Starting phenix.real_space_refine on Fri Jul 3 02:46:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.cif" model { file = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3v_36862/07_2026/8k3v_36862.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 7366 2.51 5 N 1802 2.21 5 O 2000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11248 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5536 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 679} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5536 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 679} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {' MG': 1, 'POV': 2, 'UD1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.59, per 1000 atoms: 0.23 Number of scatterers: 11248 At special positions: 0 Unit cell: (132.5, 92.22, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 6 15.00 Mg 2 11.99 O 2000 8.00 N 1802 7.00 C 7366 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: 0.89 Conformation dependent library (CDL) restraints added in 494.6 milliseconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 64.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.610A pdb=" N PHE A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.862A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.516A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.550A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.908A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.633A pdb=" N SER A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.831A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.749A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.074A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.736A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.553A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.956A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 removed outlier: 4.529A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 915 " --> pdb=" O PHE A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.549A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.586A pdb=" N ILE A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1127 removed outlier: 4.200A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 410 through 413 removed outlier: 3.610A pdb=" N PHE B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.862A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 478 removed outlier: 3.516A pdb=" N LEU B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.551A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.632A pdb=" N SER B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.831A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.749A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.074A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.565A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.736A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.553A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 894 removed outlier: 3.956A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 932 removed outlier: 4.529A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 915 " --> pdb=" O PHE B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.549A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.586A pdb=" N ILE B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B1005 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B1007 " --> pdb=" O ALA B1003 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B1008 " --> pdb=" O ASN B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1127 removed outlier: 4.200A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.694A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.670A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.693A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.671A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1902 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: 1.96 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1706 1.31 - 1.43: 3298 1.43 - 1.56: 6390 1.56 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11518 