Starting phenix.real_space_refine on Tue Jun 10 18:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ftj_50747/06_2025/9ftj_50747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ftj_50747/06_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_50747/06_2025/9ftj_50747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ftj_50747/06_2025/9ftj_50747.map" model { file = "/net/cci-nas-00/data/ceres_data/9ftj_50747/06_2025/9ftj_50747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ftj_50747/06_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-5710/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: 5.30, 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: 2.81 Conformation dependent library (CDL) restraints added in 1.5 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: 1.26 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: 3.04 Time building geometry restraints manager: 3.22 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: 1.080 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 25.690 Find NCS groups from input model: 0.250 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- 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= 0.285 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 Details of bonding type rmsd hydrogen bonds : bond 0.19942 ( 620) hydrogen bonds : angle 6.51630 ( 1785) covalent geometry : bond 0.00688 (12360) covalent geometry : angle 0.64407 (16910) *********************** 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 : 1.380 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: 0.2513 time to fit residues: 45.9028 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 : 1.492 ------------------------------------------------------------------------------- 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 = 0.110337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087446 restraints weight = 22560.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089618 restraints weight = 15517.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.091007 restraints weight = 12069.896| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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= 0.219 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 Details of bonding type rmsd hydrogen bonds : bond 0.06664 ( 620) hydrogen bonds : angle 4.82298 ( 1785) covalent geometry : bond 0.00529 (12360) covalent geometry : angle 0.59879 (16910) *********************** 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 : 1.272 Fit side-chains REVERT: A 581 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 591 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8842 (p) REVERT: C 581 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8758 (mp) REVERT: C 627 TYR cc_start: 0.8107 (t80) cc_final: 0.7772 (t80) REVERT: D 546 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8596 (tt) REVERT: D 591 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8853 (p) REVERT: E 441 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7756 (t80) REVERT: E 581 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8814 (mp) outliers start: 74 outliers final: 45 residues processed: 219 average time/residue: 0.1974 time to fit residues: 66.6000 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 : 1.283 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.112270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.089525 restraints weight = 22521.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091778 restraints weight = 15361.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093355 restraints weight = 11854.286| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12360 Z= 0.154 Angle : 0.548 5.585 16910 Z= 0.294 Chirality : 0.043 0.156 1995 Planarity : 0.003 0.036 2120 Dihedral : 4.397 15.717 1685 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.75 % Allowed : 21.48 % 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: 0.24 (0.21), residues: 1560 helix: 2.15 (0.21), residues: 560 sheet: -0.08 (0.30), residues: 325 loop : -1.49 (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 0.020 0.001 PHE D 561 TYR 0.016 0.002 TYR D 632 ARG 0.003 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 620) hydrogen bonds : angle 4.41196 ( 1785) covalent geometry : bond 0.00356 (12360) covalent geometry : angle 0.54786 (16910) *********************** 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 218 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 1.394 Fit side-chains REVERT: D 591 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8812 (p) REVERT: E 441 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7486 (t80) outliers start: 58 outliers final: 47 residues processed: 211 average time/residue: 0.1922 time to fit residues: 62.4584 Evaluate side-chains 202 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 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 623 VAL Chi-restraints excluded: chain B residue 332 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 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 412 VAL 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: 2.9990 chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.110271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.087581 restraints weight = 22453.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089761 restraints weight = 15644.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.091289 restraints weight = 12226.872| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12360 Z= 0.209 Angle : 0.578 5.862 16910 Z= 0.313 Chirality : 0.043 0.140 1995 Planarity : 0.003 0.035 2120 Dihedral : 4.427 19.873 1685 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.82 % Allowed : 21.56 % Favored : 72.62 % 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: 0.15 (0.21), residues: 1560 helix: 2.07 (0.21), residues: 560 sheet: -0.07 (0.30), residues: 325 loop : -1.57 (0.22), residues: 675 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 0.016 0.001 PHE D 561 TYR 0.014 0.002 TYR D 632 ARG 0.003 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.05928 ( 620) hydrogen bonds : angle 4.44883 ( 1785) covalent geometry : bond 0.00508 (12360) covalent geometry : angle 0.57824 (16910) *********************** 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 226 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 1.331 Fit side-chains REVERT: C 627 TYR cc_start: 0.8109 (t80) cc_final: 0.7826 (t80) REVERT: E 441 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7553 (t80) outliers start: 71 outliers final: 62 residues processed: 219 average time/residue: 0.1913 time to fit residues: 64.8631 Evaluate side-chains 212 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 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 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 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: 2.9990 chunk 55 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.110544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.087807 restraints weight = 22583.