Starting phenix.real_space_refine on Tue Jun 17 10:45:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fti_50746/06_2025/9fti_50746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fti_50746/06_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_50746/06_2025/9fti_50746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fti_50746/06_2025/9fti_50746.map" model { file = "/net/cci-nas-00/data/ceres_data/9fti_50746/06_2025/9fti_50746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fti_50746/06_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-5710/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: 9.36, per 1000 atoms: 0.47 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: 5.13 Conformation dependent library (CDL) restraints added in 2.7 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: 2.73 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: 6.23 Time building geometry restraints manager: 6.00 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: 0.17 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.600 ------------------------------------------------------------------------------- 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 20297 Z= 0.213 Angle : 0.597 9.768 27734 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 Details of bonding type rmsd hydrogen bonds : bond 0.30797 ( 735) hydrogen bonds : angle 8.92714 ( 2055) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.58999 ( 4) covalent geometry : bond 0.00506 (20295) covalent geometry : angle 0.59654 (27730) *********************** 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 : 2.150 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: 0.3133 time to fit residues: 121.6709 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 : 2.104 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.150962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107159 restraints weight = 32465.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109194 restraints weight = 20047.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109763 restraints weight = 14121.099| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 20297 Z= 0.271 Angle : 0.738 14.361 27734 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 Details of bonding type rmsd hydrogen bonds : bond 0.06560 ( 735) hydrogen bonds : angle 6.07076 ( 2055) SS BOND : bond 0.00438 ( 2) SS BOND : angle 1.75320 ( 4) covalent geometry : bond 0.00649 (20295) covalent geometry : angle 0.73733 (27730) *********************** 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 : 2.271 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 329 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6960 (mt) REVERT: B 559 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 158 LYS cc_start: 0.6349 (pttt) cc_final: 0.5769 (mptt) REVERT: A 280 CYS cc_start: 0.5642 (OUTLIER) cc_final: 0.5111 (m) REVERT: A 329 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6975 (mt) REVERT: A 431 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 615 TRP cc_start: 0.6610 (t-100) cc_final: 0.6246 (t-100) REVERT: C 559 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7112 (t80) REVERT: C 615 TRP cc_start: 0.6435 (t-100) cc_final: 0.6035 (t-100) REVERT: D 329 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7030 (mt) REVERT: E 431 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8662 (mt) outliers start: 128 outliers final: 75 residues processed: 348 average time/residue: 0.2831 time to fit residues: 155.8382 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 : 2.426 ------------------------------------------------------------------------------- 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: 3.9990 chunk 258 optimal weight: 1.9990 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: 9.9990 chunk 139 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 263 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.152907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108301 restraints weight = 32031.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110890 restraints weight = 18039.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112438 restraints weight = 12791.174| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20297 Z= 0.171 Angle : 0.645 16.414 27734 Z= 0.315 Chirality : 0.044 0.140 3330 Planarity : 0.005 0.040 3620 Dihedral : 5.045 54.477 2922 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.80 % Allowed : 29.92 % Favored : 64.28 % 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: -1.24 (0.16), residues: 2720 helix: 0.07 (0.20), residues: 585 sheet: 0.06 (0.19), residues: 795 loop : -1.82 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 482 HIS 0.002 0.001 HIS A 360 PHE 0.016 0.002 PHE B 505 TYR 0.013 0.002 TYR E 632 ARG 0.005 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 735) hydrogen bonds : angle 5.33663 ( 2055) SS BOND : bond 0.00369 ( 2) SS BOND : angle 1.58499 ( 4) covalent geometry : bond 0.00412 (20295) covalent geometry : angle 0.64470 (27730) *********************** 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 347 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 240 time to evaluate : 2.143 Fit side-chains REVERT: B 78 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5766 (tp) REVERT: B 271 LEU cc_start: 0.6216 (tp) cc_final: 0.5918 (tp) REVERT: B 329 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6934 (mt) REVERT: B 520 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8008 (tt) REVERT: B 559 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: A 158 LYS cc_start: 0.6377 (pttt) cc_final: 0.5763 (mptt) REVERT: A 271 LEU cc_start: 0.6124 (tp) cc_final: 0.5826 (tp) REVERT: A 280 CYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5201 (m) REVERT: A 329 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6947 (mt) REVERT: A 559 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7307 (t80) REVERT: C 249 LEU cc_start: 0.8176 (tp) cc_final: 0.7836 (tp) REVERT: C 271 LEU cc_start: 0.6169 (tp) cc_final: 0.5871 (tp) REVERT: C 280 CYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5683 (m) REVERT: C 559 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7020 (t80) REVERT: C 615 TRP cc_start: 0.6798 (t-100) cc_final: 0.6437 (t-100) REVERT: D 271 LEU cc_start: 0.5958 (tp) cc_final: 0.5738 (tp) REVERT: D 280 CYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5373 (m) REVERT: D 559 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: E 249 LEU cc_start: 0.8123 (tt) cc_final: 0.7804 (tp) REVERT: E 271 LEU cc_start: 0.6249 (tp) cc_final: 0.5925 (tp) REVERT: E 280 CYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5891 (m) REVERT: E 559 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7485 (m-80) outliers start: 107 outliers final: 60 residues processed: 331 average time/residue: 0.2756 time to fit residues: 144.7155 Evaluate side-chains 290 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 217 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain B residue 392 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 520 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 576 LEU 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 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 351 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 480 GLU 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 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 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 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 612 ILE 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 250 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 429 VAL 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 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 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: 9.9990 chunk 118 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 overall best weight: 4.0986 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107971 restraints weight = 32736.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110550 restraints weight = 20426.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110863 restraints weight = 13905.566| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20297 Z= 0.217 Angle : 0.683 16.105 27734 Z= 0.337 Chirality : 0.046 0.145 3330 Planarity : 0.005 0.041 3620 Dihedral : 5.267 53.873 2922 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 6.94 % Allowed : 30.57 % Favored : 62.49 % 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: -1.29 (0.16), residues: 2720 helix: 0.08 (0.20), residues: 585 sheet: 0.11 (0.19), residues: 780 loop : -1.91 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 482 HIS 0.002 0.001 HIS A 360 PHE 0.016 0.002 PHE E 443 TYR 0.016 0.002 TYR E 632 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 735) hydrogen bonds : angle 5.33267 ( 2055) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.51768 ( 4) covalent geometry : bond 0.00522 (20295) covalent geometry : angle 0.68306 (27730) *********************** 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 350 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 222 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: B 78 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5522 (tp) REVERT: B 271 LEU cc_start: 0.6127 (tp) cc_final: 0.5927 (tp) REVERT: B 282 LEU cc_start: 0.8375 (mp) cc_final: 0.8057 (mm) REVERT: B 329 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6950 (mt) REVERT: B 520 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 559 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 158 LYS cc_start: 0.6372 (pttt) cc_final: 0.5732 (mptt) REVERT: A 271 LEU cc_start: 0.6137 (tp) cc_final: 0.5912 (tp) REVERT: A 280 CYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5549 (m) REVERT: A 329 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6980 (mt) REVERT: A 520 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 559 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 520 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (tt) REVERT: C 559 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 615 TRP cc_start: 0.6773 (t-100) cc_final: 0.6450 (t-100) REVERT: D 271 LEU cc_start: 0.5962 (tp) cc_final: 0.5756 (tp) REVERT: D 280 CYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5492 (m) REVERT: D 559 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: E 431 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8638 (mt) REVERT: E 559 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7445 (m-80) outliers start: 128 outliers final: 94 residues processed: 332 average time/residue: 0.2911 time to fit residues: 152.8652 Evaluate side-chains 324 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 216 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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 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 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 612 ILE Chi-restraints excluded: chain B residue 617 LEU 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 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 480 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU 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 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 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 342 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 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 612 ILE 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 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 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 615 TRP 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 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 595 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: 7.9990 chunk 218 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 184 optimal weight: 0.2980 chunk 127 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 57 optimal weight: 0.0020 overall best weight: 1.6730 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.154723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109206 restraints weight = 32109.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112051 restraints weight = 17240.