Starting phenix.real_space_refine on Tue Nov 19 17:53:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fti_50746/11_2024/9fti_50746.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fti_50746/11_2024/9fti_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fti_50746/11_2024/9fti_50746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fti_50746/11_2024/9fti_50746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fti_50746/11_2024/9fti_50746.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fti_50746/11_2024/9fti_50746.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 12770 2.51 5 N 3415 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19935 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 3987 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 531} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 15, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 268 Restraints were copied for chains: C, B, E, D Time building chain proxies: 9.16, per 1000 atoms: 0.46 Number of scatterers: 19935 At special positions: 0 Unit cell: (136.149, 133.563, 154.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 3710 8.00 N 3415 7.00 C 12770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 373 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 3.0 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5150 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 35 sheets defined 26.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.880A pdb=" N LEU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 543 through 564 removed outlier: 3.691A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 575 through 604 removed outlier: 3.682A pdb=" N ILE B 589 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 592 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 636 removed outlier: 3.628A pdb=" N ALA B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Proline residue: B 621 - end of helix removed outlier: 4.067A pdb=" N TYR B 624 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 634 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.880A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 543 through 564 removed outlier: 3.691A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 575 through 604 removed outlier: 3.682A pdb=" N ILE A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 removed outlier: 3.628A pdb=" N ALA A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix removed outlier: 4.067A pdb=" N TYR A 624 " --> pdb=" O TYR A 620 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 634 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.879A pdb=" N LEU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 522 Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 543 through 564 removed outlier: 3.690A pdb=" N VAL C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 575 through 604 removed outlier: 3.681A pdb=" N ILE C 589 " --> pdb=" O CYS C 585 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU C 592 " --> pdb=" O ALA C 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 599 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 602 " --> pdb=" O LYS C 598 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 636 removed outlier: 3.629A pdb=" N ALA C 609 " --> pdb=" O LYS C 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 4.067A pdb=" N TYR C 624 " --> pdb=" O TYR C 620 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 633 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 634 " --> pdb=" O TRP C 630 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.880A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.902A pdb=" N ILE D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 543 through 564 removed outlier: 3.690A pdb=" N VAL D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 575 through 604 removed outlier: 3.681A pdb=" N ILE D 589 " --> pdb=" O CYS D 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 599 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 removed outlier: 3.627A pdb=" N ALA D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 615 " --> pdb=" O GLN D 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 616 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Proline residue: D 621 - end of helix removed outlier: 4.067A pdb=" N TYR D 624 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D 625 " --> pdb=" O PRO D 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 633 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG D 634 " --> pdb=" O TRP D 630 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.879A pdb=" N LEU E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 386 through 391 removed outlier: 3.901A pdb=" N ILE E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 522 Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 543 through 564 removed outlier: 3.690A pdb=" N VAL E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 575 through 604 removed outlier: 3.682A pdb=" N ILE E 589 " --> pdb=" O CYS E 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU E 592 " --> pdb=" O ALA E 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 599 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 602 " --> pdb=" O LYS E 598 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 removed outlier: 3.628A pdb=" N ALA E 609 " --> pdb=" O LYS E 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR E 614 " --> pdb=" O ALA E 610 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP E 615 " --> pdb=" O GLN E 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 616 " --> pdb=" O ILE E 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 618 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR E 620 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Proline residue: E 621 - end of helix removed outlier: 4.066A pdb=" N TYR E 624 " --> pdb=" O TYR E 620 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG E 