Starting phenix.real_space_refine on Thu Jan 23 07:28:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fti_50746/01_2025/9fti_50746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fti_50746/01_2025/9fti_50746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fti_50746/01_2025/9fti_50746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fti_50746/01_2025/9fti_50746.map" model { file = "/net/cci-nas-00/data/ceres_data/9fti_50746/01_2025/9fti_50746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fti_50746/01_2025/9fti_50746.cif" } resolution = 3.5 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 40 5.16 5 C 12770 2.51 5 N 3415 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19935 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 3987 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 531} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 15, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 268 Restraints were copied for chains: C, B, E, D Time building chain proxies: 8.57, per 1000 atoms: 0.43 Number of scatterers: 19935 At special positions: 0 Unit cell: (136.149, 133.563, 154.244, 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 40 16.00 O 3710 8.00 N 3415 7.00 C 12770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 373 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.81 Conformation dependent library (CDL) restraints added in 2.9 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5150 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 35 sheets defined 26.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.880A pdb=" N LEU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 522 through 536 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 543 through 564 removed outlier: 3.691A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 558 " --> pdb=" O LEU B 554 " (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 575 through 604 removed outlier: 3.682A pdb=" N ILE B 589 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 592 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 636 removed outlier: 3.628A pdb=" N ALA B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Proline residue: B 621 - end of helix removed outlier: 4.067A pdb=" N TYR B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 634 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.880A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 522 through 536 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 543 through 564 removed outlier: 3.691A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 558 " --> pdb=" O LEU A 554 " (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 575 through 604 removed outlier: 3.682A pdb=" N ILE A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 removed outlier: 3.628A pdb=" N ALA A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix removed outlier: 4.067A pdb=" N TYR A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 634 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.879A pdb=" N LEU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 522 Processing helix chain 'C' and resid 522 through 536 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 543 through 564 removed outlier: 3.690A pdb=" N VAL C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 558 " --> pdb=" O LEU C 554 " (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 575 through 604 removed outlier: 3.681A pdb=" N ILE C 589 " --> pdb=" O CYS C 585 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU C 592 " --> pdb=" O ALA C 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 599 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 602 " --> pdb=" O LYS C 598 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 636 removed outlier: 3.629A pdb=" N ALA C 609 " --> pdb=" O LYS C 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 4.067A pdb=" N TYR C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 633 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 634 " --> pdb=" O TRP C 630 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.880A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.902A pdb=" N ILE D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 522 through 536 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 543 through 564 removed outlier: 3.690A pdb=" N VAL D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 558 " --> pdb=" O LEU D 554 " (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 575 through 604 removed outlier: 3.681A pdb=" N ILE D 589 " --> pdb=" O CYS D 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 599 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 removed outlier: 3.627A pdb=" N ALA D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 615 " --> pdb=" O GLN D 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 616 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Proline residue: D 621 - end of helix removed outlier: 4.067A pdb=" N TYR D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D 625 " --> pdb=" O PRO D 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 633 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG D 634 " --> pdb=" O TRP D 630 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.879A pdb=" N LEU E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 522 Processing helix chain 'E' and resid 522 through 536 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 543 through 564 removed outlier: 3.690A pdb=" N VAL E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 