Starting phenix.real_space_refine on Sat Jan 18 07:01:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftj_50747/01_2025/9ftj_50747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftj_50747/01_2025/9ftj_50747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ftj_50747/01_2025/9ftj_50747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftj_50747/01_2025/9ftj_50747.map" model { file = "/net/cci-nas-00/data/ceres_data/9ftj_50747/01_2025/9ftj_50747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftj_50747/01_2025/9ftj_50747.cif" } resolution = 4.0 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 10 5.16 5 C 7970 2.51 5 N 1950 2.21 5 O 2115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12045 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2409 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 301} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.29, per 1000 atoms: 0.44 Number of scatterers: 12045 At special positions: 0 Unit cell: (103.404, 105.989, 112.021, 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 10 16.00 O 2115 8.00 N 1950 7.00 C 7970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2970 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 43.6% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.768A pdb=" N CYS A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.573A pdb=" N VAL A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.659A pdb=" N SER A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 542 through 564 removed outlier: 3.998A pdb=" N SER A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.573A pdb=" N GLY A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 637 removed outlier: 4.076A pdb=" N ALA A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 610 " --> pdb=" O GLN A 606 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) Proline residue: A 621 - end of helix removed outlier: 3.975A pdb=" N THR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.767A pdb=" N CYS B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.573A pdb=" N VAL B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 522 through 536 removed outlier: 3.659A pdb=" N SER B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 542 through 564 removed outlier: 3.998A pdb=" N SER B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.573A pdb=" N GLY B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 637 removed outlier: 4.077A pdb=" N ALA B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 610 " --> pdb=" O GLN B 606 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) Proline residue: B 621 - end of helix removed outlier: 3.975A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.768A pdb=" N CYS C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.574A pdb=" N VAL C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 522 Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.659A pdb=" N SER C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 542 through 564 removed outlier: 3.998A pdb=" N SER C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.574A pdb=" N GLY C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 637 removed outlier: 4.076A pdb=" N ALA C 609 " --> pdb=" O LYS C 605 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 610 " --> pdb=" O GLN C 606 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 611 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 3.975A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.769A pdb=" N CYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.574A pdb=" N VAL D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.659A pdb=" N SER D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 542 through 564 removed outlier: 3.998A pdb=" N SER D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.574A pdb=" N GLY D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 637 removed outlier: 4.077A pdb=" N ALA D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA D 610 " --> pdb=" O GLN D 606 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 611 " --> pdb=" O ALA D 607 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) Proline residue: D 621 - end of helix removed outlier: 3.975A pdb=" N THR D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.768A pdb=" N CYS E 371 " --> pdb=" O SER E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 391 removed outlier: 3.573A pdb=" N VAL E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 522 Processing helix chain 'E' and resid 522 through 536 removed outlier: 3.659A pdb=" N SER E 533 " --> pdb=" O ILE E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 542 through 564 removed outlier: 3.997A pdb=" N SER E 564 " --> pdb=" O ASN E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.573A pdb=" N GLY E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 637 removed outlier: 4.076A pdb=" N ALA E 609 " --> pdb=" O LYS E 605 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA E 610 " --> pdb=" O GLN E 606 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL E 618 " --> pdb=" O THR E 614 " (cutoff:3.500A) Proline residue: E 621 - end of helix removed outlier: 3.975A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.504A pdb=" N TRP A 407 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP A 359 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 335 