 0.05681 ( 1085) hydrogen bonds : angle 4.81046 ( 3060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 113 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.7032 (ptm160) REVERT: B 379 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: A 118 PHE cc_start: 0.8224 (m-10) cc_final: 0.7922 (m-80) REVERT: A 139 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6341 (mpp80) REVERT: A 281 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 329 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8732 (mt) REVERT: C 118 PHE cc_start: 0.8126 (m-10) cc_final: 0.7757 (m-80) REVERT: C 139 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6093 (tpp80) REVERT: C 301 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7210 (tpp80) REVERT: C 379 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: D 379 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: E 139 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6181 (mpp80) REVERT: E 301 ARG cc_start: 0.7378 (ttp-110) cc_final: 0.6811 (ptp-110) REVERT: E 329 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8777 (mt) REVERT: E 357 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8861 (mp) REVERT: E 379 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: E 431 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9023 (mt) outliers start: 79 outliers final: 45 residues processed: 187 average time/residue: 0.4068 time to fit residues: 92.4608 Evaluate side-chains 156 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 587 THR Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 105 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 287 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS A 160 GLN C 40 HIS C 285 HIS E 40 HIS E 160 GLN E 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.132127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083361 restraints weight = 39900.374| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.64 r_work: 0.3024 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23310 Z= 0.127 Angle : 0.544 9.313 31830 Z= 0.281 Chirality : 0.042 0.152 3685 Planarity : 0.004 0.045 4135 Dihedral : 4.114 17.435 3230 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.99 % Allowed : 26.23 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.16), residues: 3000 helix: 2.28 (0.19), residues: 740 sheet: 0.62 (0.16), residues: 1010 loop : -1.12 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 246 TYR 0.012 0.001 TYR C 441 PHE 0.015 0.001 PHE C 146 TRP 0.011 0.001 TRP C 359 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00301 (23300) covalent geometry : angle 0.54414 (31810) SS BOND : bond 0.00302 ( 10) SS BOND : angle 0.50258 ( 20) hydrogen bonds : bond 0.04203 ( 1085) hydrogen bonds : angle 4.46771 ( 3060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6982 (ptm160) REVERT: B 302 LEU cc_start: 0.8983 (tt) cc_final: 0.8732 (tt) REVERT: B 379 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: A 118 PHE cc_start: 0.8193 (m-10) cc_final: 0.7905 (m-80) REVERT: A 329 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8784 (mt) REVERT: C 118 PHE cc_start: 0.8125 (m-10) cc_final: 0.7700 (m-80) REVERT: C 301 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7189 (tpp80) REVERT: C 379 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: D 492 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8772 (p) REVERT: E 301 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.6879 (ptp-110) REVERT: E 329 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8710 (mt) REVERT: E 431 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9017 (mt) REVERT: E 580 MET cc_start: 0.8751 (tpp) cc_final: 0.8524 (mmt) REVERT: E 592 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9011 (tt) outliers start: 47 outliers final: 29 residues processed: 168 average time/residue: 0.3997 time to fit residues: 80.8328 Evaluate side-chains 143 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 600 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 42 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 120 optimal weight: 40.0000 chunk 177 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 252 optimal weight: 0.0980 chunk 285 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 391 ASN A 160 GLN A 285 HIS C 285 HIS D 285 HIS D 402 GLN E 160 GLN E 285 HIS E 391 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.081122 restraints weight = 39480.131| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.59 r_work: 0.2984 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23310 Z= 0.214 Angle : 0.607 9.699 31830 Z= 0.317 Chirality : 0.044 0.157 3685 Planarity : 0.004 0.045 4135 Dihedral : 4.383 14.693 3230 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.97 % Allowed : 25.68 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3000 helix: 2.15 (0.19), residues: 740 sheet: 0.59 (0.16), residues: 1010 loop : -1.18 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 224 TYR 0.017 0.002 TYR D 441 PHE 0.015 0.002 PHE D 118 TRP 0.010 0.001 TRP B 359 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00525 (23300) covalent geometry : angle 0.60707 (31810) SS BOND : bond 0.00405 ( 10) SS BOND : angle 0.83356 ( 20) hydrogen bonds : bond 0.05266 ( 1085) hydrogen bonds : angle 4.66438 ( 3060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 106 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6982 (ptm160) REVERT: B 302 LEU cc_start: 0.9003 (tt) cc_final: 0.8736 (tt) REVERT: B 379 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 118 PHE cc_start: 0.8304 (m-10) cc_final: 0.7990 (m-80) REVERT: A 329 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8791 (mt) REVERT: C 118 PHE cc_start: 0.8165 (m-10) cc_final: 0.7781 (m-80) REVERT: C 301 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.7208 (tpp80) REVERT: C 379 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: E 301 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.6872 (ptp-110) REVERT: E 329 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8745 (mt) REVERT: E 379 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: E 431 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9042 (mt) REVERT: E 580 MET cc_start: 0.8802 (tpp) cc_final: 0.8535 (mmt) REVERT: E 592 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9048 (tt) outliers start: 70 outliers final: 44 residues processed: 171 average time/residue: 0.4205 time to fit residues: 88.7058 Evaluate side-chains 150 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 587 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 79 optimal weight: 5.9990 chunk 284 optimal weight: 0.0470 chunk 185 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 273 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS A 160 GLN A 285 HIS C 40 HIS C 285 HIS D 285 HIS E 160 GLN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082561 restraints weight = 39863.420| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.63 r_work: 0.3009 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23310 Z= 0.146 Angle : 0.561 9.502 31830 Z= 0.290 Chirality : 0.043 0.154 3685 Planarity : 0.004 0.045 4135 Dihedral : 4.185 14.295 3230 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.33 % Allowed : 26.36 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 3000 helix: 2.32 (0.19), residues: 740 sheet: 0.59 (0.16), residues: 1010 loop : -1.13 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 301 TYR 0.014 0.001 TYR C 441 PHE 0.014 0.001 PHE C 146 TRP 0.010 0.001 TRP C 359 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00351 (23300) covalent geometry : angle 0.56047 (31810) SS BOND : bond 0.00232 ( 10) SS BOND : angle 0.68620 ( 20) hydrogen bonds : bond 0.04478 ( 1085) hydrogen bonds : angle 4.49224 ( 3060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6961 (ptm160) REVERT: B 302 LEU cc_start: 0.8990 (tt) cc_final: 0.8732 (tt) REVERT: B 379 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: A 118 PHE cc_start: 0.8283 (m-10) cc_final: 0.7940 (m-80) REVERT: A 329 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8748 (mt) REVERT: C 118 PHE cc_start: 0.8158 (m-10) cc_final: 0.7762 (m-80) REVERT: C 301 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7224 (tpp80) REVERT: C 379 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: D 492 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8809 (p) REVERT: E 329 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8725 (mt) REVERT: E 379 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: E 431 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9001 (mt) REVERT: E 580 MET cc_start: 0.8753 (tpp) cc_final: 0.8520 (mmt) REVERT: E 592 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9016 (tt) outliers start: 55 outliers final: 41 residues processed: 162 average time/residue: 0.4103 time to fit residues: 82.2638 Evaluate side-chains 152 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 65 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 chunk 296 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS A 160 GLN A 285 HIS C 285 HIS D 285 HIS E 160 GLN E 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081892 restraints weight = 39872.737| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.61 r_work: 0.3001 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23310 Z= 0.169 Angle : 0.578 9.413 31830 Z= 0.300 Chirality : 0.043 0.162 3685 Planarity : 0.004 0.046 4135 Dihedral : 4.264 14.365 3230 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.29 % Allowed : 26.48 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.16), residues: 3000 helix: 2.31 (0.19), residues: 740 sheet: 0.58 (0.16), residues: 1010 loop : -1.14 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 301 TYR 0.015 0.001 TYR C 441 PHE 0.014 0.001 PHE D 118 TRP 0.010 0.001 TRP C 359 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00411 (23300) covalent geometry : angle 0.57756 (31810) SS BOND : bond 0.00308 ( 10) SS BOND : angle 0.98581 ( 20) hydrogen bonds : bond 0.04779 ( 1085) hydrogen bonds : angle 4.53931 ( 3060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6886 (ptm160) REVERT: B 302 LEU cc_start: 0.8997 (tt) cc_final: 0.8738 (tt) REVERT: B 379 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: A 118 PHE cc_start: 0.8304 (m-10) cc_final: 0.7961 (m-80) REVERT: A 329 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8767 (mt) REVERT: C 118 PHE cc_start: 0.8178 (m-10) cc_final: 0.7781 (m-80) REVERT: C 379 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: D 492 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8831 (p) REVERT: E 329 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8736 (mt) REVERT: E 379 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: E 431 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.8999 (mt) REVERT: E 580 MET cc_start: 0.8787 (tpp) cc_final: 0.8544 (mmt) REVERT: E 592 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 54 outliers final: 44 residues processed: 160 average time/residue: 0.3831 time to fit residues: 76.1556 Evaluate side-chains 151 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 110 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS A 160 GLN A 285 HIS C 285 HIS C 391 ASN D 285 HIS E 160 GLN E 285 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081376 restraints weight = 39768.357| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.60 r_work: 0.2993 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23310 Z= 0.195 Angle : 0.600 9.603 31830 Z= 0.313 Chirality : 0.044 0.165 3685 Planarity : 0.004 0.045 4135 Dihedral : 4.401 15.442 3230 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.37 % Allowed : 26.36 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.16), residues: 3000 helix: 2.23 (0.19), residues: 740 sheet: 0.54 (0.16), residues: 1010 loop : -1.18 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 301 TYR 0.016 0.001 TYR E 441 PHE 0.016 0.001 PHE D 118 TRP 0.010 0.001 TRP C 359 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00475 (23300) covalent geometry : angle 0.59950 (31810) SS BOND : bond 0.00352 ( 10) SS BOND : angle 1.07629 ( 20) hydrogen bonds : bond 0.05125 ( 1085) hydrogen bonds : angle 4.63528 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6607.29 seconds wall clock time: 113 minutes 5.31 seconds (6785.31 seconds total)