Starting phenix.real_space_refine on Sat Jan 25 00:58:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fth_50745/01_2025/9fth_50745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fth_50745/01_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_50745/01_2025/9fth_50745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fth_50745/01_2025/9fth_50745.map" model { file = "/net/cci-nas-00/data/ceres_data/9fth_50745/01_2025/9fth_50745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fth_50745/01_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.83, per 1000 atoms: 0.48 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: 6.13 Conformation dependent library (CDL) restraints added in 3.3 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: 2.47 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: 8.13 Time building geometry restraints manager: 6.68 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: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 47.570 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- 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 23300 Z= 0.131 Angle : 0.462 10.294 31810 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 *********************** 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 : 2.604 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: 0.9330 time to fit residues: 173.6007 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 : 2.823 ------------------------------------------------------------------------------- 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 = 0.078919 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 23300 Z= 0.679 Angle : 0.784 11.176 31810 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 *********************** 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 : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 PHE cc_start: 0.8031 (m-10) cc_final: 0.7800 (m-80) REVERT: B 301 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6855 (mmm160) REVERT: B 379 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: A 118 PHE cc_start: 0.8139 (m-10) cc_final: 0.7773 (m-80) REVERT: C 379 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7675 (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: 0.9502 (OUTLIER) cc_final: 0.9077 (mt) outliers start: 101 outliers final: 32 residues processed: 212 average time/residue: 0.9221 time to fit residues: 239.3776 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 : 2.650 ------------------------------------------------------------------------------- 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: 0.0170 chunk 207 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 255 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 242 optimal weight: 0.0000 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS C 40 HIS C 160 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087890 restraints weight = 39519.832| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.63 r_work: 0.3096 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23300 Z= 0.134 Angle : 0.518 9.544 31810 Z= 0.266 Chirality : 0.041 0.149 3685 Planarity : 0.004 0.041 4135 Dihedral : 3.785 14.056 3230 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.14 % Allowed : 25.13 % 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: 0.54 (0.15), residues: 3000 helix: 2.18 (0.19), residues: 740 sheet: 0.76 (0.16), residues: 995 loop : -1.12 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.002 0.001 HIS D 144 PHE 0.008 0.001 PHE E 579 TYR 0.008 0.001 TYR A 441 ARG 0.002 0.000 ARG E 301 *********************** 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 217 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 2.631 Fit side-chains REVERT: B 118 PHE cc_start: 0.7972 (m-10) cc_final: 0.7480 (m-80) REVERT: B 301 ARG cc_start: 0.7222 (ttp-110) cc_final: 0.6919 (ttt-90) REVERT: B 390 ILE cc_start: 0.7499 (pt) cc_final: 0.7299 (pt) REVERT: A 118 PHE cc_start: 0.7998 (m-10) cc_final: 0.7666 (m-80) REVERT: A 587 THR cc_start: 0.9309 (t) cc_final: 0.9059 (t) REVERT: C 285 HIS cc_start: 0.8374 (m90) cc_final: 0.8172 (m90) REVERT: C 301 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.7081 (tpp80) REVERT: C 379 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: C 390 ILE cc_start: 0.7418 (pt) cc_final: 0.7212 (pt) REVERT: D 301 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.7066 (ptm160) REVERT: E 118 PHE cc_start: 0.7942 (m-10) cc_final: 0.7415 (m-80) REVERT: E 301 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.7152 (ttt-90) outliers start: 27 outliers final: 7 residues processed: 209 average time/residue: 0.8802 time to fit residues: 227.1219 Evaluate side-chains 136 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain E residue 236 VAL 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: 20.0000 chunk 72 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 160 GLN B 391 ASN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN D 160 GLN D 285 HIS ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 160 GLN E 391 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.080900 restraints weight = 40321.277| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.63 r_work: 0.2977 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 23300 Z= 0.384 Angle : 0.626 10.046 31810 Z= 0.328 Chirality : 0.045 0.146 3685 Planarity : 0.004 0.047 4135 Dihedral : 4.306 15.614 3230 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.92 % Allowed : 25.55 % Favored : 71.53 % 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: 0.41 (0.15), residues: 3000 helix: 2.06 (0.19), residues: 740 sheet: 0.63 (0.16), residues: 1000 loop : -1.15 (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 B 285 PHE 0.024 0.002 PHE A 146 TYR 0.018 0.002 TYR D 441 ARG 0.003 0.000 ARG A 513 *********************** 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 181 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 112 time to evaluate : 2.713 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7148 (ttp-110) cc_final: 0.6933 (ptm160) REVERT: B 379 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: A 118 PHE cc_start: 