Starting phenix.real_space_refine on Sun Aug 24 12:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fti_50746/08_2025/9fti_50746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fti_50746/08_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_50746/08_2025/9fti_50746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fti_50746/08_2025/9fti_50746.map" model { file = "/net/cci-nas-00/data/ceres_data/9fti_50746/08_2025/9fti_50746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fti_50746/08_2025/9fti_50746.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19935 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" 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, 'HIS:plan': 2, 'PHE:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 4, 'GLU:plan': 15, 'ASP:plan': 10, 'TRP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 268 Restraints were copied for chains: A, C, D, E Time building chain proxies: 3.12, per 1000 atoms: 0.16 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=10, 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 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS D 371 " - pdb=" SG CYS D 373 " distance=2.03 Simple disulfide: pdb=" SG CYS E 371 " - pdb=" SG CYS E 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: 1.78 Conformation dependent library (CDL) restraints added in 911.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.75 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: 3.70 Time building geometry restraints manager: 2.35 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: 10273 17.16 - 34.32: 1217 34.32 - 51.48: 330 51.48 - 68.64: 55 68.64 - 85.80: 25 Dihedral angle restraints: 11900 sinusoidal: 3935 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 11897 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: 2.27 - 2.80: 5363 2.80 - 3.32: 17104 3.32 - 3.85: 29270 3.85 - 4.37: 32334 4.37 - 4.90: 57584 Nonbonded interactions: 141655 Sorted by model distance: nonbonded pdb=" O SER D 108 " pdb=" OG1 THR D 111 " model vdw 2.273 3.040 nonbonded pdb=" O SER E 108 " pdb=" OG1 THR E 111 " model vdw 2.273 3.040 nonbonded pdb=" O SER B 108 " pdb=" OG1 THR B 111 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 108 " pdb=" OG1 THR A 111 " model vdw 2.274 3.040 nonbonded pdb=" O SER C 108 " pdb=" OG1 THR C 111 " model vdw 2.274 3.040 ... (remaining 141650 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- 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 20305 Z= 0.213 Angle : 0.597 9.768 27750 Z= 0.304 Chirality : 0.044 0.136 3330 Planarity : 0.004 0.044 3620 Dihedral : 16.699 85.801 6720 Min Nonbonded Distance : 2.273 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG D 406 TYR 0.013 0.002 TYR D 441 PHE 0.015 0.002 PHE C 505 TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00506 (20295) covalent geometry : angle 0.59654 (27730) SS BOND : bond 0.00194 ( 10) SS BOND : angle 0.58968 ( 20) hydrogen bonds : bond 0.30797 ( 735) hydrogen bonds : angle 8.92714 ( 2055) *********************** 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 : 0.624 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: 0.1420 time to fit residues: 55.2600 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 : 0.704 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.151423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106683 restraints weight = 32586.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109229 restraints weight = 18554.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110773 restraints weight = 13204.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111574 restraints weight = 10915.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112107 restraints weight = 9873.255| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20305 Z= 0.243 Angle : 0.710 14.615 27750 Z= 0.357 Chirality : 0.047 0.147 3330 Planarity : 0.005 0.043 3620 Dihedral : 5.409 53.893 2924 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.50 % Allowed : 27.75 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.16), residues: 2720 helix: -0.39 (0.20), residues: 585 sheet: -0.07 (0.18), residues: 800 loop : -1.82 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 248 TYR 0.017 0.002 TYR A 517 PHE 0.018 0.002 PHE E 436 TRP 0.014 0.002 TRP D 482 HIS 0.005 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00582 (20295) covalent geometry : angle 0.70866 (27730) SS BOND : bond 0.00370 ( 10) SS BOND : angle 1.70523 ( 20) hydrogen bonds : bond 0.06268 ( 735) hydrogen bonds : angle 5.95739 ( 2055) *********************** 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 370 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 250 time to evaluate : 0.782 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 329 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6960 (mt) REVERT: B 559 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: A 158 LYS cc_start: 0.6354 (pttt) cc_final: 0.5757 (mptt) REVERT: A 329 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6985 (mt) REVERT: A 431 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8662 (mt) REVERT: A 559 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7114 (t80) REVERT: A 615 TRP cc_start: 0.6729 (t-100) cc_final: 0.6306 (t-100) REVERT: C 559 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7149 (t80) REVERT: C 615 TRP cc_start: 0.6579 (t-100) cc_final: 0.6144 (t-100) REVERT: D 329 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7060 (mt) REVERT: D 559 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: E 431 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8649 (mt) REVERT: E 559 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7396 (m-80) outliers start: 120 outliers final: 66 residues processed: 340 average time/residue: 0.1206 time to fit residues: 65.2109 Evaluate side-chains 293 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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 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 559 PHE 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 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 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 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 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 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 559 PHE 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 81 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 269 optimal weight: 0.0670 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110459 restraints weight = 31940.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113131 restraints weight = 17822.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114754 restraints weight = 12522.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115669 restraints weight = 10237.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116051 restraints weight = 9210.718| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20305 Z= 0.104 Angle : 0.589 17.439 27750 Z= 0.279 Chirality : 0.042 0.138 3330 Planarity : 0.004 0.051 3620 Dihedral : 4.554 56.072 2922 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.90 % Allowed : 30.46 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.16), residues: 2720 helix: 0.52 (0.21), residues: 585 sheet: 0.11 (0.19), residues: 795 loop : -1.63 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 248 TYR 0.010 0.001 TYR C 441 PHE 0.012 0.001 PHE B 505 TRP 0.005 0.001 TRP C 359 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00248 (20295) covalent geometry : angle 0.58742 (27730) SS BOND : bond 0.00334 ( 10) SS BOND : angle 1.58704 ( 20) hydrogen bonds : bond 0.04168 ( 735) hydrogen bonds : angle 5.02141 ( 2055) *********************** 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 317 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 0.640 Fit side-chains REVERT: B 271 LEU cc_start: 0.6154 (tp) cc_final: 0.5819 (tp) REVERT: B 559 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 271 LEU cc_start: 0.6033 (tp) cc_final: 0.5711 (tp) REVERT: A 559 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 249 LEU cc_start: 0.8064 (tt) cc_final: 0.7680 (tp) REVERT: C 271 LEU cc_start: 0.5992 (tp) cc_final: 0.5658 (tp) REVERT: C 559 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7093 (t80) REVERT: C 615 TRP cc_start: 0.6845 (t-100) cc_final: 0.6464 (t-100) REVERT: D 271 LEU cc_start: 0.6088 (tp) cc_final: 0.5792 (tp) REVERT: D 559 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: E 249 LEU cc_start: 0.8105 (tt) cc_final: 0.7897 (tp) REVERT: E 271 LEU cc_start: 0.6258 (tp) cc_final: 0.5883 (tp) REVERT: E 520 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7853 (tt) REVERT: E 559 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: E 572 TYR cc_start: 0.8847 (p90) cc_final: 0.8362 (p90) outliers start: 72 outliers final: 33 residues processed: 310 average time/residue: 0.1270 time to fit residues: 62.9077 Evaluate side-chains 264 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain A residue 150 THR 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 392 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 520 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 617 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 184 optimal weight: 0.0050 chunk 3 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 273 optimal weight: 0.3980 chunk 245 optimal weight: 5.9990 chunk 220 optimal weight: 30.0000 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110735 restraints weight = 32202.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113366 restraints weight = 18138.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114971 restraints weight = 12830.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115863 restraints weight = 10546.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116240 restraints weight = 9503.605| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20305 Z= 0.103 Angle : 0.580 17.838 27750 Z= 0.270 Chirality : 0.042 0.135 3330 Planarity : 0.004 0.043 3620 Dihedral : 4.332 56.377 2922 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.07 % Allowed : 30.89 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2720 helix: 0.93 (0.22), residues: 585 sheet: 0.37 (0.19), residues: 795 loop : -1.61 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.011 0.001 TYR B 487 PHE 0.011 0.001 PHE B 505 TRP 0.006 0.001 TRP B 359 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00246 (20295) covalent geometry : angle 0.57838 (27730) SS BOND : bond 0.00360 ( 10) SS BOND : angle 1.53073 ( 20) hydrogen bonds : bond 0.03739 ( 735) hydrogen bonds : angle 4.63562 ( 2055) *********************** 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 328 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 253 time to evaluate : 0.725 Fit side-chains REVERT: B 271 LEU cc_start: 0.5998 (tp) cc_final: 0.5713 (tp) REVERT: B 329 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6897 (mt) REVERT: B 520 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7989 (tt) REVERT: B 559 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 520 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 559 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 567 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7607 (tp) REVERT: C 210 ILE cc_start: 0.6793 (pt) cc_final: 0.6567 (pt) REVERT: C 271 LEU cc_start: 0.6011 (tp) cc_final: 0.5695 (tp) REVERT: C 520 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8020 (tt) REVERT: C 559 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7078 (t80) REVERT: C 615 TRP cc_start: 0.6809 (t-100) cc_final: 0.6430 (t-100) REVERT: D 559 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: E 249 LEU cc_start: 0.8111 (tt) cc_final: 0.7878 (tp) REVERT: E 271 LEU cc_start: 0.6058 (tp) cc_final: 0.5727 (tp) REVERT: E 431 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8614 (mt) REVERT: E 520 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7769 (tt) REVERT: E 559 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7580 (m-80) outliers start: 75 outliers final: 49 residues processed: 315 average time/residue: 0.1212 time to fit residues: 60.7303 Evaluate side-chains 288 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain B residue 332 VAL 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 480 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 332 VAL 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 520 LEU 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 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 428 THR 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 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 286 VAL Chi-restraints excluded: chain D residue 329 LEU 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 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 E residue 150 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 24 optimal weight: 0.0870 chunk 179 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 overall best weight: 3.1364 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108756 restraints weight = 31957.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111332 restraints weight = 18121.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112909 restraints weight = 12861.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113636 restraints weight = 10592.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114131 restraints weight = 9592.435| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20305 Z= 0.172 Angle : 0.634 16.275 27750 Z= 0.307 Chirality : 0.044 0.165 3330 Planarity : 0.005 0.042 3620 Dihedral : 4.762 54.779 2922 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.04 % Allowed : 31.49 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.16), residues: 2720 helix: 0.72 (0.21), residues: 585 sheet: 0.38 (0.19), residues: 795 loop : -1.73 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 248 TYR 0.015 0.002 TYR A 517 PHE 0.015 0.002 PHE B 505 TRP 0.010 0.001 TRP D 482 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00416 (20295) covalent geometry : angle 0.63350 (27730) SS BOND : bond 0.00319 ( 10) SS BOND : angle 1.45676 ( 20) hydrogen bonds : bond 0.04527 ( 735) hydrogen bonds : angle 4.86370 ( 2055) *********************** 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 318 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 225 time to evaluate : 0.605 Fit side-chains REVERT: B 78 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5677 (tp) REVERT: B 271 LEU cc_start: 0.6084 (tp) cc_final: 0.5857 (tp) REVERT: B 329 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6859 (mt) REVERT: B 520 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7996 (tt) REVERT: B 559 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 78 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5824 (tp) REVERT: A 249 LEU cc_start: 0.8139 (tt) cc_final: 0.7862 (tp) REVERT: A 271 LEU cc_start: 0.6132 (tp) cc_final: 0.5826 (tp) REVERT: A 329 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6934 (mt) REVERT: A 487 TYR cc_start: 0.7705 (p90) cc_final: 0.7414 (p90) REVERT: A 520 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8063 (tt) REVERT: A 559 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7326 (t80) REVERT: C 271 LEU cc_start: 0.5981 (tp) cc_final: 0.5723 (tp) REVERT: C 520 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8049 (tt) REVERT: C 559 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7181 (t80) REVERT: D 271 LEU cc_start: 0.6069 (tp) cc_final: 0.5791 (tp) REVERT: D 559 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: E 78 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5775 (tp) REVERT: E 249 LEU cc_start: 0.8133 (tt) cc_final: 0.7874 (tp) REVERT: E 271 LEU cc_start: 0.6034 (tp) cc_final: 0.5785 (tp) REVERT: E 431 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8652 (mt) REVERT: E 559 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: E 617 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7734 (tt) outliers start: 93 outliers final: 69 residues processed: 302 average time/residue: 0.1300 time to fit residues: 62.9117 Evaluate side-chains 301 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 217 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU 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 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 591 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 219 LEU 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 351 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 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 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 249 LEU 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 392 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE 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 392 LEU 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 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 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 559 PHE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 264 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.154376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110408 restraints weight = 31823.