Starting phenix.real_space_refine on Thu Jul 31 20:45:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io4_35607/07_2025/8io4_35607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io4_35607/07_2025/8io4_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_35607/07_2025/8io4_35607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io4_35607/07_2025/8io4_35607.map" model { file = "/net/cci-nas-00/data/ceres_data/8io4_35607/07_2025/8io4_35607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io4_35607/07_2025/8io4_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-5711/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: 9.32, per 1000 atoms: 0.68 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: 3.29 Conformation dependent library (CDL) restraints added in 1.8 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: 1.33 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: 3.98 Time building geometry restraints manager: 3.94 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: 0.07 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: 4.960 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.380 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.880 ------------------------------------------------------------------------------- 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= 0.164 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 Details of bonding type rmsd hydrogen bonds : bond 0.15086 ( 742) hydrogen bonds : angle 5.84690 ( 2112) covalent geometry : bond 0.00296 (14096) covalent geometry : angle 0.74604 (19152) *********************** 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 : 1.563 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: 0.2782 time to fit residues: 141.8390 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 : 1.402 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.226176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158391 restraints weight = 21617.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.155262 restraints weight = 13494.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.155356 restraints weight = 9639.869| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 742) hydrogen bonds : angle 4.94963 ( 2112) covalent geometry : bond 0.00375 (14096) covalent geometry : angle 0.67880 (19152) *********************** 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 : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8693 (t) cc_final: 0.8378 (p) REVERT: A 538 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8128 (mmtt) REVERT: A 539 LEU cc_start: 0.8787 (tp) cc_final: 0.8247 (pp) REVERT: A 545 TYR cc_start: 0.5803 (m-10) cc_final: 0.5461 (m-10) REVERT: A 705 TRP cc_start: 0.8333 (t60) cc_final: 0.7917 (t60) REVERT: A 713 MET cc_start: 0.8364 (mpp) cc_final: 0.8129 (mpp) REVERT: C 418 VAL cc_start: 0.8690 (t) cc_final: 0.8376 (p) REVERT: C 538 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8117 (mmtt) REVERT: C 539 LEU cc_start: 0.8799 (tp) cc_final: 0.8262 (pp) REVERT: C 705 TRP cc_start: 0.8332 (t60) cc_final: 0.7916 (t60) REVERT: C 713 MET cc_start: 0.8351 (mpp) cc_final: 0.8116 (mpp) REVERT: D 418 VAL cc_start: 0.8720 (t) cc_final: 0.8410 (p) REVERT: D 538 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8207 (mmtt) REVERT: D 550 LEU cc_start: 0.8772 (mt) cc_final: 0.8411 (mp) REVERT: D 705 TRP cc_start: 0.8326 (t60) cc_final: 0.7822 (t60) REVERT: D 713 MET cc_start: 0.8411 (mpp) cc_final: 0.8162 (mpp) REVERT: D 845 TYR cc_start: 0.6184 (m-80) cc_final: 0.5957 (m-80) REVERT: B 418 VAL cc_start: 0.8721 (t) cc_final: 0.8411 (p) REVERT: B 538 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8214 (mmtt) REVERT: B 550 LEU cc_start: 0.8784 (mt) cc_final: 0.8423 (mp) REVERT: B 705 TRP cc_start: 0.8334 (t60) cc_final: 0.7830 (t60) REVERT: B 713 MET cc_start: 0.8407 (mpp) cc_final: 0.8177 (mpp) REVERT: B 845 TYR cc_start: 0.6145 (m-80) cc_final: 0.5922 (m-80) outliers start: 28 outliers final: 26 residues processed: 311 average time/residue: 0.2699 time to fit residues: 118.7740 Evaluate side-chains 290 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 264 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 136 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 141 optimal weight: 0.0070 chunk 162 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 629 ASN C 470 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.227708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.172440 restraints weight = 21720.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160077 restraints weight = 22135.