0.8064 (m-10) cc_final: 0.7775 (m-80) REVERT: A 329 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8769 (mt) REVERT: C 301 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7136 (tpp80) REVERT: C 379 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: D 379 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: D 580 MET cc_start: 0.8892 (tpp) cc_final: 0.8649 (mmt) REVERT: E 118 PHE cc_start: 0.7984 (m-10) cc_final: 0.7621 (m-80) REVERT: E 301 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.7107 (ptm160) REVERT: E 329 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8778 (mt) REVERT: E 357 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8876 (mp) REVERT: E 379 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: E 431 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9028 (mt) outliers start: 69 outliers final: 25 residues processed: 175 average time/residue: 0.9347 time to fit residues: 200.6718 Evaluate side-chains 137 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 246 ARG Chi-restraints excluded: chain A residue 274 THR 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 587 THR Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 587 THR 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: 0.0030 chunk 187 optimal weight: 9.9990 chunk 148 optimal weight: 40.0000 chunk 205 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082340 restraints weight = 40154.183| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.62 r_work: 0.3007 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23300 Z= 0.245 Angle : 0.565 9.550 31810 Z= 0.293 Chirality : 0.043 0.136 3685 Planarity : 0.004 0.045 4135 Dihedral : 4.138 16.676 3230 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.63 % Allowed : 26.10 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 3000 helix: 2.17 (0.19), residues: 740 sheet: 0.64 (0.16), residues: 1000 loop : -1.08 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 359 HIS 0.003 0.001 HIS A 285 PHE 0.021 0.001 PHE C 146 TYR 0.015 0.001 TYR C 441 ARG 0.001 0.000 ARG D 301 *********************** 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 187 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 125 time to evaluate : 2.630 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6979 (ptm160) REVERT: B 379 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: A 118 PHE cc_start: 0.8082 (m-10) cc_final: 0.7788 (m-80) REVERT: A 329 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 301 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.7141 (tpp80) REVERT: C 379 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: D 379 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: D 580 MET cc_start: 0.8857 (tpp) cc_final: 0.8636 (mmt) REVERT: E 118 PHE cc_start: 0.8088 (m-10) cc_final: 0.7796 (m-80) REVERT: E 301 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6958 (tpp80) REVERT: E 329 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8737 (mt) REVERT: E 379 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: E 431 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9011 (mt) outliers start: 62 outliers final: 35 residues processed: 178 average time/residue: 0.9006 time to fit residues: 197.1374 Evaluate side-chains 156 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL 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 392 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 431 LEU 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 350 SER Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 618 VAL 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: 5.9990 chunk 185 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 160 GLN C 391 ASN D 160 GLN E 160 GLN E 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.082670 restraints weight = 40015.613| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.61 r_work: 0.3013 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23300 Z= 0.232 Angle : 0.556 9.495 31810 Z= 0.287 Chirality : 0.043 0.168 3685 Planarity : 0.004 0.044 4135 Dihedral : 4.079 14.863 3230 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.54 % Allowed : 26.31 % Favored : 71.14 % 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: 0.54 (0.15), residues: 3000 helix: 2.26 (0.19), residues: 740 sheet: 0.66 (0.16), residues: 1000 loop : -1.07 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 359 HIS 0.004 0.001 HIS E 285 PHE 0.019 0.001 PHE C 146 TYR 0.014 0.001 TYR C 441 ARG 0.001 0.000 ARG E 301 *********************** 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 188 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 2.701 Fit side-chains revert: symmetry clash REVERT: B 301 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.7019 (ptm160) REVERT: B 379 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: A 118 PHE cc_start: 0.8131 (m-10) cc_final: 0.7823 (m-80) REVERT: A 329 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8613 (mt) REVERT: C 301 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7123 (tpp80) REVERT: C 379 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: D 379 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: D 580 MET cc_start: 0.8843 (tpp) cc_final: 0.8634 (mmt) REVERT: E 49 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7053 (mtm110) REVERT: E 118 PHE cc_start: 0.8119 (m-10) cc_final: 0.7801 (m-80) REVERT: E 301 ARG cc_start: 0.7441 (ttp-110) cc_final: 0.6897 (tpp80) REVERT: E 329 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8734 (mt) REVERT: E 379 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: E 431 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9003 (mt) outliers start: 60 outliers final: 45 residues processed: 177 average time/residue: 0.9094 time to fit residues: 197.3554 Evaluate side-chains 162 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 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 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 379 GLU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain 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 379 GLU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 431 