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113770 restraints weight = 11872.349| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20297 Z= 0.114 Angle : 0.598 18.011 27734 Z= 0.281 Chirality : 0.043 0.137 3330 Planarity : 0.004 0.049 3620 Dihedral : 4.626 55.683 2922 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.26 % Allowed : 31.92 % Favored : 62.82 % 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: -0.92 (0.16), residues: 2720 helix: 0.66 (0.21), residues: 585 sheet: 0.24 (0.19), residues: 795 loop : -1.78 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 482 HIS 0.001 0.000 HIS A 360 PHE 0.013 0.001 PHE B 505 TYR 0.010 0.001 TYR C 441 ARG 0.003 0.000 ARG B 248 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 735) hydrogen bonds : angle 4.81466 ( 2055) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.39601 ( 4) covalent geometry : bond 0.00278 (20295) covalent geometry : angle 0.59778 (27730) *********************** 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 336 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 239 time to evaluate : 2.154 Fit side-chains REVERT: B 350 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8329 (p) REVERT: B 520 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8038 (tt) REVERT: B 559 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: A 249 LEU cc_start: 0.8221 (tt) cc_final: 0.7948 (tp) REVERT: A 271 LEU cc_start: 0.5965 (tp) cc_final: 0.5734 (tp) REVERT: A 280 CYS cc_start: 0.5799 (OUTLIER) cc_final: 0.5404 (m) REVERT: A 487 TYR cc_start: 0.7672 (p90) cc_final: 0.7375 (p90) REVERT: A 520 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8033 (tt) REVERT: A 559 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7454 (t80) REVERT: C 281 GLU cc_start: 0.7219 (mt-10) cc_final: 0.7010 (mp0) REVERT: C 520 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 559 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7088 (t80) REVERT: C 615 TRP cc_start: 0.6884 (t-100) cc_final: 0.6570 (t-100) REVERT: D 155 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7209 (ptm160) REVERT: D 249 LEU cc_start: 0.8116 (tt) cc_final: 0.7792 (tp) REVERT: D 271 LEU cc_start: 0.5994 (tp) cc_final: 0.5743 (tp) REVERT: D 280 CYS cc_start: 0.5750 (OUTLIER) cc_final: 0.5448 (m) REVERT: D 559 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: E 431 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8656 (mt) REVERT: E 559 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7536 (m-80) outliers start: 97 outliers final: 66 residues processed: 319 average time/residue: 0.3035 time to fit residues: 152.3668 Evaluate side-chains 303 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 224 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 304 VAL 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 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 594 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 219 LEU 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 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU 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 279 ILE 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 475 ASP Chi-restraints excluded: chain C residue 477 LEU 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 155 ARG 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 358 SER 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 612 ILE Chi-restraints excluded: chain D residue 615 TRP 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 346 SER 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 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: 1.9990 chunk 202 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 167 optimal weight: 30.0000 chunk 103 optimal weight: 0.0670 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 0.0870 chunk 269 optimal weight: 7.9990 overall best weight: 3.0302 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.153540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109515 restraints weight = 32438.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111137 restraints weight = 21420.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111801 restraints weight = 14607.482| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20297 Z= 0.167 Angle : 0.634 16.964 27734 Z= 0.305 Chirality : 0.044 0.138 3330 Planarity : 0.005 0.044 3620 Dihedral : 4.825 54.945 2922 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.78 % Allowed : 30.95 % 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: -0.96 (0.16), residues: 2720 helix: 0.60 (0.21), residues: 585 sheet: 0.34 (0.19), residues: 775 loop : -1.85 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.002 0.000 HIS A 360 PHE 0.015 0.002 PHE B 505 TYR 0.013 0.002 TYR A 517 ARG 0.005 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 735) hydrogen bonds : angle 4.90870 ( 2055) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.37938 ( 4) covalent geometry : bond 0.00404 (20295) covalent geometry : angle 0.63356 (27730) *********************** 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 361 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 236 time to evaluate : 2.167 Fit side-chains REVERT: B 249 LEU cc_start: 0.8097 (tp) cc_final: 0.7842 (tp) REVERT: B 282 LEU cc_start: 0.8423 (mp) cc_final: 0.8162 (mm) REVERT: B 329 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6931 (mt) REVERT: B 520 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8045 (tt) REVERT: B 559 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: B 634 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5457 (mtm180) REVERT: A 329 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 487 TYR cc_start: 0.7724 (p90) cc_final: 0.7468 (p90) REVERT: A 520 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8067 (tt) REVERT: A 559 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7369 (t80) REVERT: C 158 LYS cc_start: 0.6243 (pttt) cc_final: 0.5517 (mttt) REVERT: C 281 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6924 (mp0) REVERT: C 520 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8141 (tt) REVERT: C 559 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7095 (t80) REVERT: C 615 TRP cc_start: 0.6759 (t-100) cc_final: 0.6511 (t-100) REVERT: D 436 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: D 559 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: E 155 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7058 (ptm160) REVERT: E 431 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8636 (mt) REVERT: E 436 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: E 446 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: E 559 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7423 (m-80) outliers start: 125 outliers final: 91 residues processed: 