634 " --> pdb=" O TRP E 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 635 " --> pdb=" O VAL E 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS B 204 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 236 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP B 251 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 332 removed outlier: 7.223A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 339 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER B 350 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY B 341 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN B 348 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 427 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR B 428 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER B 408 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU B 454 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 502 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 494 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 510 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER B 486 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS A 204 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 236 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP A 251 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 329 through 332 removed outlier: 7.222A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 334 through 343 removed outlier: 6.636A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A 339 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER A 350 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY A 341 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN A 348 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 427 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 428 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 408 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU A 454 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 502 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 494 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 510 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 486 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS C 204 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 236 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP C 251 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 329 through 332 removed outlier: 7.223A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 427 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR C 428 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 408 " --> pdb=" O THR C 428 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 397 through 399 removed outlier: 3.514A pdb=" N LEU C 454 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 502 " --> pdb=" O VAL C 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 494 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 510 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 486 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 40 through 45 removed outlier: 5.893A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AC6, first strand: chain 'D' and resid 204 through 210 removed outlier: 3.620A pdb=" N HIS D 204 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 236 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP D 251 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.222A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 339 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER D 350 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY D 341 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN D 348 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 427 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR D 428 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER D 408 " --> pdb=" O THR D 428 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU D 454 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 502 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 494 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 510 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER D 486 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 40 through 45 removed outlier: 5.894A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AD4, first strand: chain 'E' and resid 204 through 210 removed outlier: 3.621A pdb=" N HIS E 204 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 236 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 218 through 220 removed outlier: 5.661A pdb=" N ASP E 251 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 329 through 332 removed outlier: 7.223A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 334 through 343 removed outlier: 6.635A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE E 339 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER E 350 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY E 341 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASN E 348 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE E 427 " --> pdb=" O GLY E 353 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR E 428 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER E 408 " --> pdb=" O THR E 428 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 397 through 399 removed outlier: 3.513A pdb=" N LEU E 454 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 500 " --> pdb=" O PHE E 496 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN E 502 " --> pdb=" O VAL E 494 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 494 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 510 " --> pdb=" O SER E 486 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER E 486 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6683 1.34 - 1.46: 4203 1.46 - 1.58: 9359 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 20295 Sorted by residual: bond pdb=" CA VAL A 336 " pdb=" CB