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 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 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: 9.9990 chunk 217 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 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: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 160 GLN B 391 ASN A 285 HIS A 391 ASN C 391 ASN D 160 GLN 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 = 0.3762 r_free = 0.3762 target = 0.126739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.078334 restraints weight = 40600.715| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.59 r_work: 0.2936 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.056 23300 Z= 0.636 Angle : 0.748 10.431 31810 Z= 0.396 Chirality : 0.050 0.267 3685 Planarity : 0.005 0.047 4135 Dihedral : 4.969 19.598 3230 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.73 % Allowed : 25.51 % 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: -0.07 (0.15), residues: 3000 helix: 1.53 (0.19), residues: 745 sheet: 0.45 (0.16), residues: 1010 loop : -1.47 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 359 HIS 0.007 0.002 HIS E 285 PHE 0.020 0.002 PHE D 118 TYR 0.020 0.002 TYR D 441 ARG 0.003 0.001 ARG B 513 *********************** 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 194 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 106 time to evaluate : 2.558 Fit side-chains REVERT: B 301 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6721 (ptp-110) REVERT: B 379 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: A 139 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6364 (mpp80) REVERT: A 233 HIS cc_start: 0.7942 (t-90) cc_final: 0.7448 (t-90) REVERT: A 329 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8763 (mt) REVERT: C 139 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6071 (tpp80) REVERT: C 301 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.7162 (tpp80) REVERT: C 379 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: D 379 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: E 139 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6178 (mpp80) REVERT: E 329 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8831 (mt) REVERT: E 379 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: E 431 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9054 (mt) outliers start: 88 outliers final: 51 residues processed: 192 average time/residue: 0.9447 time to fit residues: 221.2691 Evaluate side-chains 154 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 93 time to evaluate : 3.904 ------------------------------------------------------------------------------- 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 392 LEU 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 600 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 304 VAL 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 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 431 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 600 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 139 ARG 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 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 587 THR Chi-restraints excluded: chain E residue 618 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 290 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 240 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS C 40 HIS D 160 GLN E 160 GLN E 285 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081233 restraints weight = 40006.160| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.59 r_work: 0.2982 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23300 Z= 0.286 Angle : 0.600 9.971 31810 Z= 0.312 Chirality : 0.044 0.193 3685 Planarity : 0.004 0.048 4135 Dihedral : 4.434 16.658 3230 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.71 % Allowed : 26.48 % 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: 0.22 (0.15), residues: 3000 helix: 2.02 (0.19), residues: 730 sheet: 0.52 (0.16), residues: 1010 loop : -1.34 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 359 HIS 0.004 0.001 HIS A 285 PHE 0.018 0.001 PHE C 146 TYR 0.015 0.001 TYR C 441 ARG 0.001 0.000 ARG D 301 *********************** 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 185 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 2.624 Fit side-chains REVERT: B 301 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.6957 (ptm160) REVERT: B 302 LEU cc_start: 0.8978 (tt) cc_final: 0.8707 (tt) REVERT: B 379 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: A 160 GLN cc_start: 0.8957 (tp40) cc_final: 0.8731 (tp-100) REVERT: A 233 HIS cc_start: 0.7934 (t-90) cc_final: 0.7441 (t-90) REVERT: A 329 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8610 (mt) REVERT: C 301 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.7194 (tpp80) REVERT: C 379 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: E 49 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7082 (mtm110) REVERT: E 329 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8744 (mt) REVERT: E 379 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: E 431 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.8987 (mt) REVERT: E 592 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9034 (tt) outliers start: 64 outliers final: 47 residues processed: 180 average time/residue: 0.8993 time to fit residues: 198.1990 Evaluate side-chains 161 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 392 LEU 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 600 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR 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 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 431 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 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 592 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: 0.9980 chunk 239 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 249 optimal weight: 20.