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.089997 restraints weight = 15746.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091475 restraints weight = 12293.625| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12360 Z= 0.204 Angle : 0.568 5.857 16910 Z= 0.307 Chirality : 0.043 0.141 1995 Planarity : 0.003 0.033 2120 Dihedral : 4.418 19.799 1685 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.90 % Allowed : 22.54 % 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: 0.31 (0.21), residues: 1560 helix: 2.05 (0.21), residues: 560 sheet: 0.27 (0.30), residues: 305 loop : -1.43 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 407 HIS 0.003 0.001 HIS B 360 PHE 0.016 0.001 PHE D 561 TYR 0.014 0.002 TYR D 632 ARG 0.002 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.05924 ( 620) hydrogen bonds : angle 4.41901 ( 1785) covalent geometry : bond 0.00496 (12360) covalent geometry : angle 0.56840 (16910) *********************** 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 222 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 150 time to evaluate : 1.275 Fit side-chains REVERT: C 627 TYR cc_start: 0.8149 (t80) cc_final: 0.7851 (t80) REVERT: D 591 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8842 (p) REVERT: E 441 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7512 (t80) outliers start: 72 outliers final: 62 residues processed: 214 average time/residue: 0.1971 time to fit residues: 64.6941 Evaluate side-chains 220 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 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 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 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: 10.0000 chunk 7 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.114805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.092203 restraints weight = 22340.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094566 restraints weight = 15171.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096177 restraints weight = 11632.137| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12360 Z= 0.113 Angle : 0.514 5.134 16910 Z= 0.272 Chirality : 0.041 0.135 1995 Planarity : 0.003 0.028 2120 Dihedral : 4.101 19.381 1685 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.93 % Allowed : 24.51 % 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: 0.67 (0.21), residues: 1560 helix: 2.35 (0.21), residues: 560 sheet: 0.52 (0.30), residues: 325 loop : -1.30 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 407 HIS 0.001 0.001 HIS A 360 PHE 0.018 0.001 PHE A 561 TYR 0.017 0.001 TYR D 632 ARG 0.001 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 620) hydrogen bonds : angle 3.98137 ( 1785) covalent geometry : bond 0.00238 (12360) covalent geometry : angle 0.51364 (16910) *********************** 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 214 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.147 Fit side-chains REVERT: D 591 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8712 (p) REVERT: E 441 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7333 (t80) outliers start: 48 outliers final: 35 residues processed: 212 average time/residue: 0.1947 time to fit residues: 63.2449 Evaluate side-chains 201 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL 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 B residue 352 VAL Chi-restraints excluded: chain B residue 428 THR 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 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 D residue 428 THR 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 591 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 364 LEU 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 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: 0.9980 chunk 109 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.112859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.090325 restraints weight = 22292.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.092578 restraints weight = 15391.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094145 restraints weight = 11939.175| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12360 Z= 0.150 Angle : 0.534 5.915 16910 Z= 0.284 Chirality : 0.042 0.136 1995 Planarity : 0.003 0.029 2120 Dihedral : 4.140 19.201 1685 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.59 % Allowed : 24.02 % 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: 0.66 (0.21), residues: 1560 helix: 2.33 (0.21), residues: 560 sheet: 0.43 (0.30), residues: 325 loop : -1.26 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 407 HIS 0.000 0.000 HIS E 360 PHE 0.016 0.001 PHE A 561 TYR 0.014 0.001 TYR C 627 ARG 0.001 0.000 ARG B 445 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 620) hydrogen bonds : angle 4.06935 ( 1785) covalent geometry : bond 0.00354 (12360) covalent geometry : angle 0.53366 (16910) *********************** 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 218 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 1.310 Fit side-chains REVERT: C 630 TRP cc_start: 0.8545 (t60) cc_final: 0.8306 (t60) REVERT: D 591 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8775 (p) REVERT: E 441 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7410 (t80) outliers start: 56 outliers final: 51 residues processed: 211 average time/residue: 0.2020 time to fit residues: 65.0796 Evaluate side-chains 219 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 631 VAL Chi-restraints excluded: chain B residue 352 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 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: 0.0370 overall best weight: 1.7664 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.113038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.090457 restraints weight = 22565.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092745 restraints weight = 15507.