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 397 through 399 removed outlier: 3.780A pdb=" N GLN A 446 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.504A pdb=" N TRP B 407 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP B 359 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 335 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 397 through 399 removed outlier: 3.780A pdb=" N GLN B 446 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.504A pdb=" N TRP C 407 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP C 359 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 335 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 397 through 399 removed outlier: 3.780A pdb=" N GLN C 446 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 379 removed outlier: 3.504A pdb=" N TRP D 407 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP D 359 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 335 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 397 through 399 removed outlier: 3.780A pdb=" N GLN D 446 " --> pdb=" O VAL D 511 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 376 through 379 removed outlier: 3.505A pdb=" N TRP E 407 " --> pdb=" O THR E 428 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP E 359 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA E 335 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 397 through 399 removed outlier: 3.780A pdb=" N GLN E 446 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3711 1.34 - 1.45: 1877 1.45 - 1.57: 6757 1.57 - 1.68: 0 1.68 - 1.79: 15 Bond restraints: 12360 Sorted by residual: bond pdb=" CG LEU E 546 " pdb=" CD2 LEU E 546 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CG LEU B 546 " pdb=" CD2 LEU B 546 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CG LEU C 546 " pdb=" CD2 LEU C 546 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG LEU A 546 " pdb=" CD2 LEU A 546 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG LEU D 546 " pdb=" CD2 LEU D 546 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 ... (remaining 12355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 15566 1.08 - 2.16: 1088 2.16 - 3.24: 177 3.24 - 4.32: 59 4.32 - 5.39: 20 Bond angle restraints: 16910 Sorted by residual: angle pdb=" C ASP A 541 " pdb=" N TYR A 542 " pdb=" CA TYR A 542 " ideal model delta sigma weight residual 121.54 117.44 4.10 1.91e+00 2.74e-01 4.61e+00 angle pdb=" C ASP B 541 " pdb=" N TYR B 542 " pdb=" CA TYR B 542 " ideal model delta sigma weight residual 121.54 117.44 4.10 1.91e+00 2.74e-01 4.60e+00 angle pdb=" C ASP C 541 " pdb=" N TYR C 542 " pdb=" CA TYR C 542 " ideal model delta sigma weight residual 121.54 117.45 4.09 1.91e+00 2.74e-01 4.59e+00 angle pdb=" C ASP D 541 " pdb=" N TYR D 542 " pdb=" CA TYR D 542 " ideal model delta sigma weight residual 121.54 117.45 4.09 1.91e+00 2.74e-01 4.59e+00 angle pdb=" C ASP E 541 " pdb=" N TYR E 542 " pdb=" CA TYR E 542 " ideal model delta sigma weight residual 121.54 117.48 4.06 1.91e+00 2.74e-01 4.53e+00 ... (remaining 16905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6243 17.18 - 34.35: 657 34.35 - 51.52: 170 51.52 - 68.70: 15 68.70 - 85.87: 10 Dihedral angle restraints: 7095 sinusoidal: 2500 harmonic: 4595 Sorted by residual: dihedral pdb=" CG ARG E 544 " pdb=" CD ARG E 544 " pdb=" NE ARG E 544 " pdb=" CZ ARG E 544 " ideal model delta sinusoidal sigma weight residual 180.00 135.02 44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG D 544 " pdb=" CD ARG D 544 " pdb=" NE ARG D 544 " pdb=" CZ ARG D 544 " ideal model delta sinusoidal sigma weight residual 180.00 135.02 44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG A 544 " pdb=" CD ARG A 544 " pdb=" NE ARG A 544 " pdb=" CZ ARG A 544 " ideal model delta sinusoidal sigma weight residual 180.00 135.03 44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1182 0.032 - 0.065: 527 0.065 - 0.097: 184 0.097 - 0.130: 89 0.130 - 0.162: 13 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CB ILE C 536 " pdb=" CA ILE C 536 " pdb=" CG1 ILE C 536 " pdb=" CG2 ILE C 536 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA TYR B 620 " pdb=" N TYR B 620 " pdb=" C TYR B 620 " pdb=" CB TYR B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CB ILE B 536 " pdb=" CA ILE B 536 " pdb=" CG1 ILE B 536 " pdb=" CG2 ILE B 536 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1992 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 524 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO B 525 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 525 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 525 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 524 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO D 525 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 525 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 525 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 524 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 525 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 525 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 525 " -0.032 5.00e-02 4.00e+02 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4082 2.82 - 3.34: 11553 3.34 - 3.86: 18087 3.86 - 4.38: 19267 4.38 - 4.90: 35010 Nonbonded interactions: 87999 Sorted by model distance: nonbonded pdb=" OH TYR B 423 " pdb=" OE1 GLU B 425 