Sorted by residual: bond pdb=" C4 UD1 A1503 " pdb=" N3 UD1 A1503 " ideal model delta sigma weight residual 1.386 1.277 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 UD1 B1502 " pdb=" N3 UD1 B1502 " ideal model delta sigma weight residual 1.386 1.278 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C2B UD1 A1503 " pdb=" C3B UD1 A1503 " ideal model delta sigma weight residual 1.533 1.461 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2B UD1 B1502 " pdb=" C3B UD1 B1502 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C4 UD1 B1502 " pdb=" C5 UD1 B1502 " ideal model delta sigma weight residual 1.441 1.377 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 11513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 15495 4.19 - 8.37: 83 8.37 - 12.56: 24 12.56 - 16.74: 6 16.74 - 20.93: 2 Bond angle restraints: 15610 Sorted by residual: angle pdb=" C1B UD1 A1503 " pdb=" C2B UD1 A1503 " pdb=" O2' UD1 A1503 " ideal model delta sigma weight residual 109.46 130.39 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C1B UD1 B1502 " pdb=" C2B UD1 B1502 " pdb=" O2' UD1 B1502 " ideal model delta sigma weight residual 109.46 130.38 -20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" C2B UD1 B1502 " pdb=" C1B UD1 B1502 " pdb=" O4B UD1 B1502 " ideal model delta sigma weight residual 106.74 91.14 15.60 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C2B UD1 A1503 " pdb=" C1B UD1 A1503 " pdb=" O4B UD1 A1503 " ideal model delta sigma weight residual 106.74 91.15 15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" N ARG B 912 " pdb=" CA ARG B 912 " pdb=" C ARG B 912 " ideal model delta sigma weight residual 112.54 106.72 5.82 1.22e+00 6.72e-01 2.28e+01 ... (remaining 15605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 6473 33.01 - 66.02: 211 66.02 - 99.04: 18 99.04 - 132.05: 2 132.05 - 165.06: 2 Dihedral angle restraints: 6706 sinusoidal: 2582 harmonic: 4124 Sorted by residual: dihedral pdb=" C27 POV A1502 " pdb=" C28 POV A1502 " pdb=" C29 POV A1502 " pdb="C210 POV A1502 " ideal model delta sinusoidal sigma weight residual 127.48 -67.46 -165.06 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C27 POV A1504 " pdb=" C28 POV A1504 " pdb=" C29 POV A1504 " pdb="C210 POV A1504 " ideal model delta sinusoidal sigma weight residual 127.48 -67.55 -164.97 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1526 0.090 - 0.181: 214 0.181 - 0.271: 20 0.271 - 0.362: 6 0.362 - 0.452: 4 Chirality restraints: 1770 Sorted by residual: chirality pdb=" C2B UD1 B1502 " pdb=" C1B UD1 B1502 " pdb=" C3B UD1 B1502 " pdb=" O2' UD1 B1502 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C2B UD1 A1503 " pdb=" C1B UD1 A1503 " pdb=" C3B UD1 A1503 " pdb=" O2' UD1 A1503 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C5' UD1 B1502 " pdb=" C4' UD1 B1502 " pdb=" C6' UD1 B1502 " pdb=" O5' UD1 B1502 " both_signs ideal model delta sigma weight residual False -2.52 -2.10 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1767 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2' UD1 A1503 " 0.170 2.00e-02 2.50e+03 1.37e-01 2.33e+02 pdb=" C7' UD1 A1503 " -0.055 2.00e-02 2.50e+03 pdb=" C8' UD1 A1503 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 A1503 " -0.205 2.00e-02 2.50e+03 pdb=" O7' UD1 A1503 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' UD1 B1502 " 0.169 2.00e-02 2.50e+03 1.37e-01 2.33e+02 pdb=" C7' UD1 B1502 " -0.054 2.00e-02 2.50e+03 pdb=" C8' UD1 B1502 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 B1502 " -0.205 2.00e-02 2.50e+03 pdb=" O7' UD1 B1502 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1502 " -0.041 2.00e-02 2.50e+03 7.55e-02 5.70e+01 pdb=" C29 POV A1502 " 0.099 2.00e-02 2.50e+03 pdb="C210 POV A1502 " -0.099 2.00e-02 2.50e+03 pdb="C211 POV A1502 " 0.040 2.00e-02 2.50e+03 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1947 2.76 - 3.30: 11091 3.30 - 3.83: 18126 3.83 - 4.37: 21569 4.37 - 4.90: 38362 Nonbonded interactions: 91095 Sorted by model distance: nonbonded pdb=" O HIS B 706 " pdb=" OG SER B 710 " model vdw 2.227 3.040 nonbonded pdb=" O HIS A 706 " pdb=" OG SER A 710 " model vdw 2.227 