Starting phenix.real_space_refine on Thu Jun 19 15:51:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fth_50745/06_2025/9fth_50745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fth_50745/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fth_50745/06_2025/9fth_50745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fth_50745/06_2025/9fth_50745.map" model { file = "/net/cci-nas-00/data/ceres_data/9fth_50745/06_2025/9fth_50745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fth_50745/06_2025/9fth_50745.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22780 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 134 Restraints were copied for chains: C, B, E, D Time building chain proxies: 10.37, per 1000 atoms: 0.46 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=2, 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 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: 5.03 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.55 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: 8.38 Time building geometry restraints manager: 6.11 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: 11943 17.63 - 35.26: 1272 35.26 - 52.89: 341 52.89 - 70.52: 55 70.52 - 88.14: 20 Dihedral angle restraints: 13631 sinusoidal: 4996 harmonic: 8635 Sorted by residual: 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 dihedral pdb=" CA ASP D 328 " pdb=" CB ASP D 328 " pdb=" CG ASP D 328 " pdb=" OD1 ASP D 328 " ideal model delta sinusoidal sigma weight residual -30.00 -83.95 53.95 1 2.00e+01 2.50e-03 9.88e+00 dihedral pdb=" CA ASP E 328 " pdb=" CB ASP E 328 " pdb=" CG ASP E 328 " pdb=" OD1 ASP E 328 " ideal model delta sinusoidal sigma weight residual -30.00 -83.95 53.95 1 2.00e+01 2.50e-03 9.88e+00 ... (remaining 13628 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: 2.03 - 2.60: 173 2.60 - 3.18: 17471 3.18 - 3.75: 32410 3.75 - 4.33: 42673 4.33 - 4.90: 75267 Nonbonded interactions: 167994 Sorted by model distance: nonbonded pdb=" SG CYS D 275 " pdb=" SG CYS D 280 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 275 " pdb=" SG CYS C 280 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 275 " pdb=" SG CYS E 280 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS A 275 " pdb=" SG CYS A 280 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 371 " pdb=" SG CYS E 373 " model vdw 2.032 3.760 ... (remaining 167989 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 1.300 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: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.470 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.580 ------------------------------------------------------------------------------- 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 23302 Z= 0.083 Angle : 0.462 10.294 31814 Z= 0.228 Chirality : 0.040 0.129 3685 Planarity : 0.003 0.036 4135 Dihedral : 15.685 88.144 8095 Min Nonbonded Distance : 2.029 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.000 TRP E 359 HIS 0.002 0.000 HIS E 285 PHE 0.003 0.000 PHE D 443 TYR 0.006 0.000 TYR A 441 ARG 0.001 0.000 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.29889 ( 1085) hydrogen bonds : angle 8.12127 ( 3060) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.36069 ( 4) covalent geometry : bond 0.00194 (23300) covalent geometry : angle 0.46193 (31810) *********************** 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 : 2.476 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: 0.8983 time to fit residues: 167.4678 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 : 2.352 ------------------------------------------------------------------------------- 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 253 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 153 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 144 HIS B 307 ASN B 391 ASN B 471 GLN A 69 GLN A 144 HIS A 307 ASN A 471 GLN C 69 GLN C 144 HIS C 307 ASN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 471 GLN D 69 GLN D 144 HIS D 307 ASN ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN E 69 GLN E 144 HIS E 160 GLN E 307 ASN E 471 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078921 restraints weight = 40275.069| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.60 r_work: 0.2942 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.064 23302 Z= 0.421 Angle : 0.784 11.176 31814 Z= 0.418 Chirality : 0.051 0.161 3685 Planarity : 0.005 0.042 4135 Dihedral : 4.783 22.406 3239 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.28 % Allowed : 21.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3000 helix: 1.64 (0.19), residues: 745 sheet: 0.61 (0.16), residues: 1020 loop : -1.37 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 359 HIS 0.006 0.002 HIS A 285 PHE 0.015 0.002 PHE C 584 TYR 0.019 0.002 TYR E 441 ARG 0.005 0.001 ARG E 301 Details of bonding type rmsd hydrogen bonds : bond 0.07785 ( 1085) hydrogen bonds : angle 5.66890 ( 3060) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.08225 ( 4) covalent geometry : bond 0.01028 (23300) covalent geometry : angle 0.78393 (31810) *********************** 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 225 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 124 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 PHE cc_start: 0.8030 (m-10) cc_final: 0.7799 (m-80) REVERT: B 301 ARG cc_start: 0.7121 (ttp-110) cc_final: 0.6855 (mmm160) REVERT: B 379 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 118 PHE cc_start: 0.8138 (m-10) cc_final: 0.7773 (m-80) REVERT: C 379 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: D 379 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: E 118 PHE cc_start: 0.8145 (m-10) cc_final: 0.7664 (m-80) REVERT: E 431 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9078 (mt) outliers start: 101 outliers final: 32 residues processed: 212 average time/residue: 0.8624 time to fit residues: 224.2165 Evaluate side-chains 136 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 416 THR 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 198 GLU 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 