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.094275 restraints weight = 11969.381| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12360 Z= 0.146 Angle : 0.533 5.665 16910 Z= 0.283 Chirality : 0.042 0.136 1995 Planarity : 0.003 0.027 2120 Dihedral : 4.119 19.726 1685 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.00 % Allowed : 23.44 % 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: 0.69 (0.21), residues: 1560 helix: 2.35 (0.21), residues: 560 sheet: 0.45 (0.30), residues: 325 loop : -1.23 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 407 HIS 0.002 0.000 HIS C 360 PHE 0.016 0.001 PHE A 561 TYR 0.014 0.001 TYR C 627 ARG 0.001 0.000 ARG B 445 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 620) hydrogen bonds : angle 4.04903 ( 1785) covalent geometry : bond 0.00347 (12360) covalent geometry : angle 0.53311 (16910) *********************** 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 232 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.252 Fit side-chains REVERT: C 630 TRP cc_start: 0.8600 (t60) cc_final: 0.8342 (t60) REVERT: D 591 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8783 (p) REVERT: E 441 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7395 (t80) outliers start: 61 outliers final: 55 residues processed: 223 average time/residue: 0.2073 time to fit residues: 70.1173 Evaluate side-chains 227 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 631 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 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 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 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 555 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 352 VAL Chi-restraints excluded: chain E residue 364 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 0.0040 chunk 108 optimal weight: 1.9990 overall best weight: 2.8998 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.110334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.087583 restraints weight = 22538.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.089864 restraints weight = 15371.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091470 restraints weight = 11825.886| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12360 Z= 0.206 Angle : 0.583 6.044 16910 Z= 0.312 Chirality : 0.043 0.143 1995 Planarity : 0.003 0.028 2120 Dihedral : 4.300 20.205 1685 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.33 % Allowed : 23.20 % Favored : 71.48 % 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: 0.48 (0.21), residues: 1560 helix: 2.22 (0.21), residues: 560 sheet: 0.11 (0.28), residues: 335 loop : -1.29 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.000 0.000 HIS C 360 PHE 0.014 0.001 PHE A 561 TYR 0.014 0.002 TYR C 632 ARG 0.001 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.05775 ( 620) hydrogen bonds : angle 4.27978 ( 1785) covalent geometry : bond 0.00505 (12360) covalent geometry : angle 0.58255 (16910) *********************** 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 233 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 168 time to evaluate : 1.351 Fit side-chains REVERT: C 630 TRP cc_start: 0.8664 (t60) cc_final: 0.8398 (t60) REVERT: D 591 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8829 (p) REVERT: E 441 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7519 (t80) outliers start: 65 outliers final: 62 residues processed: 222 average time/residue: 0.2009 time to fit residues: 67.6927 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 : 1.316 ------------------------------------------------------------------------------- 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 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 631 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 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 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 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 555 VAL Chi-restraints excluded: chain D residue 557 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 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 557 VAL Chi-restraints excluded: chain E residue 617 LEU Chi-restraints excluded: chain E residue 631 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 70 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 141 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.2640 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.113573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091129 restraints weight = 22295.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.093423 restraints weight = 14914.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.095050 restraints weight = 11378.140| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12360 Z= 0.128 Angle : 0.533 5.372 16910 Z= 0.284 Chirality : 0.042 0.140 1995 Planarity : 0.003 0.027 2120 Dihedral : 4.111 19.694 1685 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.08 % Allowed : 22.95 % Favored : 71.97 % 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: 2.37 (0.21), residues: 560 sheet: 0.06 (0.28), residues: 355 loop : -1.23 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 407 HIS 0.001 0.000 HIS C 360 PHE 0.017 0.001 PHE A 561 TYR 0.013 0.001 TYR C 627 ARG 0.001 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 620) hydrogen bonds : angle 4.00148 ( 1785) covalent geometry : bond 0.00292 (12360) covalent geometry : angle 0.53345 (16910) ********************** 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 234 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 1.348 Fit side-chains REVERT: D 591 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8740 (p) REVERT: E 441 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7330 (t80) outliers start: 62 outliers final: 58 residues processed: 223 average time/residue: 0.1944 time to fit residues: 65.9384 Evaluate side-chains 239 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL 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 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 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 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 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 557 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 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 557 VAL Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.0970 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 overall best weight: 1.9380 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.112582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.089857 restraints weight = 22423.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.092131 restraints weight = 15335.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.093714 restraints weight = 11844.344| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12360 Z= 0.158 Angle : 0.548 5.730 16910 Z= 0.292 Chirality : 0.042 0.141 1995 Planarity : 0.003 0.027 2120 Dihedral : 4.128 19.799 1685 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.33 % Allowed : 22.95 % 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: 0.59 (0.21), residues: 1560 helix: 2.34 (0.21), residues: 560 sheet: 0.06 (0.28), residues: 355 loop : -1.21 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 407 HIS 0.001 0.000 HIS C 360 PHE 0.014 0.001 PHE A 561 TYR 0.019 0.001 TYR E 627 ARG 0.001 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 620) hydrogen bonds : angle 4.07267 ( 1785) covalent geometry : bond 0.00380 (12360) covalent geometry : angle 0.54839 (16910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.08 seconds wall clock time: 56 minutes 36.13 seconds (3396.13 seconds total)