3.040 nonbonded pdb=" O3' UD1 B1502 " pdb=" O7' UD1 B1502 " model vdw 2.284 3.040 nonbonded pdb=" O3' UD1 A1503 " pdb=" O7' UD1 A1503 " model vdw 2.284 3.040 nonbonded pdb=" O THR B 453 " pdb=" O3B UD1 B1502 " model vdw 2.307 3.040 ... (remaining 91090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 381 through 1501) selection = (chain 'B' and resid 381 through 1501) } 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 individual isotropic 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: 2.390 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.008 0.109 11518 Z= 0.469 Angle : 1.065 20.927 15610 Z= 0.623 Chirality : 0.066 0.452 1770 Planarity : 0.006 0.137 1900 Dihedral : 15.978 165.061 4038 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.91 % Allowed : 2.37 % Favored : 92.72 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1376 helix: 0.99 (0.19), residues: 760 sheet: -1.44 (0.47), residues: 112 loop : -1.77 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 718 TYR 0.040 0.002 TYR B 696 PHE 0.020 0.002 PHE B 885 TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.47 (11518) covalent geometry : angle 1.06502 / 0.62 (15610) hydrogen bonds : bond 0.15935 / 10.66 ( 664) hydrogen bonds : angle 7.17806 / 4.97 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 0.436 Fit side-chains REVERT: A 455 TYR cc_start: 0.8101 (t80) cc_final: 0.7559 (t80) REVERT: A 471 ASP cc_start: 0.7287 (m-30) cc_final: 0.6795 (m-30) REVERT: A 610 ASP cc_start: 0.7776 (t70) cc_final: 0.7238 (t0) REVERT: A 672 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 989 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.5282 (p) REVERT: A 991 LYS cc_start: 0.3042 (OUTLIER) cc_final: 0.2651 (mmtt) REVERT: A 992 MET cc_start: 0.0382 (OUTLIER) cc_final: 0.0090 (pmm) REVERT: A 998 SER cc_start: 0.4331 (OUTLIER) cc_final: 0.3757 (t) REVERT: B 416 MET cc_start: 0.7878 (tmm) cc_final: 0.7641 (tmm) REVERT: B 455 TYR cc_start: 0.8127 (t80) cc_final: 0.7661 (t80) REVERT: B 464 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7174 (mtp-110) REVERT: B 471 ASP cc_start: 0.7176 (m-30) cc_final: 0.6794 (m-30) REVERT: B 610 ASP cc_start: 0.7753 (t70) cc_final: 0.7237 (t0) REVERT: B 700 MET cc_start: 0.5425 (tmm) cc_final: 0.5097 (tmm) REVERT: B 998 SER cc_start: 0.3779 (OUTLIER) cc_final: 0.3309 (t) outliers start: 58 outliers final: 13 residues processed: 206 average time/residue: 0.1102 time to fit residues: 32.0547 Evaluate side-chains 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 998 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 HIS A 692 GLN A1004 ASN B 540 HIS B 706 HIS B1004 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126481 restraints weight = 12936.339| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.07 r_work: 0.3330 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11518 Z= 0.123 Angle : 0.522 6.872 15610 Z= 0.276 Chirality : 0.042 0.202 1770 Planarity : 0.004 0.045 1900 Dihedral : 9.240 101.802 1612 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.86 % Allowed : 7.28 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.23), residues: 1376 helix: 1.85 (0.19), residues: 786 sheet: -0.55 (0.44), residues: 142 loop : -1.22 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.011 0.001 TYR B 399 PHE 0.018 0.001 PHE A1052 TRP 0.012 0.001 TRP B 779 HIS 0.004 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11518) covalent geometry : angle 0.52159 / 0.28 (15610) hydrogen bonds : bond 0.04444 / 2.85 ( 664) hydrogen bonds : angle 4.46416 / 3.14 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.423 Fit side-chains REVERT: A 455 TYR cc_start: 0.8161 (t80) cc_final: 0.7570 (t80) REVERT: A 464 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7543 (mtp180) REVERT: A 471 ASP cc_start: 0.7872 (m-30) cc_final: 0.7524 (m-30) REVERT: A 610 ASP cc_start: 0.7764 (t70) cc_final: 0.7171 (t0) REVERT: A 639 PHE cc_start: 0.8265 (m-80) cc_final: 0.8065 (m-80) REVERT: A 859 LYS cc_start: 0.8758 (mmmm) cc_final: 0.8308 (mppt) REVERT: A 982 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7198 (mp) REVERT: A 989 THR