416 THR 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 279 ILE Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 431 LEU 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 391 ASN Chi-restraints excluded: chain E residue 416 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 62 optimal weight: 0.0370 chunk 207 optimal weight: 20.0000 chunk 253 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN A 40 HIS C 40 HIS ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085027 restraints weight = 39568.933| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.63 r_work: 0.3049 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23302 Z= 0.110 Angle : 0.535 9.819 31814 Z= 0.277 Chirality : 0.042 0.150 3685 Planarity : 0.004 0.042 4135 Dihedral : 3.945 13.714 3230 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.48 % Allowed : 25.25 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3000 helix: 2.14 (0.19), residues: 740 sheet: 0.63 (0.16), residues: 1005 loop : -1.10 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 359 HIS 0.003 0.001 HIS D 144 PHE 0.007 0.001 PHE A 118 TYR 0.011 0.001 TYR A 441 ARG 0.001 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 1085) hydrogen bonds : angle 4.77718 ( 3060) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.42254 ( 4) covalent geometry : bond 0.00246 (23300) covalent geometry : angle 0.53529 (31810) *********************** 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 198 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 2.574 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6990 (ptm160) REVERT: B 379 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: B 390 ILE cc_start: 0.7542 (pt) cc_final: 0.7309 (pt) REVERT: A 118 PHE cc_start: 0.8075 (m-10) cc_final: 0.7734 (m-80) REVERT: C 301 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.7133 (tpp80) REVERT: C 379 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: D 301 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6848 (ttt-90) REVERT: D 379 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: E 118 PHE cc_start: 0.7954 (m-10) cc_final: 0.7440 (m-80) outliers start: 35 outliers final: 8 residues processed: 189 average time/residue: 0.9076 time to fit residues: 210.1005 Evaluate side-chains 133 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 592 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 C residue 379 GLU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain E residue 246 ARG 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 7 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 133 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 overall best weight: 2.4684 ------------------------------------------------------------------------------- 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 ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN D 160 GLN ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083102 restraints weight = 40115.509| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.63 r_work: 0.3015 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23302 Z= 0.144 Angle : 0.552 9.556 31814 Z= 0.285 Chirality : 0.042 0.145 3685 Planarity : 0.004 0.040 4135 Dihedral : 3.995 13.315 3230 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.50 % Allowed : 25.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3000 helix: 2.21 (0.19), residues: 740 sheet: 0.68 (0.16), residues: 1000 loop : -1.09 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 359 HIS 0.003 0.001 HIS E 285 PHE 0.024 0.001 PHE C 146 TYR 0.014 0.001 TYR C 441 ARG 0.001 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 1085) hydrogen bonds : angle 4.62849 ( 3060) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.50708 ( 4) covalent geometry : bond 0.00342 (23300) covalent geometry : angle 0.55167 (31810) *********************** 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 197 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 2.524 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7204 (ttp-110) cc_final: 0.6978 (ptm160) REVERT: B 379 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: A 118 PHE cc_start: 0.8044 (m-10) cc_final: 0.7751 (m-80) REVERT: A 329 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 301 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.7143 (tpp80) REVERT: C 379 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: D 301 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.6978 (ptm160) REVERT: D 379 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: E 118 PHE cc_start: 0.7967 (m-10) cc_final: 0.7641 (m-80) REVERT: E 301 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7106 (ttt-90) REVERT: E 329 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8714 (mt) REVERT: E 379 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: E 431 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9034 (mt) REVERT: E 592 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9045 (tt) outliers start: 59 outliers final: 22 residues processed: 190 average time/residue: 0.9333 time to fit residues: 215.7401 Evaluate side-chains 151 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 2.426 ------------------------------------------------------------------------------- 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 350 SER Chi-restraints excluded: chain B residue 379 GLU 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 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 431 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 350 SER 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 350 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 379 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 138 optimal weight: 20.0000 chunk 14 optimal weight: 0.0980 chunk 187 optimal weight: 9.9990 chunk 148 optimal weight: 30.0000 chunk 205 optimal weight: 7.9990 chunk 16 optimal weight: 0.0060 chunk 163 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 243 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 40 HIS C 285 HIS D 160 GLN E 40 HIS E 