558 " --> pdb=" O LEU E 554 " (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 575 through 604 removed outlier: 3.682A pdb=" N ILE E 589 " --> pdb=" O CYS E 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU E 592 " --> pdb=" O ALA E 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 599 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 602 " --> pdb=" O LYS E 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 removed outlier: 3.628A pdb=" N ALA E 609 " --> pdb=" O LYS E 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR E 614 " --> pdb=" O ALA E 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP E 615 " --> pdb=" O GLN E 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 616 " --> pdb=" O ILE E 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 618 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR E 620 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Proline residue: E 621 - end of helix removed outlier: 4.066A pdb=" N TYR E 624 " --> pdb=" O TYR E 620 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG E 634 " --> pdb=" O TRP E 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 635 " --> pdb=" O VAL E 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS B 204 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 236 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP B 251 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 332 removed outlier: 7.223A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 339 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER B 350 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY B 341 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN B 348 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 427 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR B 428 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER B 408 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU B 454 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 502 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 494 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 510 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER B 486 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS A 204 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 236 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP A 251 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 329 through 332 removed outlier: 7.222A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 334 through 343 removed outlier: 6.636A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A 339 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER A 350 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY A 341 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN A 348 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 427 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 428 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 408 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU A 454 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 502 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 494 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 510 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 486 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS C 204 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 236 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP C 251 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 329 through 332 removed outlier: 7.223A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 427 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR C 428 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 408 " --> pdb=" O THR C 428 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 397 through 399 removed outlier: 3.514A pdb=" N LEU C 454 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 502 " --> pdb=" O VAL C 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 494 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 510 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 486 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AC6, first strand: chain 'D' and resid 204 through 210 removed outlier: 3.620A pdb=" N HIS D 204 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 236 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP D 251 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.222A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 339 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER D 350 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY D 341 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN D 348 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 427 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR D 428 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER D 408 " --> pdb=" O THR D 428 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU D 454 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 502 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 494 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 510 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER D 486 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 40 through 45 removed outlier: 5.894A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AD4, first strand: chain 'E' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS E 204 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 236 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP E 251 