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113072 restraints weight = 19348.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113156 restraints weight = 14006.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113962 restraints weight = 11980.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114172 restraints weight = 11250.740| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20305 Z= 0.147 Angle : 0.612 16.595 27750 Z= 0.292 Chirality : 0.043 0.145 3330 Planarity : 0.004 0.047 3620 Dihedral : 4.668 54.964 2922 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.53 % Allowed : 31.06 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2720 helix: 0.83 (0.22), residues: 585 sheet: 0.44 (0.18), residues: 795 loop : -1.74 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.012 0.002 TYR E 517 PHE 0.013 0.001 PHE B 505 TRP 0.009 0.001 TRP D 482 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00355 (20295) covalent geometry : angle 0.61131 (27730) SS BOND : bond 0.00313 ( 10) SS BOND : angle 1.38828 ( 20) hydrogen bonds : bond 0.04188 ( 735) hydrogen bonds : angle 4.74270 ( 2055) *********************** 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 328 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 226 time to evaluate : 0.697 Fit side-chains REVERT: B 78 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5533 (tp) REVERT: B 329 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6899 (mt) REVERT: B 520 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7911 (tt) REVERT: B 559 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: A 155 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7321 (ptm160) REVERT: A 249 LEU cc_start: 0.8065 (tt) cc_final: 0.7814 (tp) REVERT: A 271 LEU cc_start: 0.6068 (tp) cc_final: 0.5791 (tp) REVERT: A 329 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6930 (mt) REVERT: A 487 TYR cc_start: 0.7688 (p90) cc_final: 0.7427 (p90) REVERT: A 520 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 559 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7355 (t80) REVERT: C 271 LEU cc_start: 0.5950 (tp) cc_final: 0.5735 (tp) REVERT: C 520 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8132 (tt) REVERT: C 559 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7156 (t80) REVERT: C 615 TRP cc_start: 0.6835 (t-100) cc_final: 0.6530 (t-100) REVERT: D 271 LEU cc_start: 0.6046 (tp) cc_final: 0.5824 (tp) REVERT: D 559 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: E 160 GLN cc_start: 0.5326 (pt0) cc_final: 0.5083 (pm20) REVERT: E 249 LEU cc_start: 0.8135 (tt) cc_final: 0.7798 (tp) REVERT: E 271 LEU cc_start: 0.5988 (tp) cc_final: 0.5739 (tp) REVERT: E 431 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8687 (mt) REVERT: E 559 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7474 (m-80) outliers start: 102 outliers final: 78 residues processed: 309 average time/residue: 0.1279 time to fit residues: 62.7173 Evaluate side-chains 310 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 219 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 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 576 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain 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 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 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 617 LEU Chi-restraints excluded: chain C residue 150 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 392 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 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 358 SER Chi-restraints excluded: chain D residue 392 LEU 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 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 615 TRP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 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 559 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 120 optimal weight: 0.5980 chunk 67 optimal weight: 40.0000 chunk 154 optimal weight: 0.1980 chunk 194 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 184 optimal weight: 0.0470 chunk 238 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 181 optimal weight: 0.0020 overall best weight: 0.9688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111587 restraints weight = 31872.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114180 restraints weight = 18133.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115782 restraints weight = 12921.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116657 restraints weight = 10631.