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.084600 restraints weight = 40232.833| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.65 r_work: 0.3017 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23302 Z= 0.118 Angle : 0.528 9.144 31814 Z= 0.271 Chirality : 0.042 0.181 3685 Planarity : 0.003 0.041 4135 Dihedral : 3.866 17.199 3230 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3000 helix: 2.35 (0.19), residues: 740 sheet: 0.73 (0.16), residues: 1000 loop : -1.03 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 359 HIS 0.003 0.001 HIS E 285 PHE 0.020 0.001 PHE C 146 TYR 0.012 0.001 TYR C 441 ARG 0.001 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 1085) hydrogen bonds : angle 4.42705 ( 3060) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.53170 ( 4) covalent geometry : bond 0.00275 (23300) covalent geometry : angle 0.52795 (31810) *********************** 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 196 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 2.361 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.7019 (ptm160) REVERT: B 379 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: A 118 PHE cc_start: 0.8083 (m-10) cc_final: 0.7735 (m-80) REVERT: C 301 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.7172 (tpp80) REVERT: C 379 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: D 301 ARG cc_start: 0.7231 (ttp-110) cc_final: 0.6919 (ptm160) REVERT: D 580 MET cc_start: 0.8835 (tpp) cc_final: 0.8612 (mmt) REVERT: E 118 PHE cc_start: 0.8005 (m-10) cc_final: 0.7711 (m-80) REVERT: E 301 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.7124 (ttt-90) REVERT: E 329 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8738 (mt) REVERT: E 379 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7755 (mt-10) outliers start: 47 outliers final: 23 residues processed: 186 average time/residue: 0.8592 time to fit residues: 196.9637 Evaluate side-chains 144 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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 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 592 LEU Chi-restraints excluded: chain A residue 123 ASP 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 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 456 VAL 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 4 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 93 optimal weight: 0.0030 chunk 217 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 257 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 chunk 211 optimal weight: 0.1980 chunk 190 optimal weight: 3.9990 overall best weight: 2.8396 ------------------------------------------------------------------------------- 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 C 285 HIS C 391 ASN D 160 GLN D 391 ASN 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 = 0.3824 r_free = 0.3824 target = 0.131243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082521 restraints weight = 40063.495| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.63 r_work: 0.3011 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23302 Z= 0.156 Angle : 0.565 9.171 31814 Z= 0.292 Chirality : 0.043 0.209 3685 Planarity : 0.004 0.044 4135 Dihedral : 4.038 14.768 3230 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.50 % Allowed : 25.93 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 3000 helix: 2.31 (0.19), residues: 740 sheet: 0.72 (0.16), residues: 1000 loop : -1.05 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 359 HIS 0.004 0.001 HIS E 285 PHE 0.018 0.001 PHE C 146 TYR 0.015 0.001 TYR C 441 ARG 0.001 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 1085) hydrogen bonds : angle 4.47852 ( 3060) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.54933 ( 4) covalent geometry : bond 0.00375 (23300) covalent geometry : angle 0.56511 (31810) *********************** 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 178 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6986 (ptm160) REVERT: B 379 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: A 118 PHE cc_start: 0.8138 (m-10) cc_final: 0.7824 (m-80) REVERT: A 329 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 301 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.7160 (tpp80) REVERT: C 379 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: D 301 ARG cc_start: 0.7340 (ttp-110) cc_final: 0.6957 (ptm160) REVERT: D 580 MET cc_start: 0.8837 (tpp) cc_final: 0.8596 (mmt) REVERT: E 118 PHE cc_start: 0.8038 (m-10) cc_final: 0.7755 (m-80) REVERT: E 329 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8718 (mt) REVERT: E 379 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: E 431 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9008 (mt) outliers start: 59 outliers final: 33 residues processed: 171 average time/residue: 0.9090 time to fit residues: 190.8728 Evaluate side-chains 148 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 2.621 ------------------------------------------------------------------------------- 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 391 ASN 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 A residue 123 ASP 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 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 535 VAL 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 261 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 145 optimal weight: 0.0470 chunk 132 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 120 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- 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 391 ASN C 285 HIS C 391 ASN D 160 GLN D 285 HIS D 391 ASN E 160 GLN E 285 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080623 restraints weight = 40293.689| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.61 r_work: 0.2980 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23302 Z= 0.222 Angle : 0.625 9.470 31814 Z= 0.326 Chirality : 0.045 0.228 3685 Planarity : 0.004 0.043 4135 Dihedral : 4.383 15.046 3230 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.09 % Allowed : 25.89 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3000 