VAL A 336 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.23e-02 6.61e+03 8.03e-01 bond pdb=" CA VAL D 336 " pdb=" CB VAL D 336 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.23e-02 6.61e+03 7.83e-01 bond pdb=" CA VAL B 336 " pdb=" CB VAL B 336 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.23e-02 6.61e+03 7.78e-01 bond pdb=" CA VAL E 336 " pdb=" CB VAL E 336 " ideal model delta sigma weight residual 1.540 1.530 0.011 1.23e-02 6.61e+03 7.61e-01 bond pdb=" CA VAL C 336 " pdb=" CB VAL C 336 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.23e-02 6.61e+03 7.28e-01 ... (remaining 20290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 27345 1.95 - 3.91: 329 3.91 - 5.86: 46 5.86 - 7.81: 5 7.81 - 9.77: 5 Bond angle restraints: 27730 Sorted by residual: angle pdb=" CA LEU B 364 " pdb=" CB LEU B 364 " pdb=" CG LEU B 364 " ideal model delta sigma weight residual 116.30 126.07 -9.77 3.50e+00 8.16e-02 7.79e+00 angle pdb=" CA LEU D 364 " pdb=" CB LEU D 364 " pdb=" CG LEU D 364 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU E 364 " pdb=" CB LEU E 364 " pdb=" CG LEU E 364 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU C 364 " pdb=" CB LEU C 364 " pdb=" CG LEU C 364 " ideal model delta sigma weight residual 116.30 126.05 -9.75 3.50e+00 8.16e-02 7.75e+00 angle pdb=" CA LEU A 364 " pdb=" CB LEU A 364 " pdb=" CG LEU A 364 " ideal model delta sigma weight residual 116.30 126.04 -9.74 3.50e+00 8.16e-02 7.75e+00 ... (remaining 27725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 10265 17.16 - 34.32: 1213 34.32 - 51.48: 318 51.48 - 68.64: 55 68.64 - 85.80: 25 Dihedral angle restraints: 11876 sinusoidal: 3911 harmonic: 7965 Sorted by residual: dihedral pdb=" CA VAL A 386 " pdb=" C VAL A 386 " pdb=" N ALA A 387 " pdb=" CA ALA A 387 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL C 386 " pdb=" C VAL C 386 " pdb=" N ALA C 387 " pdb=" CA ALA C 387 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B 386 " pdb=" C VAL B 386 " pdb=" N ALA B 387 " pdb=" CA ALA B 387 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 11873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1693 0.027 - 0.054: 1034 0.054 - 0.082: 330 0.082 - 0.109: 201 0.109 - 0.136: 72 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ILE A 339 " pdb=" N ILE A 339 " pdb=" C ILE A 339 " pdb=" CB ILE A 339 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE B 339 " pdb=" N ILE B 339 " pdb=" C ILE B 339 " pdb=" CB ILE B 339 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PRO D 417 " pdb=" N PRO D 417 " pdb=" C PRO D 417 " pdb=" CB PRO D 417 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 3327 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 160 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO E 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 161 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 161 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 160 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO B 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 160 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 161 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.024 5.00e-02 4.00e+02 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 99 2.60 - 3.18: 16292 3.18 - 3.75: 27386 3.75 - 4.33: 36436 4.33 - 4.90: 61466 Nonbonded interactions: 141679 Sorted by model distance: nonbonded pdb=" SG CYS D 275 " pdb=" SG CYS D 280 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 275 " pdb=" SG CYS C 280 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 275 " pdb=" SG CYS E 280 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS A 275 " pdb=" SG CYS A 280 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 371 " pdb=" SG CYS D 373 " model vdw 2.032 3.760 ... (remaining 141674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 42.410 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20295 Z= 0.332 Angle : 0.597 9.768 27730 Z= 0.304 Chirality : 0.044 0.136 3330 Planarity : 0.004 0.044 3620 Dihedral : 16.699 85.801 6720 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.27 % Allowed : 29.81 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2720 helix: -1.26 (0.19), residues: 585 sheet: -0.03 (0.19), residues: 740 loop : -1.79 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS D 285 PHE 0.015 0.002 PHE C 505 TYR 0.013 0.002 TYR D 441 ARG 0.001 0.000 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 2.187 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: 0.3287 time to fit residues: 127.3512 Evaluate side-chains 231 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain D residue 581 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 40.0000 chunk 208 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 285 HIS B 410 ASN B 471 GLN A 206 GLN A 285 HIS A 410 ASN A 471 GLN C 206 GLN C 285 HIS C 410 ASN C 471 GLN D 206 GLN D 285 HIS D 410 ASN D 471 GLN E 206 GLN E 285 HIS E 410 ASN E 471 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20295 Z= 0.426 Angle : 0.737 14.361 27730 Z= 0.374 Chirality : 0.048 0.151 3330 Planarity : 0.006 0.044 3620 Dihedral : 5.546 54.072 2924 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.94 % Allowed : 27.59 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2720 helix: -0.52 (0.19), residues: 585 sheet: -0.10 (0.18), residues: 800 loop : -1.88 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 482 HIS 0.005 0.001 HIS C 285 PHE 0.019 0.002 PHE E 436 TYR 0.019 0.003 TYR A 517 ARG 0.004 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 251 time to evaluate : 2.173 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 329 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6988 (mt) REVERT: B 559 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: A 158 LYS cc_start: 0.6595 (pttt) cc_final: 0.6015 (mptt) REVERT: A 280 CYS cc_start: 0.5696 (OUTLIER) cc_final: 0.5029 (m) REVERT: A 329 