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR D 423 " pdb=" OE1 GLU D 425 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR A 423 " pdb=" OE1 GLU A 425 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR C 423 " pdb=" OE1 GLU C 425 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR E 423 " pdb=" OE1 GLU E 425 " model vdw 2.305 3.040 ... (remaining 87994 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: 0.10 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 group one per residue 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: 0.770 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.007 0.044 12360 Z= 0.448 Angle : 0.644 5.394 16910 Z= 0.355 Chirality : 0.045 0.162 1995 Planarity : 0.005 0.057 2120 Dihedral : 15.415 85.874 4125 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 25.74 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.21), residues: 1560 helix: 1.84 (0.22), residues: 555 sheet: -1.16 (0.26), residues: 385 loop : -1.79 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 407 HIS 0.003 0.002 HIS D 360 PHE 0.030 0.002 PHE D 561 TYR 0.021 0.003 TYR E 620 ARG 0.003 0.000 ARG E 513 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.471 Fit side-chains REVERT: A 627 TYR cc_start: 0.7981 (t80) cc_final: 0.7658 (t80) REVERT: C 627 TYR cc_start: 0.8093 (t80) cc_final: 0.7830 (t80) REVERT: E 465 GLU cc_start: 0.8550 (pt0) cc_final: 0.8337 (pt0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2519 time to fit residues: 46.0195 Evaluate side-chains 126 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 0.0010 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 2.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 471 GLN B 360 HIS B 471 GLN C 360 HIS C 471 GLN D 360 HIS D 471 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087439 restraints weight = 22492.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.089606 restraints weight = 15668.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.090720 restraints weight = 12270.589| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12360 Z= 0.344 Angle : 0.599 6.572 16910 Z= 0.326 Chirality : 0.044 0.142 1995 Planarity : 0.004 0.046 2120 Dihedral : 4.652 16.725 1685 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.07 % Allowed : 19.18 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1560 helix: 1.91 (0.21), residues: 560 sheet: -0.82 (0.27), residues: 400 loop : -1.66 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 407 HIS 0.002 0.002 HIS B 360 PHE 0.022 0.001 PHE A 561 TYR 0.011 0.002 TYR E 517 ARG 0.005 0.001 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 151 time to evaluate : 1.398 Fit side-chains REVERT: A 581 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8738 (mp) REVERT: A 591 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8857 (p) REVERT: C 581 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 627 TYR cc_start: 0.8111 (t80) cc_final: 0.7775 (t80) REVERT: D 546 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8595 (tt) REVERT: D 591 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8868 (p) REVERT: E 441 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7755 (t80) REVERT: E 581 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (mp) outliers start: 74 outliers final: 45 residues processed: 219 average time/residue: 0.2036 time to fit residues: 67.9966 Evaluate side-chains 198 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 360 HIS Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 360 HIS C 360 HIS E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.090208 restraints weight = 22466.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092490 restraints weight = 15242.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094110 restraints weight = 11716.234| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12360 Z= 0.203 Angle : 0.539 5.418 16910 Z= 0.289 Chirality : 0.042 0.160 1995 Planarity : 0.003 0.036 2120 Dihedral : 4.361 15.791 1685 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.51 % Allowed : 21.56 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.21), residues: 1560 helix: 2.19 (0.21), residues: 560 sheet: -0.03 (0.30), residues: 325 loop : -1.47 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 407 HIS 0.004 0.002 HIS A 360 PHE 0.021 0.001 PHE D 561 TYR 0.016 0.001 TYR D 632 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 1.284 Fit side-chains REVERT: D 591 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8797 (p) REVERT: E 441 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7433 (t80) outliers start: 55 outliers final: 44 residues processed: 209 average time/residue: 0.1989 time to fit residues: 63.5685 Evaluate side-chains 200 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 360 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 0.0010 chunk 20 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 360 HIS C 360 HIS E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.089024 restraints weight = 22338.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.091262 restraints weight = 15289.