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117042 restraints weight = 9602.628| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20305 Z= 0.093 Angle : 0.566 18.043 27750 Z= 0.261 Chirality : 0.042 0.133 3330 Planarity : 0.004 0.052 3620 Dihedral : 4.200 56.464 2922 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.44 % Allowed : 32.03 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2720 helix: 1.29 (0.22), residues: 585 sheet: 0.63 (0.19), residues: 795 loop : -1.65 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 248 TYR 0.012 0.001 TYR B 487 PHE 0.010 0.001 PHE B 505 TRP 0.007 0.001 TRP E 359 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00228 (20295) covalent geometry : angle 0.56474 (27730) SS BOND : bond 0.00322 ( 10) SS BOND : angle 1.34681 ( 20) hydrogen bonds : bond 0.03285 ( 735) hydrogen bonds : angle 4.35786 ( 2055) *********************** 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 332 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 0.776 Fit side-chains REVERT: B 520 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8005 (tt) REVERT: B 559 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: B 567 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7760 (tp) REVERT: A 249 LEU cc_start: 0.8135 (tt) cc_final: 0.7868 (tp) REVERT: A 271 LEU cc_start: 0.5890 (tp) cc_final: 0.5647 (tp) REVERT: A 329 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6872 (mt) REVERT: A 487 TYR cc_start: 0.7654 (p90) cc_final: 0.7396 (p90) REVERT: A 520 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 559 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7016 (t80) REVERT: A 562 THR cc_start: 0.7594 (m) cc_final: 0.7392 (p) REVERT: A 567 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7416 (tp) REVERT: C 271 LEU cc_start: 0.5950 (tp) cc_final: 0.5698 (tp) REVERT: C 520 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8085 (tt) REVERT: C 559 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.6730 (t80) REVERT: C 562 THR cc_start: 0.7514 (m) cc_final: 0.7295 (p) REVERT: D 271 LEU cc_start: 0.6042 (tp) cc_final: 0.5802 (tp) REVERT: D 559 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: D 615 TRP cc_start: 0.6338 (t-100) cc_final: 0.5977 (t-100) REVERT: E 160 GLN cc_start: 0.5353 (pt0) cc_final: 0.5116 (pm20) REVERT: E 249 LEU cc_start: 0.8158 (tt) cc_final: 0.7861 (tp) REVERT: E 271 LEU cc_start: 0.5944 (tp) cc_final: 0.5684 (tp) REVERT: E 501 THR cc_start: 0.7361 (p) cc_final: 0.7156 (p) REVERT: E 559 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: E 572 TYR cc_start: 0.8869 (p90) cc_final: 0.8351 (p90) outliers start: 82 outliers final: 60 residues processed: 318 average time/residue: 0.1218 time to fit residues: 62.6820 Evaluate side-chains 297 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 226 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 VAL 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 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 160 GLN 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 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 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 617 LEU 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 392 LEU Chi-restraints excluded: chain C residue 428 THR 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 567 LEU Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 286 VAL 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 535 VAL Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL 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 154 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 224 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 0.0470 chunk 134 optimal weight: 9.9990 overall best weight: 3.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.156368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129671 restraints weight = 31912.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131219 restraints weight = 63438.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130901 restraints weight = 38552.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130285 restraints weight = 31880.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131364 restraints weight = 24449.344| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20305 Z= 0.185 Angle : 0.644 16.547 27750 Z= 0.313 Chirality : 0.045 0.162 3330 Planarity : 0.005 0.059 3620 Dihedral : 4.758 54.384 2922 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.20 % Allowed : 31.60 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.16), residues: 2720 helix: 0.92 (0.21), residues: 585 sheet: 0.58 (0.19), residues: 775 loop : -1.80 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 155 TYR 0.016 0.002 TYR A 517 PHE 0.016 0.002 PHE C 443 TRP 0.011 0.001 TRP D 482 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00447 (20295) covalent geometry : angle 0.64360 (27730) SS BOND : bond 0.00304 ( 10) SS BOND : angle 1.32187 ( 20) hydrogen bonds : bond 0.04436 ( 735) hydrogen bonds : angle 4.75296 ( 2055) *********************** 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 317 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 221 time to evaluate : 0.779 Fit side-chains REVERT: B 329 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7000 (mt) REVERT: B 559 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: A 78 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6133 (tp) REVERT: A 249 LEU cc_start: 0.8010 (tt) cc_final: 0.7719 (tp) REVERT: A 271 LEU cc_start: 0.5775 (tp) cc_final: 0.5479 (tp) REVERT: A 329 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7026 (mt) REVERT: A 487 TYR cc_start: 0.7578 (p90) cc_final: 0.7359 (p90) REVERT: A 559 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7698 (t80) REVERT: C 158 LYS cc_start: 0.6796 (pttt) cc_final: 0.6153 (mttt) REVERT: C 271 LEU cc_start: 0.5747 (tp) cc_final: 0.5468 (tp) REVERT: C 559 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7543 (t80) REVERT: D 271 LEU cc_start: 0.5766 (tp) cc_final: 0.5507 (tp) REVERT: D 559 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: E 249 LEU cc_start: 0.7971 (tt) cc_final: 0.7563 (tp) REVERT: E 271 LEU cc_start: 0.5795 (tp) cc_final: 0.5529 (tp) REVERT: E 559 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: E 617 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7718 (tt) outliers start: 96 outliers final: 74 residues processed: 301 average time/residue: 0.1268 time to fit residues: 60.6037 Evaluate side-chains 297 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 214 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 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 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 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 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 428 THR 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 536 ILE 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 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 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 358 SER Chi-restraints excluded: chain D residue 392 LEU 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 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU 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 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 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 591 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 48 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 81 optimal weight: 0.0030 chunk 87 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 217 optimal weight: 0.0970 chunk 22 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 464 ASN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN C 464 ASN D 464 ASN E 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131160 restraints weight = 31447.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128957 restraints weight = 58276.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129876 restraints weight = 50510.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132601 restraints weight = 30431.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132476 restraints weight = 20412.769| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20305 Z= 0.092 Angle : 0.579 18.256 27750 Z= 0.264 Chirality : 0.042 0.170 3330 Planarity : 0.004 0.055 3620 Dihedral : 4.109 56.654 2922 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.90 % Allowed : 32.74 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2720 helix: 1.46 (0.22), residues: 585 sheet: 0.74 (0.19), residues: 800 loop : -1.62 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.011 0.001 TYR B 487 PHE 0.015 0.001 PHE E 159 TRP 0.009 0.001 TRP D 359 HIS 0.002 0.000 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00224 (20295) covalent geometry : angle 0.57786 (27730) SS BOND : bond 0.00340 ( 10) SS BOND : angle 1.30716 ( 20) hydrogen bonds : bond 0.03028 ( 735) hydrogen bonds : angle 4.22727 ( 2055) *********************** 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 327 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 255 time to evaluate : 0.786 Fit side-chains REVERT: B 249 LEU cc_start: 0.7843 (tt) cc_final: 0.7554 (tp) REVERT: B 493 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6461 (mt-10) REVERT: B 520 LEU cc_start: 0.8238 (tt) cc_final: 0.7946 (mt) REVERT: B 559 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: B 567 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7525 (tp) REVERT: A 249 LEU cc_start: 0.8030 (tt) cc_final: 0.7697 (tp) REVERT: A 271 LEU cc_start: 0.5681 (tp) cc_final: 0.5420 (tp) REVERT: A 487 TYR cc_start: 0.7465 (p90) cc_final: 0.7222 (p90) REVERT: A 559 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7638 (t80) REVERT: A 567 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7326 (tp) REVERT: C 158 LYS cc_start: 0.6664 (pttt) cc_final: 0.6152 (mttt) REVERT: C 249 LEU cc_start: 0.7861 (tt) cc_final: 0.7358 (tp) REVERT: C 271 LEU cc_start: 0.5816 (tp) cc_final: 0.5508 (tp) REVERT: C 559 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7311 (t80) REVERT: D 271 LEU cc_start: 0.5761 (tp) cc_final: 0.5502 (tp) REVERT: D 493 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6355 (mt-10) REVERT: D 615 TRP cc_start: 0.6537 (t-100) cc_final: 0.6263 (t-100) REVERT: E 249 LEU cc_start: 0.7873 (tt) cc_final: 0.7568 (tp) REVERT: E 271 LEU cc_start: 0.5735 (tp) cc_final: 0.5491 (tp) REVERT: E 431 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8599 (mt) REVERT: E 493 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6560 (mt-10) REVERT: E 501 THR cc_start: 0.7416 (p) cc_final: 0.7198 (p) REVERT: E 559 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7723 (m-80) outliers start: 72 outliers final: 57 residues processed: 314 average time/residue: 0.1137 time to fit residues: 57.7276 Evaluate side-chains 302 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 286 VAL Chi-restraints excluded: chain B residue 304 VAL 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 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 617 LEU 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 428 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 501 THR 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 594 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 351 VAL 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 535 VAL 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 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 591 VAL 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 97 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 chunk 218 optimal weight: 5.9990 chunk 178 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128106 restraints weight = 31812.