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7010 (mt) REVERT: A 431 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 615 TRP cc_start: 0.6770 (t-100) cc_final: 0.6382 (t-100) REVERT: C 559 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7367 (t80) REVERT: C 615 TRP cc_start: 0.6598 (t-100) cc_final: 0.6175 (t-100) REVERT: D 329 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7070 (mt) REVERT: E 431 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (mt) outliers start: 128 outliers final: 75 residues processed: 348 average time/residue: 0.3044 time to fit residues: 167.9971 Evaluate side-chains 299 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 475 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 chunk 207 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20295 Z= 0.190 Angle : 0.603 17.335 27730 Z= 0.288 Chirality : 0.043 0.138 3330 Planarity : 0.004 0.044 3620 Dihedral : 4.719 55.559 2922 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.39 % Allowed : 30.51 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2720 helix: 0.34 (0.21), residues: 585 sheet: 0.10 (0.19), residues: 790 loop : -1.73 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 482 HIS 0.002 0.000 HIS A 360 PHE 0.013 0.001 PHE B 505 TYR 0.010 0.001 TYR E 441 ARG 0.006 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 2.365 Fit side-chains REVERT: B 271 LEU cc_start: 0.6102 (tp) cc_final: 0.5808 (tp) REVERT: B 520 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (tt) REVERT: B 559 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 271 LEU cc_start: 0.6091 (tp) cc_final: 0.5784 (tp) REVERT: A 280 CYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5310 (m) REVERT: A 559 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7655 (t80) REVERT: C 249 LEU cc_start: 0.8239 (tp) cc_final: 0.7906 (tp) REVERT: C 271 LEU cc_start: 0.6145 (tp) cc_final: 0.5833 (tp) REVERT: C 280 CYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5783 (m) REVERT: C 559 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7278 (t80) REVERT: C 615 TRP cc_start: 0.6857 (t-100) cc_final: 0.6494 (t-100) REVERT: D 232 PHE cc_start: 0.7155 (t80) cc_final: 0.6953 (t80) REVERT: D 271 LEU cc_start: 0.5961 (tp) cc_final: 0.5719 (tp) REVERT: D 280 CYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5369 (m) REVERT: D 559 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: E 249 LEU cc_start: 0.8091 (tt) cc_final: 0.7817 (tp) REVERT: E 271 LEU cc_start: 0.6324 (tp) cc_final: 0.5965 (tp) REVERT: E 280 CYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5897 (m) REVERT: E 559 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7666 (m-80) outliers start: 81 outliers final: 41 residues processed: 318 average time/residue: 0.2933 time to fit residues: 148.1059 Evaluate side-chains 275 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 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 250 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 6.9990 chunk 188 optimal weight: 0.0570 chunk 129 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 265 optimal weight: 0.0370 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20295 Z= 0.143 Angle : 0.569 18.938 27730 Z= 0.260 Chirality : 0.042 0.133 3330 Planarity : 0.004 0.046 3620 Dihedral : 4.211 56.830 2922 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.50 % Allowed : 30.95 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2720 helix: 1.03 (0.22), residues: 585 sheet: 0.35 (0.19), residues: 795 loop : -1.59 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.002 0.000 HIS B 285 PHE 0.010 0.001 PHE B 505 TYR 0.012 0.001 TYR E 487 ARG 0.005 0.000 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 2.216 Fit side-chains REVERT: B 271 LEU cc_start: 0.6012 (tp) cc_final: 0.5724 (tp) REVERT: B 329 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6957 (mt) REVERT: B 559 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: A 280 CYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5497 (m) REVERT: A 329 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6957 (mt) REVERT: A 501 THR cc_start: 0.7731 (p) cc_final: 0.7346 (p) REVERT: A 520 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 559 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 567 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7462 (tp) REVERT: C 249 LEU cc_start: 0.8192 (tp) cc_final: 0.7925 (tp) REVERT: C 271 LEU cc_start: 0.6045 (tp) cc_final: 0.5745 (tp) REVERT: C 280 CYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5790 (m) REVERT: C 559 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 567 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7333 (tp) REVERT: C 615 TRP cc_start: 0.6870 (t-100) cc_final: 0.6642 (t-100) REVERT: D 280 CYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5567 (m) REVERT: D 559 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: D 615 TRP cc_start: 0.6411 (t-100) cc_final: 0.6078 (t-100) REVERT: E 249 LEU cc_start: 0.8109 (tt) cc_final: 0.7883 (tp) REVERT: E 271 LEU cc_start: 0.5973 (tp) cc_final: 0.5667 (tp) REVERT: E 280 CYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5873 (m) REVERT: E 559 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: E 567 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7499 (tp) REVERT: E 572 TYR cc_start: 0.8797 (p90) cc_final: 0.8369 (p90) outliers start: 83 outliers final: 50 residues processed: 327 average time/residue: 0.2944 time to fit residues: 152.8811 Evaluate side-chains 306 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain B residue 332 VAL 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 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 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 520 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 210 ILE Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 567 LEU 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 280 CYS 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 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 559 PHE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 595 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 226 optimal weight: 0.0770 chunk 183 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 135 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 overall best weight: 6.