helix: 2.14 (0.19), residues: 730 sheet: 0.61 (0.16), residues: 1000 loop : -1.21 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 359 HIS 0.006 0.001 HIS A 285 PHE 0.017 0.002 PHE C 146 TYR 0.018 0.002 TYR D 441 ARG 0.002 0.000 ARG E 301 Details of bonding type rmsd hydrogen bonds : bond 0.05551 ( 1085) hydrogen bonds : angle 4.71147 ( 3060) SS BOND : bond 0.00371 ( 2) SS BOND : angle 0.70029 ( 4) covalent geometry : bond 0.00541 (23300) covalent geometry : angle 0.62513 (31810) *********************** 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 190 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 117 time to evaluate : 2.413 Fit side-chains REVERT: B 301 ARG cc_start: 0.7302 (ttp-110) cc_final: 0.7008 (ptm160) REVERT: B 379 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: A 118 PHE cc_start: 0.8187 (m-10) cc_final: 0.7855 (m-80) REVERT: C 301 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7129 (tpp80) REVERT: C 379 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: D 379 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: D 580 MET cc_start: 0.8873 (tpp) cc_final: 0.8639 (mmt) REVERT: E 329 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8766 (mt) REVERT: E 357 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8858 (mp) REVERT: E 379 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: E 431 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9025 (mt) outliers start: 73 outliers final: 42 residues processed: 184 average time/residue: 0.8361 time to fit residues: 190.2013 Evaluate side-chains 148 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 99 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ASP 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 391 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain A residue 123 ASP 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 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 GLN 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 535 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 379 GLU 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 600 LEU Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 290 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 240 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 C 285 HIS C 391 ASN D 160 GLN 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 = 0.3817 r_free = 0.3817 target = 0.130833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082365 restraints weight = 39969.228| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.61 r_work: 0.2988 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23302 Z= 0.154 Angle : 0.577 9.545 31814 Z= 0.298 Chirality : 0.043 0.196 3685 Planarity : 0.004 0.044 4135 Dihedral : 4.175 16.165 3230 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.42 % Allowed : 26.53 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 3000 helix: 2.30 (0.19), residues: 730 sheet: 0.62 (0.16), residues: 1010 loop : -1.15 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 359 HIS 0.004 0.001 HIS E 285 PHE 0.017 0.001 PHE C 146 TYR 0.015 0.001 TYR C 441 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 1085) hydrogen bonds : angle 4.51191 ( 3060) SS BOND : bond 0.00278 ( 2) SS BOND : angle 1.20446 ( 4) covalent geometry : bond 0.00369 (23300) covalent geometry : angle 0.57653 (31810) *********************** 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 180 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 2.515 Fit side-chains REVERT: B 301 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.7030 (ptm160) REVERT: B 379 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: A 118 PHE cc_start: 0.8171 (m-10) cc_final: 0.7838 (m-80) REVERT: A 233 HIS cc_start: 0.7881 (t-90) cc_final: 0.7408 (t-90) REVERT: A 329 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8613 (mt) REVERT: A 498 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8202 (ttp80) REVERT: C 301 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7151 (tpp80) REVERT: C 379 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: D 580 MET cc_start: 0.8865 (tpp) cc_final: 0.8643 (mmt) REVERT: E 49 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7046 (mtm110) REVERT: E 329 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8737 (mt) REVERT: E 357 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8824 (mp) REVERT: E 379 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7624 (mt-10) outliers start: 57 outliers final: 37 residues processed: 173 average time/residue: 0.9248 time to fit residues: 195.6543 Evaluate side-chains 148 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 379 GLU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 587 THR 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 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 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL 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 123 ASP Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 379 GLU 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 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 20 optimal weight: 20.0000 chunk 286 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 249 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 285 HIS C 285 HIS C 391 ASN D 160 GLN D 285 HIS D 391 ASN E 160 GLN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080774 restraints weight = 40315.552| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.61 r_work: 0.2976 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23302 Z= 0.213 Angle : 0.622 9.558 31814 Z= 0.324 Chirality : 0.045 0.186 3685 Planarity : 0.004 0.044 4135 Dihedral : 4.380 15.321 3230 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.54 % Allowed : 26.69 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 3000 helix: 2.19 (0.19), residues: 730 sheet: 0.57 (0.16), residues: 1010 loop : -1.23 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 359 HIS 0.004 0.001 HIS C 285 PHE 0.016 0.002 PHE C 146 TYR 0.017 0.002 TYR D 441 ARG 0.002 0.000 ARG E 301 Details of bonding type