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159496 restraints weight = 16093.345| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2379 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= 0.138 Angle : 0.625 8.348 19152 Z= 0.315 Chirality : 0.041 0.145 2176 Planarity : 0.004 0.046 2376 Dihedral : 4.335 15.811 1876 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.01 % Favored : 92.76 % Rotamer: Outliers : 2.75 % Allowed : 13.26 % Favored : 84.00 % 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: -0.84 (0.20), residues: 1684 helix: 0.40 (0.16), residues: 1032 sheet: -1.35 (0.59), residues: 64 loop : -2.18 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 705 HIS 0.006 0.001 HIS D 731 PHE 0.012 0.001 PHE A 720 TYR 0.014 0.001 TYR D 707 ARG 0.002 0.000 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 742) hydrogen bonds : angle 4.72407 ( 2112) covalent geometry : bond 0.00295 (14096) covalent geometry : angle 0.62509 (19152) *********************** 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 325 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8612 (t) cc_final: 0.8315 (p) REVERT: A 550 LEU cc_start: 0.8617 (mt) cc_final: 0.8329 (mp) REVERT: A 705 TRP cc_start: 0.8265 (t60) cc_final: 0.7840 (t60) REVERT: A 713 MET cc_start: 0.8190 (mpp) cc_final: 0.7968 (mpp) REVERT: C 418 VAL cc_start: 0.8627 (t) cc_final: 0.8333 (p) REVERT: C 545 TYR cc_start: 0.5694 (m-10) cc_final: 0.5400 (m-10) REVERT: C 705 TRP cc_start: 0.8257 (t60) cc_final: 0.7832 (t60) REVERT: C 713 MET cc_start: 0.8177 (mpp) cc_final: 0.7955 (mpp) REVERT: D 418 VAL cc_start: 0.8593 (t) cc_final: 0.8312 (p) REVERT: D 550 LEU cc_start: 0.8706 (mt) cc_final: 0.8370 (mp) REVERT: D 705 TRP cc_start: 0.8248 (t60) cc_final: 0.7830 (t60) REVERT: D 713 MET cc_start: 0.8358 (mpp) cc_final: 0.8120 (mpp) REVERT: D 842 LEU cc_start: 0.7374 (mm) cc_final: 0.6965 (pp) REVERT: B 418 VAL cc_start: 0.8598 (t) cc_final: 0.8315 (p) REVERT: B 550 LEU cc_start: 0.8705 (mt) cc_final: 0.8371 (mp) REVERT: B 705 TRP cc_start: 0.8249 (t60) cc_final: 0.7835 (t60) REVERT: B 713 MET cc_start: 0.8344 (mpp) cc_final: 0.8111 (mpp) REVERT: B 842 LEU cc_start: 0.7336 (mm) cc_final: 0.6943 (pp) outliers start: 40 outliers final: 28 residues processed: 305 average time/residue: 0.2480 time to fit residues: 109.1385 Evaluate side-chains 279 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 644 VAL 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 644 VAL 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 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 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 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 79 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.226957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.172976 restraints weight = 21586.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164169 restraints weight = 25803.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163714 restraints weight = 21891.712| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2712 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= 0.145 Angle : 0.619 7.491 19152 Z= 0.313 Chirality : 0.041 0.151 2176 Planarity : 0.004 0.045 2376 Dihedral : 4.268 16.416 1876 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.48 % Favored : 92.04 % Rotamer: Outliers : 4.26 % Allowed : 13.67 % Favored : 82.07 % 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: -0.80 (0.20), residues: 1684 helix: 0.46 (0.16), residues: 1032 sheet: -3.43 (0.41), residues: 40 loop : -2.01 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 705 HIS 0.006 0.001 HIS A 731 PHE 0.020 0.002 PHE D 701 TYR 0.012 0.001 TYR A 545 ARG 0.003 0.000 ARG C 685 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 742) hydrogen bonds : angle 4.70678 ( 2112) covalent geometry : bond 0.00320 (14096) covalent geometry : angle 0.61901 (19152) *********************** 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 346 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8446 (t) cc_final: 0.8191 (p) REVERT: A 550 LEU cc_start: 0.8803 (mt) cc_final: 0.8570 (mp) REVERT: A 705 TRP cc_start: 0.8156 (t60) cc_final: 0.7829 (t60) REVERT: A 713 MET cc_start: 0.8198 (mpp) cc_final: 0.7967 (mpp) REVERT: C 418 VAL cc_start: 0.8456 (t) cc_final: 0.8199 (p) REVERT: C 545 TYR cc_start: 0.5617 (m-10) cc_final: 0.5261 (m-10) REVERT: C 550 LEU cc_start: 0.8779 (mt) cc_final: 0.8547 (mp) REVERT: C 705 TRP cc_start: 0.8138 (t60) cc_final: 0.7817 (t60) REVERT: C 713 MET cc_start: 0.8208 (mpp) cc_final: 0.7979 (mpp) REVERT: D 418 VAL cc_start: 0.8455 (t) cc_final: 0.8196 (p) REVERT: D 550 LEU cc_start: 0.8709 (mt) cc_final: 0.8403 (mp) REVERT: D 552 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7921 (tt) REVERT: D 698 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8237 (mm-30) REVERT: D 705 TRP cc_start: 0.8183 (t60) cc_final: 0.7842 (t60) REVERT: D 713 MET cc_start: 0.8298 (mpp) cc_final: 0.8055 (mpp) REVERT: B 418 VAL cc_start: 0.8467 (t) cc_final: 0.8206 (p) REVERT: B 550 LEU cc_start: 0.8714 (mt) cc_final: 0.8405 (mp) REVERT: B 552 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7919 (tt) REVERT: B 698 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 705 TRP cc_start: 0.8182 (t60) cc_final: 0.7839 (t60) REVERT: B 713 MET cc_start: 0.8291 (mpp) cc_final: 0.8055 (mpp) outliers start: 62 outliers final: 46 residues processed: 314 average time/residue: 0.2461 time to fit residues: 112.4145 Evaluate side-chains 307 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 7.9990 chunk 36 optimal weight: 0.0970 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 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 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.225964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170605 restraints weight = 21644.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162059 restraints weight = 24589.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162005 restraints weight = 19639.653| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14096 Z= 0.161 Angle : 0.655 9.191 19152 Z= 0.332 Chirality : 0.042 0.145 2176 Planarity : 0.004 0.043 2376 Dihedral : 4.328 16.135 1876 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.07 % Favored : 92.46 % Rotamer: Outliers : 3.98 % Allowed : 15.59 % Favored : 80.43 % 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: -0.65 (0.20), residues: 1684 helix: 0.47 (0.16), residues: 1036 sheet: -3.28 (0.43), residues: 40 loop : -1.75 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 705 HIS 0.007 0.001 HIS D 703 PHE 0.023 0.001 PHE C 701 TYR 0.017 0.002 TYR A 700 ARG 0.004 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 742) hydrogen bonds : angle 4.74563 ( 2112) covalent geometry : bond 0.00359 (14096) covalent geometry : angle 0.65486 (19152) *********************** 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 330 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8367 (t) cc_final: 0.8156 (p) REVERT: A 705 TRP cc_start: 0.7945 (t60) cc_final: 0.7736 (t60) REVERT: C 418 VAL cc_start: 0.8371 (t) cc_final: 0.8161 (p) REVERT: C 705 TRP cc_start: 0.7939 (t60) cc_final: 0.7738 (t60) REVERT: D 418 VAL cc_start: 0.8366 (t) cc_final: 0.8161 (p) REVERT: D 552 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7959 (tt) REVERT: D 705 TRP cc_start: 0.8026 (t60) cc_final: 0.7816 (t60) REVERT: D 842 LEU cc_start: 0.6829 (mm) cc_final: 0.6457 (pp) REVERT: B 418 VAL cc_start: 0.8372 (t) cc_final: 0.8169 (p) REVERT: B 552 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7954 (tt) REVERT: B 842 LEU cc_start: 0.6814 (mm) cc_final: 0.6440 (pp) outliers start: 58 outliers final: 48 residues processed: 300 average time/residue: 0.2795 time to fit residues: 122.9999 Evaluate side-chains 304 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 630 VAL 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 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 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 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 630 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.227622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174686 restraints weight = 21783.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.163592 restraints weight = 25373.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163155 restraints weight = 21545.175| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14096 Z= 0.134 Angle : 0.651 9.232 19152 Z= 0.327 Chirality : 0.041 0.149 2176 Planarity : 0.004 0.042 2376 Dihedral : 4.196 15.898 1876 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.77 % Favored : 92.76 % Rotamer: Outliers : 3.09 % Allowed : 17.93 % Favored : 78.98 % 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: 0.58 (0.16), residues: 1032 sheet: -3.28 (0.43), residues: 40 loop : -1.84 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 705 HIS 0.005 0.001 HIS D 703 PHE 0.026 0.001 PHE B 701 TYR 0.016 0.001 TYR C 700 ARG 0.002 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 742) hydrogen bonds : angle 4.67075 ( 2112) covalent geometry : bond 0.00294 (14096) covalent geometry : angle 0.65106 (19152) *********************** 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 334 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8414 (t) cc_final: 0.8163 (p) REVERT: A 545 TYR cc_start: 0.5681 (m-80) cc_final: 0.5406 (m-10) REVERT: A 705 TRP cc_start: 0.8158 (t60) cc_final: 0.7805 (t60) REVERT: C 418 VAL