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 20295 Z= 0.492 Angle : 0.763 15.227 27730 Z= 0.383 Chirality : 0.049 0.190 3330 Planarity : 0.006 0.044 3620 Dihedral : 5.493 53.128 2922 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.50 % Allowed : 31.17 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2720 helix: 0.09 (0.20), residues: 585 sheet: 0.26 (0.19), residues: 780 loop : -1.90 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 482 HIS 0.003 0.001 HIS A 360 PHE 0.022 0.003 PHE E 443 TYR 0.023 0.003 TYR C 517 ARG 0.005 0.001 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 234 time to evaluate : 2.229 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 78 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5623 (tp) REVERT: B 271 LEU cc_start: 0.6083 (tp) cc_final: 0.5868 (tp) REVERT: B 329 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6920 (mt) REVERT: B 520 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 158 LYS cc_start: 0.6514 (pttt) cc_final: 0.5834 (mttt) REVERT: A 249 LEU cc_start: 0.8048 (tt) cc_final: 0.7825 (tp) REVERT: A 280 CYS cc_start: 0.5875 (OUTLIER) cc_final: 0.5508 (m) REVERT: A 329 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7032 (mt) REVERT: A 520 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 559 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7508 (t80) REVERT: C 78 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5932 (tp) REVERT: C 559 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7317 (t80) REVERT: C 615 TRP cc_start: 0.6968 (t-100) cc_final: 0.6658 (t-100) REVERT: D 78 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5641 (tp) REVERT: D 271 LEU cc_start: 0.6007 (tp) cc_final: 0.5772 (tp) REVERT: D 280 CYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5484 (m) REVERT: D 559 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: E 78 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5752 (tp) REVERT: E 280 CYS cc_start: 0.6338 (OUTLIER) cc_final: 0.6118 (m) REVERT: E 431 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8653 (mt) REVERT: E 559 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: E 617 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7704 (tt) outliers start: 120 outliers final: 84 residues processed: 330 average time/residue: 0.2916 time to fit residues: 151.6777 Evaluate side-chains 320 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 219 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 350 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 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 562 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 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 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 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 351 VAL 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 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 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 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 52 optimal weight: 0.0050 chunk 156 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 220 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20295 Z= 0.180 Angle : 0.598 17.319 27730 Z= 0.283 Chirality : 0.043 0.134 3330 Planarity : 0.004 0.051 3620 Dihedral : 4.631 55.261 2922 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.58 % Allowed : 31.44 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2720 helix: 0.78 (0.22), residues: 585 sheet: 0.40 (0.19), residues: 795 loop : -1.76 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 482 HIS 0.001 0.000 HIS A 360 PHE 0.013 0.001 PHE B 505 TYR 0.010 0.001 TYR D 441 ARG 0.004 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 230 time to evaluate : 2.155 Fit side-chains REVERT: B 78 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5767 (tp) REVERT: B 271 LEU cc_start: 0.6061 (tp) cc_final: 0.5847 (tp) REVERT: B 329 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6943 (mt) REVERT: B 520 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8138 (tt) REVERT: B 559 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: B 634 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5410 (mtm180) REVERT: A 329 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6971 (mt) REVERT: A 559 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7651 (t80) REVERT: C 78 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.6068 (tp) REVERT: C 249 LEU cc_start: 0.8118 (tp) cc_final: 0.7913 (tp) REVERT: C 559 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7369 (t80) REVERT: C 615 TRP cc_start: 0.6931 (t-100) cc_final: 0.6619 (t-100) REVERT: D 271 LEU cc_start: 0.6067 (tp) cc_final: 0.5821 (tp) REVERT: D 280 CYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5464 (m) REVERT: D 559 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: E 78 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5797 (tp) REVERT: E 431 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8642 (mt) REVERT: E 559 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: E 617 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7647 (tt) outliers start: 103 outliers final: 67 residues processed: 314 average time/residue: 0.3014 time to fit residues: 148.6817 Evaluate side-chains 303 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 221 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 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 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 