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 329 through 332 removed outlier: 7.223A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE E 339 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER E 350 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY E 341 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASN E 348 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE E 427 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR E 428 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER E 408 " --> pdb=" O THR E 428 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU E 454 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 500 " --> pdb=" O PHE E 496 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN E 502 " --> pdb=" O VAL E 494 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 494 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 510 " --> pdb=" O SER E 486 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER E 486 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2055 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: 6.45 Time building geometry restraints manager: 5.62 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: 6683 1.34 - 1.46: 4203 1.46 - 1.58: 9359 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 20295 Sorted by residual: bond pdb=" CA VAL A 336 " pdb=" CB VAL A 336 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.23e-02 6.61e+03 8.03e-01 bond pdb=" CA VAL D 336 " pdb=" CB VAL D 336 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.23e-02 6.61e+03 7.83e-01 bond pdb=" CA VAL B 336 " pdb=" CB VAL B 336 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.23e-02 6.61e+03 7.78e-01 bond pdb=" CA VAL E 336 " pdb=" CB VAL E 336 " ideal model delta sigma weight residual 1.540 1.530 0.011 1.23e-02 6.61e+03 7.61e-01 bond pdb=" CA VAL C 336 " pdb=" CB VAL C 336 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.23e-02 6.61e+03 7.28e-01 ... (remaining 20290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 27345 1.95 - 3.91: 329 3.91 - 5.86: 46 5.86 - 7.81: 5 7.81 - 9.77: 5 Bond angle restraints: 27730 Sorted by residual: angle pdb=" CA LEU B 364 " pdb=" CB LEU B 364 " pdb=" CG LEU B 364 " ideal model delta sigma weight residual 116.30 126.07 -9.77 3.50e+00 8.16e-02 7.79e+00 angle pdb=" CA LEU D 364 " pdb=" CB LEU D 364 " pdb=" CG LEU D 364 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU E 364 " pdb=" CB LEU E 364 " pdb=" CG LEU E 364 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU C 364 " pdb=" CB LEU C 364 " pdb=" CG LEU C 364 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.75e+00 angle pdb=" CA LEU A 364 " pdb=" CB LEU A 364 " pdb=" CG LEU A 364 " ideal model delta sigma weight residual 116.30 126.04 -9.74 3.50e+00 8.16e-02 7.75e+00 ... (remaining 27725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 10265 17.16 - 34.32: 1213 34.32 - 51.48: 318 51.48 - 68.64: 55 68.64 - 85.80: 25 Dihedral angle restraints: 11876 sinusoidal: 3911 harmonic: 7965 Sorted by residual: dihedral pdb=" CA VAL A 386 " pdb=" C VAL A 386 " pdb=" N ALA A 387 " pdb=" CA ALA A 387 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL C 386 " pdb=" C VAL C 386 " pdb=" N ALA C 387 " pdb=" CA ALA C 387 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B 386 " pdb=" C VAL B 386 " pdb=" N ALA B 387 " pdb=" CA ALA B 387 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 11873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1693 0.027 - 0.054: 1034 0.054 - 0.082: 330 0.082 - 0.109: 201 0.109 - 0.136: 72 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ILE A 339 " pdb=" N ILE A 339 " pdb=" C ILE A 339 " pdb=" CB ILE A 339 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE B 339 " pdb=" N ILE B 339 " pdb=" C ILE B 339 " pdb=" CB ILE B 339 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PRO D 417 " pdb=" N PRO D 417 " pdb=" C PRO D 417 " pdb=" CB PRO D 417 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 3327 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 160 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO E 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 161 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 161 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 160 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO B 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 160 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 161 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.024 5.00e-02 4.00e+02 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 99 2.60 - 3.18: 16292 3.18 - 3.75: 27386 3.75 - 4.33: 36436 4.33 - 4.90: 61466 Nonbonded interactions: 141679 Sorted by model distance: nonbonded pdb=" SG CYS D 275 " pdb=" SG CYS D 280 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 275 " pdb=" SG CYS C 280 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 275 " pdb=" SG CYS E 280 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS A 275 " pdb=" SG CYS A 280 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 371 " pdb=" SG CYS D 373 " model vdw 2.032 3.760 ... (remaining 141674 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 41.780 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.005 0.040 20295 Z= 0.332 Angle : 0.597 9.768 27730 Z= 0.304 Chirality : 0.044 0.136 3330 Planarity : 0.004 0.044 3620 Dihedral : 16.699 85.801 6720 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.27 % Allowed : 29.81 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.77 (0.15), residues: 2720 