rmsd hydrogen bonds : bond 0.05292 ( 1085) hydrogen bonds : angle 4.66125 ( 3060) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.42160 ( 4) covalent geometry : bond 0.00521 (23300) covalent geometry : angle 0.62188 (31810) *********************** 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 167 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 107 time to evaluate : 2.371 Fit side-chains REVERT: B 301 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6982 (ptm160) REVERT: B 379 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 118 PHE cc_start: 0.8276 (m-10) cc_final: 0.7934 (m-80) REVERT: A 233 HIS cc_start: 0.7915 (t-90) cc_final: 0.7417 (t-90) REVERT: A 329 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8795 (mt) REVERT: C 301 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7177 (tpp80) REVERT: C 379 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: D 580 MET cc_start: 0.8881 (tpp) cc_final: 0.8651 (mmt) REVERT: E 49 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7061 (mtm110) REVERT: E 329 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8756 (mt) REVERT: E 357 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8852 (mp) REVERT: E 379 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: E 431 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9028 (mt) outliers start: 60 outliers final: 45 residues processed: 165 average time/residue: 0.8895 time to fit residues: 180.2591 Evaluate side-chains 150 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 98 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 379 GLU Chi-restraints excluded: chain B residue 391 ASN 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 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 456 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL 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 618 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 379 GLU 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 553 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 228 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN A 285 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS C 391 ASN D 160 GLN 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 = 0.3812 r_free = 0.3812 target = 0.130495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082021 restraints weight = 40096.981| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.61 r_work: 0.3004 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23302 Z= 0.157 Angle : 0.584 9.524 31814 Z= 0.302 Chirality : 0.043 0.175 3685 Planarity : 0.004 0.045 4135 Dihedral : 4.215 14.599 3230 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.08 % Allowed : 27.12 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 3000 helix: 2.31 (0.19), residues: 730 sheet: 0.57 (0.16), residues: 1010 loop : -1.19 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 359 HIS 0.004 0.001 HIS C 285 PHE 0.016 0.001 PHE C 146 TYR 0.015 0.001 TYR C 441 ARG 0.001 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 1085) hydrogen bonds : angle 4.52748 ( 3060) SS BOND : bond 0.00124 ( 2) SS BOND : angle 1.07059 ( 4) covalent geometry : bond 0.00379 (23300) covalent geometry : angle 0.58420 (31810) ********************** 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 164 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 2.664 Fit side-chains REVERT: B 301 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6968 (ptm160) REVERT: B 379 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: A 118 PHE cc_start: 0.8261 (m-10) cc_final: 0.7916 (m-80) REVERT: A 233 HIS cc_start: 0.7881 (t-90) cc_final: 0.7391 (t-90) REVERT: A 329 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 379 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: D 580 MET cc_start: 0.8837 (tpp) cc_final: 0.8614 (mmt) REVERT: E 49 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7050 (mtm110) REVERT: E 329 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8732 (mt) REVERT: E 357 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8827 (mp) REVERT: E 379 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7613 (mt-10) outliers start: 49 outliers final: 40 residues processed: 159 average time/residue: 0.9125 time to fit residues: 176.9052 Evaluate side-chains 150 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 379 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 532 VAL 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 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 535 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL 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 123 ASP Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 379 GLU 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 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 237 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 15 optimal weight: 0.0020 chunk 233 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN D 285 HIS D 391 ASN E 160 GLN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081991 restraints weight = 39903.761| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.59 r_work: 0.2983 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 23302 Z= 0.179 Angle : 0.722 59.020 31814 Z= 0.405 Chirality : 0.046 0.872 3685 Planarity : 0.004 0.053 4135 Dihedral : 4.222 15.311 3230 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.16 % Allowed : 27.08 % Favored : 70.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 3000 helix: 2.31 (0.19), residues: 730 sheet: 0.57 (0.16), residues: 1010 loop : -1.19 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 359 HIS 0.004 0.001 HIS A 285 PHE 0.015 0.001 PHE C 146 TYR 0.015 0.001 TYR C 441 ARG 0.001 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 1085) hydrogen bonds : angle 4.54473 ( 3060) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.95119 ( 4) covalent geometry : bond 0.00419 (23300) covalent geometry : angle 0.72238 (31810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14707.87 seconds wall clock time: 250 minutes 41.97 seconds (15041.97 seconds total)