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS A 285 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN D 391 ASN E 160 GLN E 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.080663 restraints weight = 40268.494| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.59 r_work: 0.2973 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23300 Z= 0.345 Angle : 0.625 9.884 31810 Z= 0.326 Chirality : 0.045 0.193 3685 Planarity : 0.004 0.048 4135 Dihedral : 4.525 17.150 3230 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.46 % Allowed : 26.78 % 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: 0.20 (0.15), residues: 3000 helix: 2.02 (0.19), residues: 730 sheet: 0.60 (0.16), residues: 1000 loop : -1.42 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 359 HIS 0.004 0.001 HIS A 285 PHE 0.017 0.002 PHE C 146 TYR 0.017 0.002 TYR D 441 ARG 0.002 0.000 ARG C 301 *********************** 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 170 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 2.564 Fit side-chains REVERT: B 301 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6741 (ptp-110) REVERT: B 302 LEU cc_start: 0.8991 (tt) cc_final: 0.8728 (tt) REVERT: B 379 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: A 160 GLN cc_start: 0.8985 (tp40) cc_final: 0.8785 (tp-100) REVERT: A 233 HIS cc_start: 0.7924 (t-90) cc_final: 0.7414 (t-90) REVERT: A 329 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8767 (mt) REVERT: C 301 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.7132 (tpp80) REVERT: C 379 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: E 329 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8780 (mt) REVERT: E 379 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: E 431 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9003 (mt) REVERT: E 592 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9061 (tt) outliers start: 58 outliers final: 46 residues processed: 167 average time/residue: 0.8479 time to fit residues: 176.2507 Evaluate side-chains 159 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 392 LEU 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 600 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR 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 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 431 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 350 SER Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 592 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: 2.9990 chunk 86 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS A 285 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN D 391 ASN E 160 GLN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080981 restraints weight = 40129.940| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.59 r_work: 0.2979 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23300 Z= 0.330 Angle : 0.617 10.823 31810 Z= 0.321 Chirality : 0.044 0.182 3685 Planarity : 0.004 0.048 4135 Dihedral : 4.470 16.970 3230 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.33 % Allowed : 26.99 % Favored : 70.68 % 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: 0.21 (0.16), residues: 3000 helix: 2.08 (0.19), residues: 730 sheet: 0.50 (0.16), residues: 1010 loop : -1.36 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 359 HIS 0.004 0.001 HIS A 285 PHE 0.017 0.001 PHE C 146 TYR 0.016 0.002 TYR C 441 ARG 0.001 0.000 ARG E 301 ********************** 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 160 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 2.530 Fit side-chains REVERT: B 301 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6788 (ptp-110) REVERT: B 302 LEU cc_start: 0.8990 (tt) cc_final: 0.8726 (tt) REVERT: B 379 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: A 233 HIS cc_start: 0.7934 (t-90) cc_final: 0.7420 (t-90) REVERT: A 329 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8572 (mt) REVERT: C 301 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.7152 (tpp80) REVERT: C 379 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: E 329 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8749 (mt) REVERT: E 379 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: E 431 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9005 (mt) REVERT: E 592 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9047 (tt) outliers start: 55 outliers final: 46 residues processed: 155 average time/residue: 0.8977 time to fit residues: 171.8415 Evaluate side-chains 154 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 2.781 ------------------------------------------------------------------------------- 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 392 LEU 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 600 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR 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 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 431 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 350 SER Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 592 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: 9.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 233 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 597 GLN A 40 HIS A 160 GLN A 285 HIS A 307 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 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 = 0.3857 r_free = 0.3857 target = 0.133873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086679 restraints weight = 39788.450| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.60 r_work: 0.3081 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23300 Z= 0.150 Angle : 0.536 10.150 31810 Z= 0.273 Chirality : 0.042 0.146 3685 Planarity : 0.004 0.048 4135 Dihedral : 3.877 13.843 3230 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.14 % Allowed : 28.14 % Favored : 70.72 % 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: 0.55 (0.16), residues: 3000 helix: 2.45 (0.20), residues: 735 sheet: 0.60 (0.16), residues: 1010 loop : -1.15 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 359 HIS 0.004 0.001 HIS B 40 PHE 0.016 0.001 PHE C 146 TYR 0.007 0.001 TYR C 441 ARG 0.002 0.000 ARG A 513 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14871.25 seconds wall clock time: 263 minutes 51.77 seconds (15831.77 seconds total)