344 average time/residue: 0.3133 time to fit residues: 167.3284 Evaluate side-chains 334 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 227 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 576 LEU 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 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 274 THR 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 520 LEU 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 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 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 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 612 ILE 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 250 THR 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 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 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 615 TRP 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 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 436 PHE Chi-restraints excluded: chain E residue 446 GLN 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 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: 6.9990 chunk 239 optimal weight: 8.9990 chunk 171 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 187 optimal weight: 10.0000 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 = 0.153853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108293 restraints weight = 32009.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111058 restraints weight = 17409.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112767 restraints weight = 12056.146| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20297 Z= 0.156 Angle : 0.623 17.014 27734 Z= 0.298 Chirality : 0.044 0.137 3330 Planarity : 0.004 0.040 3620 Dihedral : 4.780 54.989 2922 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 7.26 % Allowed : 30.41 % Favored : 62.33 % 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: -0.91 (0.16), residues: 2720 helix: 0.69 (0.21), residues: 585 sheet: 0.32 (0.19), residues: 795 loop : -1.85 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 482 HIS 0.002 0.000 HIS A 360 PHE 0.015 0.001 PHE B 505 TYR 0.012 0.002 TYR A 517 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 735) hydrogen bonds : angle 4.82989 ( 2055) SS BOND : bond 0.00348 ( 2) SS BOND : angle 1.35416 ( 4) covalent geometry : bond 0.00379 (20295) covalent geometry : angle 0.62319 (27730) *********************** 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 367 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 233 time to evaluate : 2.103 Fit side-chains REVERT: B 249 LEU cc_start: 0.8133 (tp) cc_final: 0.7883 (tp) REVERT: B 282 LEU cc_start: 0.8404 (mp) cc_final: 0.8203 (mm) REVERT: B 329 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6941 (mt) REVERT: B 436 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6297 (m-10) REVERT: B 520 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 559 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: A 329 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6982 (mt) REVERT: A 487 TYR cc_start: 0.7655 (p90) cc_final: 0.7428 (p90) REVERT: A 520 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 559 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7445 (t80) REVERT: C 158 LYS cc_start: 0.6323 (pttt) cc_final: 0.5600 (mttt) REVERT: C 520 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 559 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7170 (t80) REVERT: D 155 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7316 (ptm160) REVERT: D 255 LYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5555 (pttp) REVERT: D 559 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: E 431 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8645 (mt) REVERT: E 436 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: E 446 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7938 (mm-40) REVERT: E 559 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: E 617 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7691 (tt) outliers start: 134 outliers final: 98 residues processed: 345 average time/residue: 0.3032 time to fit residues: 163.1981 Evaluate side-chains 348 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 233 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 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 250 THR 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 520 LEU 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 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 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 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 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 615 TRP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 274 THR 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 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 475 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 194 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 255 optimal weight: 5.9990 chunk 256 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 220 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 overall best weight: 1.7102 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.155110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110160 restraints weight = 32411.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112602 restraints weight = 20231.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113801 restraints weight = 14290.378| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20297 Z= 0.114 Angle : 0.589 17.933 27734 Z= 0.275 Chirality : 0.043 0.136 3330 Planarity : 0.004 0.042 3620 Dihedral : 4.441 55.293 2922 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.96 % Allowed : 31.49 % Favored : 62.55 % 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: -0.68 (0.16), residues: 2720 helix: 1.02 (0.22), residues: 585 sheet: 0.48 (0.19), residues: 795 loop : -1.78 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 482 HIS 0.002 0.001 HIS E 285 PHE 0.013 0.001 PHE B 505 TYR 0.011 0.001 TYR B 487 ARG 0.003 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 735) hydrogen bonds : angle 4.54826 ( 2055) SS BOND : bond 0.00329 ( 2) SS BOND : angle 1.32449 ( 4) covalent geometry : bond 0.00281 (20295) covalent geometry : angle 0.58864 (27730) *********************** 