helix: -1.26 (0.19), residues: 585 sheet: -0.03 (0.19), residues: 740 loop : -1.79 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS D 285 PHE 0.015 0.002 PHE C 505 TYR 0.013 0.002 TYR D 441 ARG 0.001 0.000 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 2.171 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 224 ARG cc_start: 0.7064 (mmt90) cc_final: 0.6757 (mmm-85) REVERT: A 615 TRP cc_start: 0.6948 (t-100) cc_final: 0.6628 (t-100) REVERT: C 615 TRP cc_start: 0.6745 (t-100) cc_final: 0.6390 (t-100) REVERT: D 232 PHE cc_start: 0.7164 (t80) cc_final: 0.6832 (t80) outliers start: 5 outliers final: 2 residues processed: 253 average time/residue: 0.3344 time to fit residues: 130.1218 Evaluate side-chains 231 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain D residue 581 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 40.0000 chunk 208 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 285 HIS B 410 ASN B 471 GLN A 206 GLN A 285 HIS A 410 ASN A 471 GLN C 206 GLN C 285 HIS C 410 ASN C 471 GLN D 206 GLN D 285 HIS D 410 ASN D 471 GLN E 206 GLN E 285 HIS E 410 ASN E 471 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.150818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106173 restraints weight = 32430.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108690 restraints weight = 18358.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110236 restraints weight = 13101.915| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20295 Z= 0.426 Angle : 0.737 14.361 27730 Z= 0.374 Chirality : 0.048 0.151 3330 Planarity : 0.006 0.044 3620 Dihedral : 5.546 54.072 2924 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.94 % Allowed : 27.59 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.56 (0.16), residues: 2720 helix: -0.52 (0.19), residues: 585 sheet: -0.10 (0.18), residues: 800 loop : -1.88 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 482 HIS 0.005 0.001 HIS C 285 PHE 0.019 0.002 PHE E 436 TYR 0.019 0.003 TYR A 517 ARG 0.004 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 251 time to evaluate : 2.195 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 329 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6968 (mt) REVERT: B 559 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: A 158 LYS cc_start: 0.6392 (pttt) cc_final: 0.5809 (mptt) REVERT: A 280 CYS cc_start: 0.5654 (OUTLIER) cc_final: 0.4910 (m) REVERT: A 329 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6976 (mt) REVERT: A 431 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8581 (mt) REVERT: A 615 TRP cc_start: 0.6721 (t-100) cc_final: 0.6334 (t-100) REVERT: C 559 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 615 TRP cc_start: 0.6550 (t-100) cc_final: 0.6121 (t-100) REVERT: D 329 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7033 (mt) REVERT: E 431 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8649 (mt) outliers start: 128 outliers final: 75 residues processed: 348 average time/residue: 0.2954 time to fit residues: 162.5672 Evaluate side-chains 299 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 38 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 40.0000 chunk 161 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 182 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.153457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108796 restraints weight = 31945.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111390 restraints weight = 17972.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112980 restraints weight = 12715.674| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20295 Z= 0.228 Angle : 0.622 16.778 27730 Z= 0.301 Chirality : 0.043 0.137 3330 Planarity : 0.004 0.044 3620 Dihedral : 4.886 55.068 2922 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.15 % Allowed : 30.35 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.15 (0.16), residues: 2720 helix: 0.19 (0.21), residues: 585 sheet: 0.09 (0.19), residues: 795 loop : -1.77 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 482 HIS 0.002 0.000 HIS A 360 PHE 0.014 0.001 PHE B 505 TYR 0.011 0.002 TYR E 441 ARG 0.005 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 242 time to evaluate : 2.045 Fit side-chains REVERT: B 78 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5819 (tp) REVERT: B 271 LEU cc_start: 0.6206 (tp) cc_final: 0.5893 (tp) REVERT: B 329 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6935 (mt) REVERT: B 559 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: A 271 LEU cc_start: 0.6145 (tp) cc_final: 0.5831 (tp) REVERT: A 280 CYS cc_start: 0.5791 (OUTLIER) cc_final: 0.5186 (m) REVERT: A 329 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6946 (mt) REVERT: A 559 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7347 (t80) REVERT: C 249 LEU cc_start: 0.8214 (tp) cc_final: 0.7887 (tp) REVERT: C 271 LEU cc_start: 0.6183 (tp) cc_final: 0.5871 (tp) REVERT: C 280 CYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5640 (m) REVERT: C 559 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7025 (t80) REVERT: C 615 TRP cc_start: 0.6815 (t-100) cc_final: 0.6448 (t-100) REVERT: D 271 LEU cc_start: 0.6032 (tp) cc_final: 0.5766 (tp) REVERT: D 280 CYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5358 (m) REVERT: D 329 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6978 (mt) REVERT: D 559 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: E 249 LEU cc_start: 0.8079 (tt) cc_final: 0.7768 (tp) REVERT: E 271 LEU cc_start: 0.6262 (tp) cc_final: 0.5920 (tp) REVERT: E 280 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5778 (m) REVERT: E 559 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7506 (m-80) outliers start: 95 outliers final: 47 residues processed: 322 average time/residue: 0.2952 time to fit residues: 150.3669 Evaluate side-chains 283 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 166 optimal weight: 30.0000 chunk 265 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.151144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106366 restraints weight = 32756.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108910 restraints weight = 18639.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110400 restraints weight = 13276.402| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 20295 Z= 0.442 Angle : 0.741 15.445 27730 Z= 0.371 Chirality : 0.048 0.158 3330 Planarity : 0.006 0.042 3620 Dihedral : 5.567 53.192 2922 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 7.26 % Allowed : 30.46 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.42 (0.16), residues: 2720 helix: -0.10 (0.20), residues: 580 sheet: 0.08 (0.19), residues: 780 loop : -1.99 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 482 HIS 0.003 0.001 HIS A 360 PHE 0.020 0.002 PHE E 443 TYR 0.019 0.003 TYR A 517 ARG 0.004 0.001 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 231 time to evaluate : 2.112 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 78 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5704 (tp) REVERT: B 271 LEU cc_start: 0.6244 (tp) cc_final: 0.5993 (tp) REVERT: B 282 LEU cc_start: 0.8349 (mp) cc_final: 0.8104 (mm) REVERT: B 329 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6954 (mt) REVERT: B 520 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7958 (tt) REVERT: B 559 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7461 (m-80) REVERT: A 158 LYS cc_start: 0.6461 (pttt) cc_final: 0.5864 (mptt) REVERT: A 271 LEU cc_start: 0.6092 (tp) cc_final: 0.5852 (tp) REVERT: A 280 CYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5350 (m) REVERT: A 329 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7017 (mt) REVERT: A 559 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7275 (t80) REVERT: C 271 LEU cc_start: 0.6184 (tp) cc_final: 0.5953 (tp) REVERT: C 280 CYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5580 (m) REVERT: C 520 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8103 (tt) REVERT: C 559 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7042 (t80) REVERT: C 615 TRP cc_start: 0.6867 (t-100) cc_final: 0.6562 (t-100) REVERT: D 78 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5642 (tp) REVERT: D 271 LEU cc_start: 0.6059 (tp) cc_final: 0.5843 (tp) REVERT: D 280 CYS cc_start: 0.5946 (OUTLIER) cc_final: 0.5349 (m) REVERT: D 559 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: E 280 CYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5911 (m) REVERT: E 431 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8623 (mt) REVERT: E 559 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7420 (m-80) outliers start: 134 outliers final: 97 residues processed: 347 average time/residue: 0.2801 time to fit residues: 154.1216 Evaluate side-chains 330 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 217 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 253 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 184 optimal weight: 0.0980 chunk 127 optimal weight: 40.0000 chunk 105 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 164 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 57 optimal weight: 0.0020 overall best weight: 1.2792 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.155456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110397 restraints weight = 32019.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113073 restraints weight = 17616.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114735 restraints weight = 12324.752| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20295 Z= 0.168 Angle : 0.598 17.946 27730 Z= 0.280 Chirality : 0.042 0.136 3330 Planarity : 0.004 0.052 3620 Dihedral : 4.586 55.924 2922 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.55 % Allowed : 32.79 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.90 (0.16), residues: 2720 helix: 0.68 (0.21), residues: 585 sheet: 0.22 (0.19), residues: 800 loop : -1.75 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 482 HIS 0.002 0.001 HIS B 285 PHE 0.016 0.001 PHE D 579 TYR 0.010 0.001 TYR D 441 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 245 time to evaluate : 2.112 Fit side-chains REVERT: B 271 LEU cc_start: 0.6141 (tp) cc_final: 0.5901 (tp) REVERT: B 282 LEU cc_start: 0.8364 (mp) cc_final: 0.8148 (mm) REVERT: B 520 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 559 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 634 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5380 (mtm180) REVERT: A 155 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7092 (ptm160) REVERT: A 249 LEU cc_start: 0.8275 (tt) cc_final: 0.7996 (tp) REVERT: A 271 LEU cc_start: 0.5971 (tp) cc_final: 0.5723 (tp) REVERT: A 280 CYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5382 (m) REVERT: A 559 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7446 (t80) REVERT: C 249 LEU cc_start: 0.8143 (tp) cc_final: 0.7907 (tp) REVERT: C 271 LEU cc_start: 0.5919 (tp) cc_final: 0.5677 (tp) REVERT: C 280 CYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5598 (m) REVERT: C 520 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8132 (tt) REVERT: C 559 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7159 (t80) REVERT: C 611 GLN cc_start: 0.5737 (tm-30) cc_final: 0.5435 (tm-30) REVERT: D 249 LEU cc_start: 0.8134 (tt) cc_final: 0.7788 (tp) REVERT: D 271 LEU cc_start: 0.5993 (tp) cc_final: 0.5764 (tp) REVERT: D 280 CYS cc_start: 0.5789 (OUTLIER) cc_final: 0.5476 (m) REVERT: D 559 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: E 280 CYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5967 (m) REVERT: E 431 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8653 (mt) REVERT: E 559 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7532 (m-80) outliers start: 84 outliers final: 59 residues processed: 312 average time/residue: 0.3091 time to fit residues: 149.5107 Evaluate side-chains 298 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 225 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 206 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 0.0070 chunk 269 optimal weight: 5.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.151941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107127 restraints weight = 32342.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109645 restraints weight = 18414.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111197 restraints weight = 13108.400| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20295 Z= 0.350 Angle : 0.685 16.080 27730 Z= 0.336 Chirality : 0.046 0.146 3330 Planarity : 0.005 0.041 3620 Dihedral : 5.182 54.021 2922 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 6.67 % Allowed : 31.60 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.16 (0.16), residues: 2720 helix: 0.33 (0.21), residues: 585 sheet: 0.25 (0.19), residues: 775 loop : -1.95 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 482 HIS 0.002 0.001 HIS A 360 PHE 0.022 0.002 PHE D 579 TYR 0.017 0.002 TYR A 517 ARG 0.004 0.000 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 233 time to evaluate : 2.073 Fit side-chains REVERT: B 78 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5701 (tp) REVERT: B 271 LEU cc_start: 0.6198 (tp) cc_final: 0.5990 (tp) REVERT: B 329 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6952 (mt) REVERT: B 520 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 559 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: A 158 LYS cc_start: 0.6338 (pttt) cc_final: 0.5741 (mptt) REVERT: A 249 LEU cc_start: 0.8057 (tt) cc_final: 0.7799 (tp) REVERT: A 271 LEU cc_start: 0.5963 (tp) cc_final: 0.5737 (tp) REVERT: A 280 CYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5426 (m) REVERT: A 329 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 559 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7293 (t80) REVERT: C 158 LYS cc_start: 0.6444 (pttt) cc_final: 0.5708 (mttt) REVERT: C 520 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8079 (tt) REVERT: C 559 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7127 (t80) REVERT: D 78 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5601 (tp) REVERT: D 280 CYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5436 (m) REVERT: D 436 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: D 559 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: E 155 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7227 (ptm160) REVERT: E 280 CYS cc_start: 0.6296 (OUTLIER) cc_final: 0.6020 (m) REVERT: E 431 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8646 (mt) REVERT: E 559 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7393 (m-80) outliers start: 123 outliers final: 86 residues processed: 338 average time/residue: 0.3188 time to fit residues: 167.0546 Evaluate side-chains 331 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 228 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 ARG Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 4 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 171 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 123 optimal weight: 40.0000 chunk 187 optimal weight: 9.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109819 restraints weight = 32258.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111551 restraints weight = 21803.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112142 restraints weight = 14593.316| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20295 Z= 0.239 Angle : 0.625 17.027 27730 Z= 0.299 Chirality : 0.044 0.137 3330 Planarity : 0.004 0.042 3620 Dihedral : 4.847 55.080 2922 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.83 % Allowed : 31.06 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.99 (0.16), residues: 2720 helix: 0.61 (0.21), residues: 585 sheet: 0.25 (0.19), residues: 795 loop : -1.86 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 482 HIS 0.002 0.000 HIS A 360 PHE 0.019 0.001 PHE D 579 TYR 0.012 0.002 TYR A 517 ARG 0.004 0.000 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 230 time to evaluate : 2.219 Fit side-chains REVERT: B 78 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5586 (tp) REVERT: B 271 LEU cc_start: 0.6100 (tp) cc_final: 0.5897 (tp) REVERT: B 282 LEU cc_start: 0.8447 (mp) cc_final: 0.8175 (mm) REVERT: B 329 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6955 (mt) REVERT: B 436 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6323 (m-10) REVERT: B 520 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8003 (tt) REVERT: B 559 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: A 329 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6978 (mt) REVERT: A 559 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 158 LYS cc_start: 0.6298 (pttt) cc_final: 0.5558 (mttt) REVERT: C 520 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8173 (tt) REVERT: C 559 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7202 (t80) REVERT: D 155 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7274 (ptm160) REVERT: D 255 LYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5493 (pttp) REVERT: D 559 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: E 431 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8705 (mt) REVERT: E 436 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6307 (m-80) REVERT: E 446 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: E 559 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: E 617 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7632 (tt) outliers start: 126 outliers final: 87 residues processed: 335 average time/residue: 0.3070 time to fit residues: 161.2004 Evaluate side-chains 331 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 227 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 194 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 255 optimal weight: 0.0270 chunk 256 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 overall best weight: 2.1042 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.154777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109537 restraints weight = 32134.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112238 restraints weight = 17795.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113877 restraints weight = 12429.731| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20295 Z= 0.205 Angle : 0.606 17.577 27730 Z= 0.286 Chirality : 0.043 0.139 3330 Planarity : 0.004 0.041 3620 Dihedral : 4.625 55.115 2922 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.50 % Allowed : 31.22 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.83 (0.16), residues: 2720 helix: 0.83 (0.22), residues: 585 sheet: 0.37 (0.19), residues: 795 loop : -1.83 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.002 0.000 HIS A 360 PHE 0.021 0.001 PHE D 579 TYR 0.011 0.002 TYR C 487 ARG 0.004 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 241 time to evaluate : 2.258 Fit side-chains REVERT: B 78 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5696 (tp) REVERT: B 282 LEU cc_start: 0.8407 (mp) cc_final: 0.8183 (mm) REVERT: B 329 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6947 (mt) REVERT: B 436 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6285 (m-10) REVERT: B 520 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8031 (tt) REVERT: B 559 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: A 155 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7178 (ptm160) REVERT: A 329 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6991 (mt) REVERT: A 559 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7439 (t80) REVERT: C 158 LYS cc_start: 0.6324 (pttt) cc_final: 0.5605 (mttt) REVERT: C 520 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 559 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7219 (t80) REVERT: D 155 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7296 (ptm160) REVERT: D 255 LYS cc_start: 0.5946 (OUTLIER) cc_final: 0.5565 (pttp) REVERT: D 559 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: E 431 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8674 (mt) REVERT: E 436 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6177 (m-80) REVERT: E 446 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7965 (mm-40) REVERT: E 559 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: E 617 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7624 (tt) outliers start: 120 outliers final: 92 residues processed: 340 average time/residue: 0.2942 time to fit residues: 157.4683 Evaluate side-chains 342 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 232 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 156 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 40.0000 chunk 231 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 262 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.149945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105400 restraints weight = 32585.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107853 restraints weight = 18810.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109339 restraints weight = 13495.033| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 20295 Z= 0.625 Angle : 0.842 14.233 27730 Z= 0.429 Chirality : 0.053 0.224 3330 Planarity : 0.007 0.051 3620 Dihedral : 6.008 52.686 2922 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 7.48 % Allowed : 31.22 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.66 (0.15), residues: 2720 helix: -0.31 (0.19), residues: 580 sheet: 0.08 (0.19), residues: 780 loop : -2.24 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 482 HIS 0.003 0.001 HIS D 360 PHE 0.026 0.003 PHE E 443 TYR 0.028 0.004 TYR A 517 ARG 0.005 0.001 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 232 time to evaluate : 2.224 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE C 636 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE D 636 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE E 636 " (corrupted residue). Skipping it. REVERT: B 78 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5596 (tp) REVERT: B 329 