cc_start: 0.8436 (t) cc_final: 0.8189 (p) REVERT: C 541 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7371 (tpt-90) REVERT: C 705 TRP cc_start: 0.8126 (t60) cc_final: 0.7787 (t60) REVERT: C 842 LEU cc_start: 0.7085 (mm) cc_final: 0.6667 (pp) REVERT: D 418 VAL cc_start: 0.8394 (t) cc_final: 0.8171 (p) REVERT: D 705 TRP cc_start: 0.8211 (t60) cc_final: 0.7880 (t60) REVERT: D 842 LEU cc_start: 0.7067 (mm) cc_final: 0.6690 (pp) REVERT: B 418 VAL cc_start: 0.8410 (t) cc_final: 0.8190 (p) REVERT: B 842 LEU cc_start: 0.7055 (mm) cc_final: 0.6702 (pp) outliers start: 45 outliers final: 36 residues processed: 306 average time/residue: 0.2582 time to fit residues: 113.6125 Evaluate side-chains 296 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 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 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 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 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET 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 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET 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: 0.3980 chunk 49 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 573 ASN A 629 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN C 573 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN D 573 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS B 573 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.222299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.166233 restraints weight = 21688.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153653 restraints weight = 25698.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151672 restraints weight = 23346.167| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14096 Z= 0.253 Angle : 0.764 10.508 19152 Z= 0.392 Chirality : 0.046 0.212 2176 Planarity : 0.005 0.037 2376 Dihedral : 4.596 17.348 1876 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.42 % Favored : 91.86 % Rotamer: Outliers : 4.12 % Allowed : 19.37 % Favored : 76.51 % 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: -0.78 (0.20), residues: 1684 helix: 0.32 (0.16), residues: 1024 sheet: -3.10 (0.46), residues: 40 loop : -1.71 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 705 HIS 0.011 0.002 HIS D 834 PHE 0.026 0.002 PHE A 701 TYR 0.014 0.002 TYR B 652 ARG 0.005 0.001 ARG B 752 Details of bonding type rmsd hydrogen bonds : bond 0.05252 ( 742) hydrogen bonds : angle 5.01985 ( 2112) covalent geometry : bond 0.00578 (14096) covalent geometry : angle 0.76365 (19152) *********************** 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 341 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8639 (t) cc_final: 0.8432 (p) REVERT: A 452 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5027 (mm) REVERT: A 541 ARG cc_start: 0.7236 (ttp80) cc_final: 0.7034 (tmm-80) REVERT: C 418 VAL cc_start: 0.8625 (t) cc_final: 0.8421 (p) REVERT: C 452 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5029 (mm) REVERT: C 541 ARG cc_start: 0.7649 (ttp80) cc_final: 0.7261 (tpt-90) REVERT: D 542 TYR cc_start: 0.6827 (m-80) cc_final: 0.6597 (m-80) REVERT: D 685 ARG cc_start: 0.7985 (tmm160) cc_final: 0.7638 (ttp80) REVERT: B 542 TYR cc_start: 0.6824 (m-80) cc_final: 0.6591 (m-80) REVERT: B 685 ARG cc_start: 0.7914 (tmm160) cc_final: 0.7562 (ttp80) REVERT: B 705 TRP cc_start: 0.8363 (t60) cc_final: 0.7979 (t60) outliers start: 60 outliers final: 51 residues processed: 317 average time/residue: 0.2821 time to fit residues: 131.3903 Evaluate side-chains 317 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 573 ASN 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 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 452 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 573 ASN 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 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 750 CYS 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 573 ASN 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 573 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 91 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** B 762 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.225330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.169786 restraints weight = 21710.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.156691 restraints weight = 23933.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156608 restraints weight = 17698.291| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14096 Z= 0.152 Angle : 0.719 9.950 19152 Z= 0.362 Chirality : 0.043 0.202 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.411 17.462 1876 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.71 % Favored : 92.81 % Rotamer: Outliers : 3.50 % Allowed : 21.57 % 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: -0.75 (0.20), residues: 1684 helix: 0.32 (0.16), residues: 1024 sheet: -3.03 (0.48), residues: 40 loop : -1.64 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 705 HIS 0.008 0.001 HIS B 703 PHE 0.024 0.001 PHE A 701 TYR 0.026 0.002 TYR B 673 ARG 0.004 0.000 ARG C 685 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 742) hydrogen bonds : angle 4.91672 ( 2112) covalent geometry : bond 0.00339 (14096) covalent geometry : angle 0.71892 (19152) *********************** 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 328 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9033 (tt) REVERT: C 542 TYR cc_start: 0.6858 (m-80) cc_final: 0.6193 (m-80) REVERT: D 415 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7494 (tp) REVERT: D 550 LEU cc_start: 0.8626 (mt) cc_final: 0.8252 (mp) REVERT: D 685 ARG cc_start: 0.7846 (tmm160) cc_final: 0.7553 (ttp80) REVERT: D 842 LEU cc_start: 0.7102 (mm) cc_final: 0.6581 (pp) REVERT: B 415 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7505 (tp) REVERT: B 550 LEU cc_start: 0.8644 (mt) cc_final: 0.8271 (mp) REVERT: B 705 TRP cc_start: 0.8136 (t60) cc_final: 0.7619 (t60) REVERT: B 842 LEU cc_start: 0.7110 (mm) cc_final: 0.6592 (pp) outliers start: 51 outliers final: 39 residues processed: 300 average time/residue: 0.2864 time to fit residues: 123.4940 Evaluate side-chains 300 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 613 THR Chi-restraints excluded: chain A residue 618 THR 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 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR 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 415 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS 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 415 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 35 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** D 762 HIS ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.225926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170739 restraints weight = 21709.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158722 restraints weight = 22538.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.159276 restraints weight = 17274.945| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14096 Z= 0.151 Angle : 0.722 10.374 19152 Z= 0.358 Chirality : 0.043 0.190 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.303 16.814 1876 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.71 % Favored : 92.76 % Rotamer: Outliers : 3.57 % Allowed : 20.81 % Favored : 75.62 % 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: 0.33 (0.16), residues: 1024 sheet: -2.75 (0.54), residues: 40 loop : -1.66 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 412 HIS 0.008 0.001 HIS D 703 PHE 0.025 0.001 PHE A 701 TYR 0.017 0.001 TYR C 700 ARG 0.004 0.000 ARG C 541 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 742) hydrogen bonds : angle 4.85273 ( 2112) covalent geometry : bond 0.00341 (14096) covalent geometry : angle 0.72162 (19152) *********************** 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 326 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9027 (tt) REVERT: A 842 LEU cc_start: 0.7011 (mm) cc_final: 0.6619 (pp) REVERT: C 532 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9057 (tt) REVERT: C 842 LEU cc_start: 0.7027 (mm) cc_final: 0.6629 (pp) REVERT: D 532 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9051 (tt) REVERT: D 550 LEU cc_start: 0.8691 (mt) cc_final: 0.8322 (mp) REVERT: D 552 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7968 (tt) REVERT: D 685 ARG cc_start: 0.7876 (tmm160) cc_final: 0.7605 (ttp80) REVERT: D 705 TRP cc_start: 0.8351 (t60) cc_final: 0.8057 (t60) REVERT: D 842 LEU cc_start: 0.7117 (mm) cc_final: 0.6621 (pp) REVERT: B 532 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9040 (tt) REVERT: B 550 LEU cc_start: 0.8681 (mt) cc_final: 0.8314 (mp) REVERT: B 552 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7949 (tt) REVERT: B 705 TRP cc_start: 0.8334 (t60) cc_final: 0.7922 (t60) REVERT: B 842 LEU cc_start: 0.7135 (mm) cc_final: 0.6636 (pp) outliers start: 52 outliers final: 35 residues processed: 297 average time/residue: 0.3319 time to fit residues: 144.0825 Evaluate side-chains 306 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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 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 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR 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 552 LEU Chi-restraints excluded: chain D residue 566 CYS 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 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 113 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 674 HIS ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C 674 HIS ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 HIS ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.226816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.168952 restraints weight = 21855.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156891 restraints weight = 22133.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.157138 restraints weight = 14660.249| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3907 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= 0.142 Angle : 0.727 11.659 19152 Z= 0.362 Chirality : 0.043 0.204 2176 Planarity : 0.004 0.038 2376 Dihedral : 4.204 16.591 1876 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.12 % Favored : 93.35 % Rotamer: Outliers : 2.82 % Allowed : 21.77 % Favored : 75.41 % 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: -0.67 (0.20), residues: 1684 helix: 0.42 (0.16), residues: 1016 sheet: -2.59 (0.58), residues: 40 loop : -1.67 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 705 HIS 0.025 0.002 HIS D 674 PHE 0.026 0.001 PHE A 701 TYR 0.017 0.001 TYR C 700 ARG 0.004 0.000 ARG C 685 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 742) hydrogen bonds : angle 4.85234 ( 2112) covalent geometry : bond 0.00318 (14096) covalent geometry : angle 0.72737 (19152) ********************** 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 305 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8998 (tt) REVERT: A 705 TRP cc_start: 0.8193 (t60) cc_final: 0.7613 (t60) REVERT: A 842 LEU cc_start: 0.7024 (mm) cc_final: 0.6647 (pp) REVERT: C 532 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9016 (tt) REVERT: C 705 TRP cc_start: 0.8165 (t60) cc_final: 0.7594 (t60) REVERT: C 842 LEU cc_start: 0.7003 (mm) cc_final: 0.6626 (pp) REVERT: D 532 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9014 (tt) REVERT: D 550 LEU cc_start: 0.8609 (mt) cc_final: 0.8271 (mp) REVERT: D 685 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7631 (ttp80) REVERT: D 705 TRP cc_start: 0.8305 (t60) cc_final: 0.8008 (t60) REVERT: D 842 LEU cc_start: 0.7112 (mm) cc_final: 0.6621 (pp) REVERT: B 532 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9031 (tt) REVERT: B 550 LEU cc_start: 0.8634 (mt) cc_final: 0.8295 (mp) REVERT: B 705 TRP cc_start: 0.8255 (t60) cc_final: 0.7722 (t60) REVERT: B 842 LEU cc_start: 0.7112 (mm) cc_final: 0.6599 (pp) outliers start: 41 outliers final: 35 residues processed: 279 average time/residue: 0.2700 time to fit residues: 109.3643 Evaluate side-chains 299 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 618 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 674 HIS 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 618 THR Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 645 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 532 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 644 VAL Chi-restraints excluded: chain D residue 645 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 0.0010 chunk 48 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 635 ASN A 674 HIS ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN C 635 ASN C 674 HIS D 674 HIS ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.219618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148660 restraints weight = 24941.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144831 restraints weight = 14414.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145497 restraints weight = 11083.107| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3938 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= 0.137 Angle : 0.725 12.046 19152 Z= 0.360 Chirality : 0.042 0.196 2176 Planarity : 0.004 0.038 2376 Dihedral : 4.114 16.142 1876 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.00 % Favored : 93.47 % Rotamer: Outliers : 2.27 % Allowed : 22.46 % 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: -0.65 (0.20), residues: 1684 helix: 0.42 (0.16), residues: 1016 sheet: -2.63 (0.59), residues: 40 loop : -1.65 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 705 HIS 0.024 0.002 HIS D 674 PHE 0.027 0.001 PHE A 701 TYR 0.017 0.001 TYR A 700 ARG 0.004 0.000 ARG C 685 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 742) hydrogen bonds : angle 4.80742 ( 2112) covalent geometry : bond 0.00301 (14096) covalent geometry : angle 0.72509 (19152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5772.60 seconds wall clock time: 104 minutes 40.07 seconds (6280.07 seconds total)