634 ARG 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 429 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 78 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 304 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 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 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 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 559 PHE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 150 THR 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 484 VAL Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 165 optimal weight: 30.0000 chunk 161 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20295 Z= 0.206 Angle : 0.607 17.544 27730 Z= 0.287 Chirality : 0.043 0.137 3330 Planarity : 0.004 0.041 3620 Dihedral : 4.581 54.917 2922 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.12 % Allowed : 31.38 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2720 helix: 0.92 (0.22), residues: 585 sheet: 0.49 (0.19), residues: 795 loop : -1.77 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.002 0.000 HIS A 360 PHE 0.013 0.001 PHE B 505 TYR 0.013 0.002 TYR A 517 ARG 0.004 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 234 time to evaluate : 2.354 Fit side-chains REVERT: B 78 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5702 (tp) REVERT: B 329 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6956 (mt) REVERT: B 520 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 559 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: B 634 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5467 (mtm180) REVERT: A 155 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7360 (ptm160) REVERT: A 329 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7012 (mt) REVERT: A 559 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7660 (t80) REVERT: C 158 LYS cc_start: 0.6441 (pttt) cc_final: 0.5717 (mttt) REVERT: C 559 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7398 (t80) REVERT: D 155 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7274 (ptm160) REVERT: D 271 LEU cc_start: 0.6039 (tp) cc_final: 0.5826 (tp) REVERT: D 280 CYS cc_start: 0.5708 (OUTLIER) cc_final: 0.5401 (m) REVERT: D 282 LEU cc_start: 0.8523 (mp) cc_final: 0.8205 (mm) REVERT: D 559 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: E 431 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8660 (mt) REVERT: E 559 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: E 617 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7639 (tt) outliers start: 113 outliers final: 83 residues processed: 328 average time/residue: 0.3087 time to fit residues: 158.9374 Evaluate side-chains 319 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 221 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 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 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 594 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 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 536 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 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 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 591 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 163 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 20295 Z= 0.369 Angle : 0.694 15.628 27730 Z= 0.342 Chirality : 0.047 0.145 3330 Planarity : 0.005 0.045 3620 Dihedral : 5.193 53.673 2922 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.78 % Allowed : 31.11 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2720 helix: 0.46 (0.21), residues: 585 sheet: 0.38 (0.19), residues: 775 loop : -1.94 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 482 HIS 0.002 0.001 HIS A 360 PHE 0.018 0.002 PHE E 443 TYR 0.018 0.002 TYR A 517 ARG 0.004 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 226 time to evaluate : 2.242 Fit side-chains TARDY: cannot create tardy model for: "PHE B 636 " (corrupted residue). Skipping it. REVERT: B 78 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5727 (tp) REVERT: B 329 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7042 (mt) REVERT: B 520 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (tt) REVERT: B 559 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: A 158 LYS cc_start: 0.6553 (pttt) cc_final: 0.5879 (mttt) REVERT: A 249 LEU cc_start: 0.8005 (tt) cc_final: 0.7755 (tp) REVERT: A 329 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7040 (mt) REVERT: A 559 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 158 LYS cc_start: 0.6488 (pttt) cc_final: 0.5769 (mttt) REVERT: C 559 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7376 (t80) REVERT: D 78 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5530 (tp) REVERT: D 271 LEU cc_start: 0.6071 (tp) cc_final: 0.5866 (tp) REVERT: D 280 CYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5627 (m) REVERT: D 559 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: D 579 PHE cc_start: 0.8028 (t80) cc_final: 0.7625 (t80) REVERT: E 431 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8646 (mt) REVERT: E 559 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: E 617 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7671 (tt) outliers start: 125 outliers final: 94 residues processed: 331 average time/residue: 0.3105 time to fit residues: 158.1916 Evaluate side-chains 322 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 215 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 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 536 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 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 559 PHE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 231 optimal weight: 0.0370 chunk 246 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 233 optimal weight: 30.0000 chunk 162 optimal weight: 0.0980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: