Starting phenix.real_space_refine on Mon Dec 30 19:35:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io4_35607/12_2024/8io4_35607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io4_35607/12_2024/8io4_35607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8io4_35607/12_2024/8io4_35607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io4_35607/12_2024/8io4_35607.map" model { file = "/net/cci-nas-00/data/ceres_data/8io4_35607/12_2024/8io4_35607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io4_35607/12_2024/8io4_35607.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= 0.014 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 68 5.16 5 C 9008 2.51 5 N 2324 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 9.11, per 1000 atoms: 0.66 Number of scatterers: 13736 At special positions: 0 Unit cell: (111.219, 111.219, 118.86, 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 68 16.00 O 2336 8.00 N 2324 7.00 C 9008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 65.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 removed outlier: 3.675A pdb=" N ALA A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 470 Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 525 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.870A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.726A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 576 removed outlier: 3.763A pdb=" N PHE A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 623 removed outlier: 4.579A pdb=" N THR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 687 removed outlier: 3.723A pdb=" N LYS A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.074A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.010A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 removed outlier: 3.547A pdb=" N ALA A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.804A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 845 removed outlier: 3.613A pdb=" N TYR A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 removed outlier: 3.587A pdb=" N SER A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.675A pdb=" N ALA C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 470 Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU C 524 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 525 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.870A pdb=" N ALA C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.726A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 547 through 576 removed outlier: 3.763A pdb=" N PHE C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 606 through 623 removed outlier: 4.579A pdb=" N THR C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 687 removed outlier: 3.723A pdb=" N LYS C 638 " --> pdb=" O THR C 634 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.074A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.010A pdb=" N VAL C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 720 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 732 removed outlier: 3.547A pdb=" N ALA C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS C 729 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 731 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 732 " --> pdb=" O ILE C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 747 through 757 removed outlier: 3.804A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 removed outlier: 3.612A pdb=" N TYR C 845 " --> pdb=" O VAL C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 855 removed outlier: 3.587A pdb=" N SER C 855 " --> pdb=" O HIS C 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.680A pdb=" N ALA D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 470 Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU D 524 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.860A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 576 removed outlier: 3.587A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 623 removed outlier: 4.580A pdb=" N THR D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 687 removed outlier: 3.719A pdb=" N LYS D 638 " --> pdb=" O THR D 634 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE D 639 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.205A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 3.903A pdb=" N VAL D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 720 " --> pdb=" O VAL D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 732 removed outlier: 4.240A pdb=" N ILE D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS D 731 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 746 removed outlier: 3.651A pdb=" N ALA D 746 " --> pdb=" O PHE D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 757 removed outlier: 3.862A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 removed outlier: 3.618A pdb=" N TYR D 845 " --> pdb=" O VAL D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 855 removed outlier: 3.569A pdb=" N SER D 855 " --> pdb=" O HIS D 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.680A pdb=" N ALA B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 470 Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU B 524 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.859A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 576 removed outlier: 3.587A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 606 through 623 removed outlier: 4.580A pdb=" N THR B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 687 removed outlier: 3.719A pdb=" N LYS B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 639 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.205A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 3.903A pdb=" N VAL B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 732 removed outlier: 4.239A pdb=" N ILE B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B 729 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 731 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 746 removed outlier: 3.649A pdb=" N ALA B 746 " --> pdb=" O PHE B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 removed outlier: 3.863A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 845 removed outlier: 3.618A pdb=" N TYR B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 855 removed outlier: 3.569A pdb=" N SER B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA2, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.435A pdb=" N ILE A 787 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 798 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 805 through 806 removed outlier: 3.829A pdb=" N GLY A 806 " --> pdb=" O PHE A 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 759 through 761 Processing sheet with id=AA5, first strand: chain 'C' and resid 787 through 790 removed outlier: 6.435A pdb=" N ILE C 787 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C 798 " --> pdb=" O ILE C 787 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 805 through 806 removed outlier: 3.828A pdb=" N GLY C 806 " --> pdb=" O PHE C 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 759 through 761 Processing sheet with id=AA8, first strand: chain 'D' and resid 787 through 790 removed outlier: 6.443A pdb=" N ILE D 787 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 798 " --> pdb=" O ILE D 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 805 through 806 removed outlier: 3.779A pdb=" N GLY D 806 " --> pdb=" O PHE D 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 759 through 761 Processing sheet with id=AB2, first strand: chain 'B' and resid 787 through 790 removed outlier: 6.443A pdb=" N ILE B 787 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 798 " --> pdb=" O ILE B 787 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 805 through 806 removed outlier: 3.779A pdb=" N GLY B 806 " --> pdb=" O PHE B 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 742 hydrogen bonds defined for protein. 2112 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: 4.36 Time building geometry restraints manager: 3.91 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: 4252 1.34 - 1.46: 2501 1.46 - 1.58: 7239 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 14096 Sorted by residual: bond pdb=" C THR C 425 " pdb=" N PRO C 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C THR B 425 " pdb=" N PRO B 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C THR A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C THR D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C GLN A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.28e-02 6.10e+03 5.27e+00 ... (remaining 14091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18236 1.60 - 3.20: 758 3.20 - 4.81: 119 4.81 - 6.41: 28 6.41 - 8.01: 11 Bond angle restraints: 19152 Sorted by residual: angle pdb=" N GLY B 806 " pdb=" CA GLY B 806 " pdb=" C GLY B 806 " ideal model delta sigma weight residual 110.20 114.59 -4.39 1.32e+00 5.74e-01 1.11e+01 angle pdb=" N GLY D 806 " pdb=" CA GLY D 806 " pdb=" C GLY D 806 " ideal model delta sigma weight residual 110.20 114.59 -4.39 1.32e+00 5.74e-01 1.11e+01 angle pdb=" C CYS C 449 " pdb=" N GLN C 450 " pdb=" CA GLN C 450 " ideal model delta sigma weight residual 121.80 129.81 -8.01 2.44e+00 1.68e-01 1.08e+01 angle pdb=" C CYS A 449 " pdb=" N GLN A 450 " pdb=" CA GLN A 450 " ideal model delta sigma weight residual 121.80 129.81 -8.01 2.44e+00 1.68e-01 1.08e+01 angle pdb=" C CYS D 449 " pdb=" N GLN D 450 " pdb=" CA GLN D 450 " ideal model delta sigma weight residual 121.80 129.81 -8.01 2.44e+00 1.68e-01 1.08e+01 ... (remaining 19147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7444 17.93 - 35.86: 646 35.86 - 53.79: 102 53.79 - 71.72: 8 71.72 - 89.64: 8 Dihedral angle restraints: 8208 sinusoidal: 3192 harmonic: 5016 Sorted by residual: dihedral pdb=" CA TYR B 542 " pdb=" C TYR B 542 " pdb=" N SER B 543 " pdb=" CA SER B 543 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR D 542 " pdb=" C TYR D 542 " pdb=" N SER D 543 " pdb=" CA SER D 543 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU C 544 " pdb=" C GLU C 544 " pdb=" N TYR C 545 " pdb=" CA TYR C 545 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1320 0.031 - 0.062: 539 0.062 - 0.092: 246 0.092 - 0.123: 55 0.123 - 0.154: 16 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CA THR B 425 " pdb=" N THR B 425 " pdb=" C THR B 425 " pdb=" CB THR B 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA THR A 425 " pdb=" N THR A 425 " pdb=" C THR A 425 " pdb=" CB THR A 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA THR C 425 " pdb=" N THR C 425 " pdb=" C THR C 425 " pdb=" CB THR C 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2173 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 412 " -0.012 2.00e-02 2.50e+03 9.84e-03 2.42e+00 pdb=" CG TRP B 412 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 412 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 412 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 412 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 412 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 412 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 412 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 412 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 412 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 807 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO B 808 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 808 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 808 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 807 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO D 808 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 808 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 808 " 0.021 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 841 2.73 - 3.28: 14837 3.28 - 3.82: 22598 3.82 - 4.36: 25292 4.36 - 4.90: 43040 Nonbonded interactions: 106608 Sorted by model distance: nonbonded pdb=" OG1 THR D 761 " pdb=" NZ LYS D 832 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR B 761 " pdb=" NZ LYS B 832 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR A 761 " pdb=" NZ LYS A 832 " model vdw 2.211 3.120 nonbonded pdb=" OG1 THR C 761 " pdb=" NZ LYS C 832 " model vdw 2.212 3.120 nonbonded pdb=" O HIS C 703 " pdb=" OG SER C 706 " model vdw 2.231 3.040 ... (remaining 106603 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' } 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: 4.800 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 32.330 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.003 0.036 14096 Z= 0.197 Angle : 0.746 8.012 19152 Z= 0.419 Chirality : 0.042 0.154 2176 Planarity : 0.004 0.038 2376 Dihedral : 13.371 89.645 4976 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.52 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1684 helix: 0.36 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -2.09 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 412 HIS 0.007 0.001 HIS B 831 PHE 0.025 0.001 PHE A 852 TYR 0.018 0.001 TYR B 845 ARG 0.006 0.000 ARG D 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 GLU cc_start: 0.7308 (pp20) cc_final: 0.6781 (pp20) REVERT: A 545 TYR cc_start: 0.5719 (m-10) cc_final: 0.5518 (m-80) REVERT: A 550 LEU cc_start: 0.8585 (mt) cc_final: 0.8315 (mp) REVERT: A 698 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 705 TRP cc_start: 0.7972 (t60) cc_final: 0.7513 (t60) REVERT: C 544 GLU cc_start: 0.7307 (pp20) cc_final: 0.6778 (pp20) REVERT: C 550 LEU cc_start: 0.8579 (mt) cc_final: 0.8313 (mp) REVERT: C 698 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8243 (mm-30) REVERT: C 705 TRP cc_start: 0.7956 (t60) cc_final: 0.7499 (t60) REVERT: D 550 LEU cc_start: 0.8592 (mt) cc_final: 0.8318 (mp) REVERT: D 699 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7025 (tm-30) REVERT: D 845 TYR cc_start: 0.5622 (m-80) cc_final: 0.5406 (m-80) REVERT: B 550 LEU cc_start: 0.8604 (mt) cc_final: 0.8336 (mp) REVERT: B 699 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 845 TYR cc_start: 0.5615 (m-80) cc_final: 0.5397 (m-80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2926 time to fit residues: 148.8722 Evaluate side-chains 270 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN D 635 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 HIS B 635 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14096 Z= 0.243 Angle : 0.679 9.049 19152 Z= 0.343 Chirality : 0.043 0.151 2176 Planarity : 0.005 0.047 2376 Dihedral : 4.484 16.620 1876 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.95 % Favored : 92.64 % Rotamer: Outliers : 1.92 % Allowed : 12.98 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1684 helix: 0.34 (0.16), residues: 1000 sheet: -0.75 (0.78), residues: 40 loop : -2.08 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 705 HIS 0.010 0.002 HIS B 731 PHE 0.019 0.002 PHE D 701 TYR 0.013 0.002 TYR B 652 ARG 0.004 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8433 (t) cc_final: 0.8154 (p) REVERT: A 539 LEU cc_start: 0.8703 (tp) cc_final: 0.8203 (pp) REVERT: A 545 TYR cc_start: 0.5715 (m-10) cc_final: 0.5383 (m-10) REVERT: A 705 TRP cc_start: 0.8131 (t60) cc_final: 0.7801 (t60) REVERT: C 418 VAL cc_start: 0.8427 (t) cc_final: 0.8145 (p) REVERT: C 539 LEU cc_start: 0.8709 (tp) cc_final: 0.8214 (pp) REVERT: C 705 TRP cc_start: 0.8120 (t60) cc_final: 0.7790 (t60) REVERT: D 418 VAL cc_start: 0.8451 (t) cc_final: 0.8177 (p) REVERT: D 550 LEU cc_start: 0.8632 (mt) cc_final: 0.8329 (mp) REVERT: D 705 TRP cc_start: 0.8116 (t60) cc_final: 0.7699 (t60) REVERT: D 713 MET cc_start: 0.8283 (mpp) cc_final: 0.8077 (mpp) REVERT: B 418 VAL cc_start: 0.8442 (t) cc_final: 0.8165 (p) REVERT: B 550 LEU cc_start: 0.8639 (mt) cc_final: 0.8344 (mp) REVERT: B 705 TRP cc_start: 0.8130 (t60) cc_final: 0.7711 (t60) outliers start: 28 outliers final: 26 residues processed: 311 average time/residue: 0.2885 time to fit residues: 126.3881 Evaluate side-chains 288 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS B 470 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14096 Z= 0.456 Angle : 0.790 8.882 19152 Z= 0.404 Chirality : 0.048 0.177 2176 Planarity : 0.005 0.044 2376 Dihedral : 5.031 17.890 1876 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.37 % Favored : 90.97 % Rotamer: Outliers : 4.33 % Allowed : 13.39 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1684 helix: -0.04 (0.15), residues: 1048 sheet: -3.52 (0.43), residues: 40 loop : -2.33 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 568 HIS 0.008 0.002 HIS D 731 PHE 0.027 0.003 PHE A 619 TYR 0.019 0.003 TYR A 652 ARG 0.009 0.001 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 1.619 Fit side-chains REVERT: A 713 MET cc_start: 0.8175 (mpp) cc_final: 0.7937 (mpp) REVERT: C 713 MET cc_start: 0.8167 (mpp) cc_final: 0.7932 (mpp) REVERT: D 713 MET cc_start: 0.8397 (mpp) cc_final: 0.8030 (mpp) REVERT: B 713 MET cc_start: 0.8336 (mpp) cc_final: 0.8085 (mpp) outliers start: 63 outliers final: 46 residues processed: 323 average time/residue: 0.2633 time to fit residues: 123.5367 Evaluate side-chains 287 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14096 Z= 0.212 Angle : 0.673 8.461 19152 Z= 0.344 Chirality : 0.043 0.160 2176 Planarity : 0.004 0.042 2376 Dihedral : 4.589 17.079 1876 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.98 % Rotamer: Outliers : 3.64 % Allowed : 16.96 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1684 helix: 0.16 (0.15), residues: 1060 sheet: -3.28 (0.45), residues: 40 loop : -2.25 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 705 HIS 0.007 0.001 HIS B 731 PHE 0.018 0.002 PHE D 701 TYR 0.012 0.001 TYR B 616 ARG 0.003 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 1.681 Fit side-chains REVERT: A 538 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8097 (mmtt) REVERT: A 552 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7921 (tt) REVERT: C 538 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8117 (mmtt) REVERT: C 552 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7896 (tt) REVERT: D 552 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7937 (tt) REVERT: D 713 MET cc_start: 0.8310 (mpp) cc_final: 0.7997 (mpp) REVERT: B 552 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7932 (tt) REVERT: B 713 MET cc_start: 0.8269 (mpp) cc_final: 0.8046 (mpp) outliers start: 53 outliers final: 39 residues processed: 306 average time/residue: 0.2563 time to fit residues: 113.8440 Evaluate side-chains 304 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN C 733 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14096 Z= 0.213 Angle : 0.667 9.412 19152 Z= 0.339 Chirality : 0.042 0.150 2176 Planarity : 0.004 0.042 2376 Dihedral : 4.434 15.973 1876 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.24 % Favored : 92.28 % Rotamer: Outliers : 4.26 % Allowed : 18.96 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1684 helix: 0.39 (0.16), residues: 1032 sheet: -3.12 (0.46), residues: 40 loop : -1.94 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 705 HIS 0.006 0.001 HIS B 703 PHE 0.012 0.001 PHE D 656 TYR 0.013 0.001 TYR D 616 ARG 0.003 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 1.754 Fit side-chains REVERT: A 552 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7895 (tt) REVERT: A 705 TRP cc_start: 0.8205 (t60) cc_final: 0.7833 (t60) REVERT: C 552 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7869 (tt) REVERT: C 705 TRP cc_start: 0.8188 (t60) cc_final: 0.7819 (t60) REVERT: D 552 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7907 (tt) REVERT: D 705 TRP cc_start: 0.8267 (t60) cc_final: 0.7893 (t60) REVERT: D 713 MET cc_start: 0.8371 (mpp) cc_final: 0.8088 (mpp) REVERT: D 842 LEU cc_start: 0.7092 (mm) cc_final: 0.6661 (pp) REVERT: B 552 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7902 (tt) REVERT: B 705 TRP cc_start: 0.8276 (t60) cc_final: 0.7929 (t60) REVERT: B 713 MET cc_start: 0.8237 (mpp) cc_final: 0.8031 (mpp) REVERT: B 842 LEU cc_start: 0.7149 (mm) cc_final: 0.6729 (pp) outliers start: 62 outliers final: 52 residues processed: 311 average time/residue: 0.2674 time to fit residues: 122.7621 Evaluate side-chains 318 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14096 Z= 0.252 Angle : 0.693 10.484 19152 Z= 0.352 Chirality : 0.043 0.174 2176 Planarity : 0.004 0.039 2376 Dihedral : 4.462 17.733 1876 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.24 % Favored : 92.28 % Rotamer: Outliers : 4.67 % Allowed : 19.57 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1684 helix: 0.43 (0.16), residues: 1028 sheet: -3.07 (0.46), residues: 40 loop : -1.97 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 705 HIS 0.008 0.001 HIS D 703 PHE 0.027 0.002 PHE D 701 TYR 0.014 0.001 TYR B 707 ARG 0.004 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 271 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 538 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8051 (mmtt) REVERT: A 550 LEU cc_start: 0.8740 (mt) cc_final: 0.8416 (mp) REVERT: A 552 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7961 (tt) REVERT: A 842 LEU cc_start: 0.7259 (mm) cc_final: 0.6804 (pp) REVERT: C 550 LEU cc_start: 0.8729 (mt) cc_final: 0.8412 (mp) REVERT: C 552 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7928 (tt) REVERT: C 842 LEU cc_start: 0.7253 (mm) cc_final: 0.6800 (pp) REVERT: D 550 LEU cc_start: 0.8757 (mt) cc_final: 0.8515 (mp) REVERT: D 552 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7941 (tt) REVERT: D 713 MET cc_start: 0.8370 (mpp) cc_final: 