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6987 (mt) REVERT: B 436 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6361 (m-10) REVERT: B 520 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7896 (tt) REVERT: B 559 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: A 158 LYS cc_start: 0.6417 (pttt) cc_final: 0.5758 (mttt) REVERT: A 249 LEU cc_start: 0.8017 (tt) cc_final: 0.7776 (tp) REVERT: A 329 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7110 (mt) REVERT: A 436 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: A 559 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7127 (t80) REVERT: C 158 LYS cc_start: 0.6445 (pttt) cc_final: 0.5724 (mttt) REVERT: C 559 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6991 (t80) REVERT: D 255 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5732 (pttp) REVERT: D 436 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: D 559 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: E 431 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (mt) REVERT: E 436 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: E 446 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: E 559 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7311 (m-80) outliers start: 138 outliers final: 107 residues processed: 349 average time/residue: 0.2924 time to fit residues: 160.8017 Evaluate side-chains 342 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 219 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 32 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 117 optimal weight: 40.0000 chunk 180 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.153266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108327 restraints weight = 32522.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110854 restraints weight = 18743.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112241 restraints weight = 13460.848| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20295 Z= 0.282 Angle : 0.661 16.035 27730 Z= 0.320 Chirality : 0.045 0.176 3330 Planarity : 0.005 0.056 3620 Dihedral : 5.212 54.116 2922 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 6.12 % Allowed : 32.30 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.28 (0.16), residues: 2720 helix: 0.27 (0.21), residues: 585 sheet: 0.18 (0.19), residues: 775 loop : -2.05 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 482 HIS 0.002 0.000 HIS A 360 PHE 0.019 0.002 PHE D 579 TYR 0.014 0.002 TYR C 517 ARG 0.004 0.000 ARG A 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 224 time to evaluate : 2.043 Fit side-chains REVERT: B 78 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5678 (tp) REVERT: B 282 LEU cc_start: 0.8428 (mp) cc_final: 0.8151 (mm) REVERT: B 329 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7001 (mt) REVERT: B 436 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: B 520 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 559 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 158 LYS cc_start: 0.6327 (pttt) cc_final: 0.5711 (mttt) REVERT: A 329 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6992 (mt) REVERT: A 559 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7257 (t80) REVERT: C 158 LYS cc_start: 0.6314 (pttt) cc_final: 0.5547 (mttt) REVERT: C 559 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7041 (t80) REVERT: D 155 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7308 (ptm160) REVERT: D 255 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5767 (pttp) REVERT: D 436 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: D 446 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7568 (mm-40) REVERT: D 559 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: E 431 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8668 (mt) REVERT: E 436 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: E 446 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7934 (mm-40) REVERT: E 559 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7471 (m-80) outliers start: 113 outliers final: 91 residues processed: 319 average time/residue: 0.3013 time to fit residues: 151.5183 Evaluate side-chains 325 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 217 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 436 PHE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 436 PHE Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 267 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 67 optimal weight: 0.0050 chunk 149 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 234 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128350 restraints weight = 31597.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122710 restraints weight = 39266.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124241 restraints weight = 45274.080| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20295 Z= 0.152 Angle : 0.596 18.341 27730 Z= 0.276 Chirality : 0.042 0.176 3330 Planarity : 0.004 0.058 3620 Dihedral : 4.437 55.514 2922 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.61 % Allowed : 33.82 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.77 (0.16), residues: 2720 helix: 0.97 (0.22), residues: 585 sheet: 0.45 (0.19), residues: 775 loop : -1.84 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.002 0.001 HIS B 285 PHE 0.020 0.001 PHE D 579 TYR 0.013 0.001 TYR E 487 ARG 0.004 0.000 ARG A 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6636.43 seconds wall clock time: 119 minutes 10.59 seconds (7150.59 seconds total)