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 352 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 242 time to evaluate : 2.276 Fit side-chains REVERT: B 249 LEU cc_start: 0.8081 (tp) cc_final: 0.7831 (tp) REVERT: B 282 LEU cc_start: 0.8435 (mp) cc_final: 0.8204 (mm) REVERT: B 329 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6905 (mt) REVERT: B 436 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6280 (m-10) REVERT: B 520 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8009 (tt) REVERT: B 559 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 160 GLN cc_start: 0.5511 (pt0) cc_final: 0.5201 (pm20) REVERT: A 329 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6942 (mt) REVERT: A 487 TYR cc_start: 0.7635 (p90) cc_final: 0.7395 (p90) REVERT: A 520 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 559 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7438 (t80) REVERT: C 158 LYS cc_start: 0.6247 (pttt) cc_final: 0.5618 (mttt) REVERT: C 520 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8118 (tt) REVERT: C 559 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7138 (t80) REVERT: D 255 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5400 (pttp) REVERT: D 436 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: D 559 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: E 155 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7036 (ptm160) REVERT: E 431 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8683 (mt) REVERT: E 446 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: E 559 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7478 (m-80) outliers start: 110 outliers final: 84 residues processed: 332 average time/residue: 0.2957 time to fit residues: 155.3600 Evaluate side-chains 326 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 226 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 346 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 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 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 582 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 520 LEU 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 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 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 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 612 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 150 THR 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 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 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 554 LEU 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 E residue 150 THR Chi-restraints excluded: chain E residue 155 ARG 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 446 GLN Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 562 THR 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: 3.9990 chunk 123 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 30.0000 chunk 231 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.152555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107463 restraints weight = 32346.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109919 restraints weight = 18720.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111450 restraints weight = 13520.877| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20297 Z= 0.214 Angle : 0.670 15.919 27734 Z= 0.329 Chirality : 0.046 0.153 3330 Planarity : 0.005 0.042 3620 Dihedral : 5.057 54.113 2922 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.50 % Allowed : 31.76 % 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: -1.00 (0.16), residues: 2720 helix: 0.57 (0.21), residues: 585 sheet: 0.40 (0.19), residues: 775 loop : -1.94 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 482 HIS 0.002 0.001 HIS A 360 PHE 0.017 0.002 PHE B 505 TYR 0.016 0.002 TYR A 517 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 735) hydrogen bonds : angle 4.96112 ( 2055) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.35400 ( 4) covalent geometry : bond 0.00518 (20295) covalent geometry : angle 0.67002 (27730) *********************** 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 353 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 233 time to evaluate : 2.289 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 282 LEU cc_start: 0.8427 (mp) cc_final: 0.8155 (mm) REVERT: B 329 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7049 (mt) REVERT: B 436 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: B 520 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 559 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: A 158 LYS cc_start: 0.6254 (pttt) cc_final: 0.5609 (mttt) REVERT: A 329 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6961 (mt) REVERT: A 487 TYR cc_start: 0.7691 (p90) cc_final: 0.7470 (p90) REVERT: A 520 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 559 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 158 LYS cc_start: 0.6307 (pttt) cc_final: 0.5635 (mttt) REVERT: C 520 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8144 (tt) REVERT: C 559 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7094 (t80) REVERT: D 155 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7337 (ptm160) REVERT: D 255 LYS cc_start: 0.5889 (OUTLIER) cc_final: 0.5513 (pttp) REVERT: D 436 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: D 559 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: D 579 PHE cc_start: 0.7965 (t80) cc_final: 0.7537 (t80) REVERT: E 155 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7302 (ptm160) REVERT: E 431 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8641 (mt) REVERT: E 436 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: E 446 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7947 (mm-40) REVERT: E 559 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: E 617 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7652 (tt) outliers start: 120 outliers final: 93 residues processed: 335 average time/residue: 0.2923 time to fit residues: 154.6991 Evaluate side-chains 342 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 230 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 346 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 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 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 582 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 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 520 LEU 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 582 VAL 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 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 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 91 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 155 ARG 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 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 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 155 ARG Chi-restraints excluded: chain E residue 274 THR 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 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 562 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 180 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.153451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109259 restraints weight = 32528.