0.8079 (mpp) REVERT: D 842 LEU cc_start: 0.7046 (mm) cc_final: 0.6660 (pp) REVERT: B 550 LEU cc_start: 0.8765 (mt) cc_final: 0.8532 (mp) REVERT: B 552 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7936 (tt) REVERT: B 713 MET cc_start: 0.8255 (mpp) cc_final: 0.8019 (mpp) REVERT: B 842 LEU cc_start: 0.7098 (mm) cc_final: 0.6722 (pp) outliers start: 68 outliers final: 50 residues processed: 303 average time/residue: 0.2714 time to fit residues: 119.2455 Evaluate side-chains 307 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14096 Z= 0.243 Angle : 0.707 10.874 19152 Z= 0.358 Chirality : 0.043 0.211 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.445 17.067 1876 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.48 % Favored : 92.04 % Rotamer: Outliers : 4.60 % Allowed : 20.33 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1684 helix: 0.42 (0.16), residues: 1012 sheet: -3.00 (0.48), residues: 40 loop : -1.81 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 705 HIS 0.007 0.001 HIS D 703 PHE 0.023 0.001 PHE A 701 TYR 0.014 0.001 TYR D 707 ARG 0.004 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 270 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 550 LEU cc_start: 0.8730 (mt) cc_final: 0.8414 (mp) REVERT: A 552 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7924 (tt) REVERT: A 842 LEU cc_start: 0.7216 (mm) cc_final: 0.6810 (pp) REVERT: C 550 LEU cc_start: 0.8722 (mt) cc_final: 0.8410 (mp) REVERT: C 552 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7899 (tt) REVERT: C 842 LEU cc_start: 0.7212 (mm) cc_final: 0.6816 (pp) REVERT: D 550 LEU cc_start: 0.8735 (mt) cc_final: 0.8507 (mp) REVERT: D 552 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7934 (tt) REVERT: D 705 TRP cc_start: 0.8272 (t60) cc_final: 0.8010 (t60) REVERT: D 713 MET cc_start: 0.8355 (mpp) cc_final: 0.8078 (mpp) REVERT: B 550 LEU cc_start: 0.8740 (mt) cc_final: 0.8517 (mp) REVERT: B 552 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7926 (tt) REVERT: B 705 TRP cc_start: 0.8310 (t60) cc_final: 0.7910 (t60) REVERT: B 713 MET cc_start: 0.8253 (mpp) cc_final: 0.8027 (mpp) outliers start: 67 outliers final: 49 residues processed: 298 average time/residue: 0.3029 time to fit residues: 131.3939 Evaluate side-chains 305 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.0570 chunk 32 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14096 Z= 0.228 Angle : 0.715 11.580 19152 Z= 0.363 Chirality : 0.043 0.212 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.397 16.861 1876 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.58 % Rotamer: Outliers : 2.88 % Allowed : 22.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1684 helix: 0.41 (0.16), residues: 1012 sheet: -2.84 (0.54), residues: 40 loop : -1.79 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 412 HIS 0.007 0.001 HIS D 703 PHE 0.024 0.001 PHE C 701 TYR 0.013 0.001 TYR D 616 ARG 0.007 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 538 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8044 (mmtm) REVERT: A 550 LEU cc_start: 0.8739 (mt) cc_final: 0.8433 (mp) REVERT: A 722 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6973 (tm-30) REVERT: A 842 LEU cc_start: 0.7158 (mm) cc_final: 0.6811 (pp) REVERT: C 532 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9069 (tt) REVERT: C 550 LEU cc_start: 0.8734 (mt) cc_final: 0.8437 (mp) REVERT: C 722 GLU cc_start: 0.7240 (tm-30) cc_final: 0.7008 (tm-30) REVERT: C 842 LEU cc_start: 0.7150 (mm) cc_final: 0.6805 (pp) REVERT: D 705 TRP cc_start: 0.8327 (t60) cc_final: 0.8025 (t60) REVERT: D 713 MET cc_start: 0.8364 (mpp) cc_final: 0.8090 (mpp) REVERT: B 532 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9070 (tt) outliers start: 42 outliers final: 34 residues processed: 274 average time/residue: 0.2734 time to fit residues: 106.7043 Evaluate side-chains 289 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.5980 chunk 158 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 0.4980 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14096 Z= 0.199 Angle : 0.712 12.277 19152 Z= 0.356 Chirality : 0.043 0.218 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.237 15.967 1876 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.29 % Favored : 93.17 % Rotamer: Outliers : 1.79 % Allowed : 23.01 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1684 helix: 0.51 (0.16), residues: 1012 sheet: -2.70 (0.58), residues: 40 loop : -1.68 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 412 HIS 0.008 0.001 HIS D 703 PHE 0.026 0.001 PHE A 701 TYR 0.014 0.001 TYR B 707 ARG 0.003 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 705 TRP cc_start: 0.8127 (t60) cc_final: 0.7614 (t60) REVERT: A 842 LEU cc_start: 0.7002 (mm) cc_final: 0.6760 (pp) REVERT: C 532 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9036 (tt) REVERT: C 705 TRP cc_start: 0.8086 (t60) cc_final: 0.7612 (t60) REVERT: C 722 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6890 (tm-30) REVERT: C 842 LEU cc_start: 0.6995 (mm) cc_final: 0.6755 (pp) REVERT: D 532 LEU cc_start: 0.9364 (tp) cc_final: 0.9029 (tt) REVERT: D 713 MET cc_start: 0.8357 (mpp) cc_final: 0.8118 (mpp) REVERT: B 532 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9013 (tt) REVERT: B 705 TRP cc_start: 0.8295 (t60) cc_final: 0.8043 (t60) outliers start: 26 outliers final: 20 residues processed: 276 average time/residue: 0.2688 time to fit residues: 106.4820 Evaluate side-chains 277 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 171 optimal weight: 0.0170 chunk 157 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 HIS ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 HIS ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS B 674 HIS ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14096 Z= 0.199 Angle : 0.716 11.603 19152 Z= 0.357 Chirality : 0.042 0.181 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.194 16.010 1876 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.18 % Favored : 93.17 % Rotamer: Outliers : 1.99 % Allowed : 22.73 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1684 helix: 0.50 (0.16), residues: 1012 sheet: -2.58 (0.60), residues: 40 loop : -1.66 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 412 HIS 0.027 0.002 HIS C 674 PHE 0.027 0.001 PHE C 701 TYR 0.014 0.001 TYR A 707 ARG 0.004 0.000 ARG D 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 705 TRP cc_start: 0.8042 (t60) cc_final: 0.7555 (t60) REVERT: A 722 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6823 (tm-30) REVERT: C 532 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9013 (tt) REVERT: C 705 TRP cc_start: 0.8027 (t60) cc_final: 0.7540 (t60) REVERT: C 722 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6818 (tm-30) REVERT: D 532 LEU cc_start: 0.9352 (tp) cc_final: 0.9024 (tt) REVERT: D 705 TRP cc_start: 0.8293 (t60) cc_final: 0.7858 (t60) REVERT: D 713 MET cc_start: 0.8328 (mpp) cc_final: 0.8059 (mpp) REVERT: B 532 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9027 (tt) REVERT: B 705 TRP cc_start: 0.8302 (t60) cc_final: 0.7973 (t60) outliers start: 29 outliers final: 27 residues processed: 270 average time/residue: 0.2767 time to fit residues: 106.9330 Evaluate side-chains 280 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 674 HIS Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 674 HIS Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS C 674 HIS ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 HIS D 674 HIS ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 HIS ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.216806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135075 restraints weight = 23564.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137868 restraints weight = 11711.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139346 restraints weight = 6501.716| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14096 Z= 0.268 Angle : 0.746 11.430 19152 Z= 0.374 Chirality : 0.044 0.179 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.338 16.059 1876 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.65 % Favored : 92.64 % Rotamer: Outliers : 3.02 % Allowed : 22.32 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1684 helix: 0.31 (0.16), residues: 1020 sheet: -2.58 (0.61), residues: 40 loop : -1.69 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 412 HIS 0.026 0.002 HIS D 674 PHE 0.027 0.002 PHE B 701 TYR 0.022 0.002 TYR D 707 ARG 0.004 0.000 ARG D 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.23 seconds wall clock time: 59 minutes 53.49 seconds (3593.49 seconds total)