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092840 restraints weight = 11804.118| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12360 Z= 0.266 Angle : 0.549 5.402 16910 Z= 0.297 Chirality : 0.042 0.140 1995 Planarity : 0.003 0.033 2120 Dihedral : 4.344 20.219 1685 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.98 % Allowed : 20.25 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.21), residues: 1560 helix: 2.16 (0.21), residues: 560 sheet: 0.24 (0.30), residues: 315 loop : -1.48 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 407 HIS 0.002 0.001 HIS B 360 PHE 0.017 0.001 PHE D 561 TYR 0.013 0.002 TYR C 627 ARG 0.002 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 157 time to evaluate : 1.304 Fit side-chains REVERT: A 591 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8802 (p) REVERT: E 441 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7564 (t80) outliers start: 73 outliers final: 65 residues processed: 224 average time/residue: 0.1958 time to fit residues: 67.3016 Evaluate side-chains 218 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 360 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 631 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 90 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 117 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 360 HIS C 360 HIS E 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.086973 restraints weight = 22552.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.089191 restraints weight = 15476.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.090727 restraints weight = 11972.186| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12360 Z= 0.381 Angle : 0.593 5.894 16910 Z= 0.321 Chirality : 0.043 0.140 1995 Planarity : 0.003 0.033 2120 Dihedral : 4.460 19.548 1685 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.66 % Allowed : 22.46 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.21), residues: 1560 helix: 2.06 (0.21), residues: 560 sheet: -0.19 (0.29), residues: 335 loop : -1.46 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 407 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.001 PHE A 561 TYR 0.014 0.002 TYR D 627 ARG 0.002 0.000 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 1.323 Fit side-chains REVERT: A 591 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 627 TYR cc_start: 0.8096 (t80) cc_final: 0.7809 (t80) REVERT: D 591 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8837 (p) REVERT: E 441 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7569 (t80) outliers start: 69 outliers final: 60 residues processed: 212 average time/residue: 0.2071 time to fit residues: 67.2718 Evaluate side-chains 218 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 155 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 631 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.091212 restraints weight = 22402.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093488 restraints weight = 15391.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.095068 restraints weight = 11904.042| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12360 Z= 0.173 Angle : 0.519 5.286 16910 Z= 0.276 Chirality : 0.042 0.135 1995 Planarity : 0.003 0.029 2120 Dihedral : 4.189 21.441 1685 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.67 % Allowed : 23.93 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.21), residues: 1560 helix: 2.33 (0.21), residues: 560 sheet: 0.38 (0.30), residues: 325 loop : -1.32 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 407 HIS 0.001 0.001 HIS A 360 PHE 0.019 0.001 PHE A 561 TYR 0.014 0.001 TYR D 627 ARG 0.001 0.000 ARG B 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 1.316 Fit side-chains REVERT: A 591 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8749 (p) REVERT: D 591 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8780 (p) REVERT: E 441 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7378 (t80) outliers start: 57 outliers final: 49 residues processed: 213 average time/residue: 0.2036 time to fit residues: 66.1113 Evaluate side-chains 215 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 109 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.090835 restraints weight = 22308.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093086 restraints weight = 15351.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094631 restraints weight = 11869.303| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12360 Z= 0.202 Angle : 0.526 5.606 16910 Z= 0.279 Chirality : 0.042 0.136 1995 Planarity : 0.003 0.028 2120 Dihedral : 4.155 20.188 1685 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.66 % Allowed : 23.20 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.21), residues: 1560 helix: 2.36 (0.21), residues: 560 sheet: 0.42 (0.30), residues: 325 loop : -1.24 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 407 HIS 0.001 0.000 HIS E 360 PHE 0.017 0.001 PHE A 561 TYR 0.015 0.001 TYR A 627 ARG 0.001 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 163 time to evaluate : 1.407 Fit side-chains REVERT: A 591 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 630 TRP cc_start: 0.8599 (t60) cc_final: 0.8308 (t60) REVERT: D 447 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8352 (ttmm) REVERT: D 591 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8771 (p) REVERT: E 441 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7436 (t80) outliers start: 69 outliers final: 59 residues processed: 223 average time/residue: 0.1948 time to fit residues: 66.0217 Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 TYR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.0040 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.089621 restraints weight = 22600.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091887 restraints weight = 15444.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093481 restraints weight = 11902.404| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12360 Z= 0.243 Angle : 0.540 5.744 16910 Z= 0.288 Chirality : 0.042 0.138 1995 Planarity : 0.003 0.028 2120 Dihedral : 4.177 19.950 1685 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.57 % Allowed : 23.03 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.21), residues: 1560 helix: 2.33 (0.21), residues: 560 sheet: 0.39 (0.30), residues: 325 loop : -1.21 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 407 HIS 0.000 0.000 HIS E 360 PHE 0.016 0.001 PHE A 561 TYR 0.015 0.001 TYR C 627 ARG 0.001 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 1.305 Fit side-chains REVERT: A 591 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 630 TRP cc_start: 0.8649 (t60) cc_final: 0.8358 (t60) REVERT: D 591 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8785 (p) REVERT: E 441 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7431 (t80) outliers start: 68 outliers final: 61 residues processed: 227 average time/residue: 0.2057 time to fit residues: 71.0016 Evaluate side-chains 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 TYR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.086583 restraints weight = 22721.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.088852 restraints weight = 15510.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.090402 restraints weight = 11948.190| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12360 Z= 0.430 Angle : 0.636 6.339 16910 Z= 0.343 Chirality : 0.044 0.145 1995 Planarity : 0.004 0.030 2120 Dihedral : 4.552 20.854 1685 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.57 % Allowed : 22.87 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.21), residues: 1560 helix: 2.03 (0.21), residues: 560 sheet: -0.13 (0.28), residues: 335 loop : -1.32 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.001 0.000 HIS B 360 PHE 0.016 0.002 PHE D 559 TYR 0.014 0.002 TYR B 620 ARG 0.002 0.000 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 167 time to evaluate : 1.421 Fit side-chains REVERT: B 627 TYR cc_start: 0.8182 (t80) cc_final: 0.7958 (t80) REVERT: C 630 TRP cc_start: 0.8726 (t60) cc_final: 0.8456 (t60) REVERT: D 591 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8868 (p) REVERT: E 441 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7540 (t80) outliers start: 68 outliers final: 64 residues processed: 224 average time/residue: 0.2200 time to fit residues: 74.7145 Evaluate side-chains 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 572 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 TYR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 70 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.090432 restraints weight = 22400.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.092737 restraints weight = 15149.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094361 restraints weight = 11615.954| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12360 Z= 0.197 Angle : 0.541 5.531 16910 Z= 0.289 Chirality : 0.042 0.144 1995 Planarity : 0.003 0.027 2120 Dihedral : 4.198 20.201 1685 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.57 % Allowed : 22.62 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1560 helix: 2.32 (0.21), residues: 560 sheet: -0.04 (0.29), residues: 350 loop : -1.19 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 407 HIS 0.001 0.000 HIS B 360 PHE 0.018 0.001 PHE A 561 TYR 0.013 0.001 TYR C 627 ARG 0.001 0.000 ARG D 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 1.338 Fit side-chains REVERT: D 591 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8798 (p) REVERT: E 441 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7305 (t80) outliers start: 68 outliers final: 62 residues processed: 230 average time/residue: 0.2072 time to fit residues: 72.3201 Evaluate side-chains 242 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 572 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 572 TYR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 623 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.093747 restraints weight = 22208.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.096129 restraints weight = 15152.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097768 restraints weight = 11653.466| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12360 Z= 0.172 Angle : 0.526 5.306 16910 Z= 0.279 Chirality : 0.041 0.137 1995 Planarity : 0.003 0.027 2120 Dihedral : 4.005 19.144 1685 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.92 % Allowed : 23.36 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.22), residues: 1560 helix: 2.49 (0.21), residues: 560 sheet: 0.14 (0.29), residues: 355 loop : -1.14 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.000 0.000 HIS A 360 PHE 0.016 0.001 PHE A 561 TYR 0.015 0.001 TYR A 627 ARG 0.002 0.000 ARG D 513 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.65 seconds wall clock time: 51 minutes 44.96 seconds (3104.96 seconds total)