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111905 restraints weight = 19953.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112113 restraints weight = 14304.008| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20297 Z= 0.178 Angle : 0.646 16.469 27734 Z= 0.312 Chirality : 0.045 0.139 3330 Planarity : 0.005 0.049 3620 Dihedral : 4.946 54.405 2922 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.45 % Allowed : 31.54 % Favored : 62.01 % 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: -0.98 (0.16), residues: 2720 helix: 0.63 (0.21), residues: 585 sheet: 0.39 (0.19), residues: 775 loop : -1.93 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 482 HIS 0.002 0.000 HIS A 360 PHE 0.015 0.002 PHE B 505 TYR 0.014 0.002 TYR A 517 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04468 ( 735) hydrogen bonds : angle 4.87070 ( 2055) SS BOND : bond 0.00358 ( 2) SS BOND : angle 1.34332 ( 4) covalent geometry : bond 0.00434 (20295) covalent geometry : angle 0.64555 (27730) ********************** 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: 119 poor density : 218 time to evaluate : 2.166 Fit side-chains REVERT: B 272 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6702 (t0) REVERT: B 329 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7019 (mt) REVERT: B 436 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6263 (m-10) REVERT: B 520 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7990 (tt) REVERT: B 559 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 158 LYS cc_start: 0.6187 (pttt) cc_final: 0.5608 (mptt) REVERT: A 329 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6965 (mt) REVERT: A 487 TYR cc_start: 0.7650 (p90) cc_final: 0.7428 (p90) REVERT: A 520 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 559 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7355 (t80) REVERT: A 634 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5396 (mtm180) REVERT: C 158 LYS cc_start: 0.6269 (pttt) cc_final: 0.5594 (mttt) REVERT: C 520 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8157 (tt) REVERT: C 559 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7152 (t80) REVERT: D 155 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7254 (ptm160) REVERT: D 255 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5509 (pttp) REVERT: D 436 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: D 559 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: D 579 PHE cc_start: 0.7924 (t80) cc_final: 0.7492 (t80) REVERT: E 155 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7190 (ptm160) REVERT: E 431 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8667 (mt) REVERT: E 436 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: E 446 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: E 559 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: E 617 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7616 (tt) outliers start: 119 outliers final: 98 residues processed: 316 average time/residue: 0.2967 time to fit residues: 147.2977 Evaluate side-chains 335 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 216 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 272 ASN 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 346 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 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 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 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 520 LEU 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 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 A residue 634 ARG 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 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 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 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 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 155 ARG 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 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 436 PHE Chi-restraints excluded: chain E residue 446 GLN Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 562 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 267 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.153797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110212 restraints weight = 32474.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111377 restraints weight = 22132.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112357 restraints weight = 14553.433| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20297 Z= 0.164 Angle : 0.633 16.671 27734 Z= 0.305 Chirality : 0.044 0.138 3330 Planarity : 0.005 0.050 3620 Dihedral : 4.855 54.437 2922 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.83 % Allowed : 31.22 % Favored : 61.95 % 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: -0.95 (0.16), residues: 2720 helix: 0.71 (0.21), residues: 585 sheet: 0.38 (0.19), residues: 775 loop : -1.92 (0.16), residues: 1360 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 0.015 0.002 PHE B 505 TYR 0.013 0.002 TYR A 517 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 735) hydrogen bonds : angle 4.80079 ( 2055) SS BOND : bond 0.00355 ( 2) SS BOND : angle 1.33122 ( 4) covalent geometry : bond 0.00400 (20295) covalent geometry : angle 0.63309 (27730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6931.26 seconds wall clock time: 119 minutes 54.08 seconds (7194.08 seconds total)