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126523 restraints weight = 60148.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127077 restraints weight = 50901.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131073 restraints weight = 33623.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130047 restraints weight = 18933.049| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20305 Z= 0.173 Angle : 0.643 16.482 27750 Z= 0.310 Chirality : 0.045 0.182 3330 Planarity : 0.005 0.043 3620 Dihedral : 4.666 54.184 2922 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.07 % Allowed : 32.41 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2720 helix: 1.06 (0.21), residues: 585 sheet: 0.65 (0.19), residues: 775 loop : -1.78 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.017 0.002 TYR B 517 PHE 0.016 0.002 PHE B 505 TRP 0.013 0.001 TRP C 482 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00422 (20295) covalent geometry : angle 0.64204 (27730) SS BOND : bond 0.00299 ( 10) SS BOND : angle 1.31025 ( 20) hydrogen bonds : bond 0.04301 ( 735) hydrogen bonds : angle 4.65168 ( 2055) ********************** 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 298 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 0.615 Fit side-chains REVERT: B 249 LEU cc_start: 0.7922 (tt) cc_final: 0.7658 (tp) REVERT: B 559 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: A 78 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6088 (tp) REVERT: A 158 LYS cc_start: 0.6815 (pttt) cc_final: 0.6303 (mttt) REVERT: A 249 LEU cc_start: 0.8030 (tt) cc_final: 0.7720 (tp) REVERT: A 271 LEU cc_start: 0.5793 (tp) cc_final: 0.5515 (tp) REVERT: A 329 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7019 (mt) REVERT: A 487 TYR cc_start: 0.7576 (p90) cc_final: 0.7338 (p90) REVERT: A 559 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7788 (t80) REVERT: C 158 LYS cc_start: 0.6788 (pttt) cc_final: 0.6173 (mttt) REVERT: C 271 LEU cc_start: 0.5788 (tp) cc_final: 0.5522 (tp) REVERT: C 559 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7461 (t80) REVERT: D 615 TRP cc_start: 0.6562 (t-100) cc_final: 0.6281 (t-100) REVERT: E 158 LYS cc_start: 0.6852 (pttt) cc_final: 0.6272 (mttt) REVERT: E 249 LEU cc_start: 0.7944 (tt) cc_final: 0.7564 (tp) REVERT: E 271 LEU cc_start: 0.5801 (tp) cc_final: 0.5555 (tp) REVERT: E 431 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (mt) REVERT: E 559 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: E 617 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7730 (tt) outliers start: 75 outliers final: 64 residues processed: 286 average time/residue: 0.1174 time to fit residues: 54.3870 Evaluate side-chains 287 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 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 535 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 329 LEU 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 535 VAL 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 617 LEU Chi-restraints excluded: chain C residue 150 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 428 THR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 501 THR 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 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 D residue 150 THR 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 351 VAL Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 535 VAL 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 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 591 VAL 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 175 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 266 optimal weight: 0.0770 chunk 186 optimal weight: 0.0060 chunk 258 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130053 restraints weight = 31466.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128101 restraints weight = 55207.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128763 restraints weight = 51854.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131912 restraints weight = 33768.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131816 restraints weight = 19699.260| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20305 Z= 0.092 Angle : 0.583 18.110 27750 Z= 0.267 Chirality : 0.042 0.170 3330 Planarity : 0.004 0.057 3620 Dihedral : 4.074 56.144 2922 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.58 % Allowed : 33.12 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2720 helix: 1.61 (0.23), residues: 580 sheet: 0.79 (0.19), residues: 800 loop : -1.65 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.011 0.001 TYR E 487 PHE 0.009 0.001 PHE D 232 TRP 0.008 0.001 TRP D 359 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00226 (20295) covalent geometry : angle 0.58187 (27730) SS BOND : bond 0.00321 ( 10) SS BOND : angle 1.29519 ( 20) hydrogen bonds : bond 0.03010 ( 735) hydrogen bonds : angle 4.18739 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.16 seconds wall clock time: 57 minutes 27.37 seconds (3447.37 seconds total)