cc_start: 0.6426 (OUTLIER) cc_final: 0.6180 (p) REVERT: A 991 LYS cc_start: 0.3776 (OUTLIER) cc_final: 0.3191 (mttm) REVERT: B 455 TYR cc_start: 0.8203 (t80) cc_final: 0.7624 (t80) REVERT: B 471 ASP cc_start: 0.7923 (m-30) cc_final: 0.7559 (m-30) REVERT: B 529 ASN cc_start: 0.6996 (m-40) cc_final: 0.6789 (m-40) REVERT: B 610 ASP cc_start: 0.7775 (t70) cc_final: 0.7226 (t0) REVERT: B 700 MET cc_start: 0.5725 (tmm) cc_final: 0.5426 (tmm) REVERT: B 859 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8233 (mppt) REVERT: B 982 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7014 (mp) outliers start: 22 outliers final: 10 residues processed: 151 average time/residue: 0.1184 time to fit residues: 25.1758 Evaluate side-chains 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 963 ASN A1004 ASN B 963 ASN B1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126101 restraints weight = 13099.626| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.06 r_work: 0.3292 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11518 Z= 0.136 Angle : 0.490 7.980 15610 Z= 0.262 Chirality : 0.041 0.141 1770 Planarity : 0.003 0.043 1900 Dihedral : 8.046 78.516 1587 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.52 % Allowed : 9.31 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1376 helix: 2.22 (0.19), residues: 786 sheet: -0.38 (0.43), residues: 148 loop : -1.12 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.010 0.001 TYR A 925 PHE 0.019 0.002 PHE B1052 TRP 0.008 0.001 TRP B 779 HIS 0.006 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11518) covalent geometry : angle 0.48984 / 0.26 (15610) hydrogen bonds : bond 0.04326 / 2.79 ( 664) hydrogen bonds : angle 4.16275 / 2.92 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.483 Fit side-chains REVERT: A 455 TYR cc_start: 0.8279 (t80) cc_final: 0.7870 (t80) REVERT: A 471 ASP cc_start: 0.7845 (m-30) cc_final: 0.7493 (m-30) REVERT: A 610 ASP cc_start: 0.7673 (t70) cc_final: 0.7465 (t70) REVERT: A 700 MET cc_start: 0.5347 (tmm) cc_final: 0.5097 (tmm) REVERT: A 982 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 989 THR cc_start: 0.6325 (OUTLIER) cc_final: 0.6061 (p) REVERT: A 991 LYS cc_start: 0.4102 (OUTLIER) cc_final: 0.3125 (mttm) REVERT: A 1105 VAL cc_start: 0.8081 (t) cc_final: 0.7834 (p) REVERT: B 464 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7463 (mtp180) REVERT: B 471 ASP cc_start: 0.7850 (m-30) cc_final: 0.7507 (m-30) REVERT: B 529 ASN cc_start: 0.7402 (m-40) cc_final: 0.7161 (m-40) REVERT: B 610 ASP cc_start: 0.7849 (t70) cc_final: 0.7620 (t70) REVERT: B 700 MET cc_start: 0.5875 (tmm) cc_final: 0.5474 (tmm) REVERT: B 800 PHE cc_start: 0.7844 (t80) cc_final: 0.7637 (t80) REVERT: B 859 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8292 (mppt) REVERT: B 982 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6993 (mp) REVERT: B 1105 VAL cc_start: 0.8091 (t) cc_final: 0.7840 (p) outliers start: 18 outliers final: 8 residues processed: 150 average time/residue: 0.1030 time to fit residues: 22.0102 Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1004 ASN B1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121629 restraints weight = 13136.124| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.08 r_work: 0.3264 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11518 Z= 0.151 Angle : 0.499 6.110 15610 Z= 0.266 Chirality : 0.041 0.140 1770 Planarity : 0.003 0.042 1900 Dihedral : 8.071 80.524 1581 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.95 % Allowed : 10.66 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.23), residues: 1376 helix: 2.25 (0.18), residues: 786 sheet: -0.28 (0.44), residues: 148 loop : -1.23 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 787 TYR 0.017 0.001 TYR B 827 PHE 0.017 0.002 PHE B1052 TRP 0.008 0.001 TRP A 779 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (11518) covalent geometry : angle 0.49937 / 0.27 (15610) hydrogen bonds : bond 0.04452 / 2.86 ( 664) hydrogen bonds : angle 4.13634 / 2.90 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.267 Fit side-chains REVERT: A 455 TYR cc_start: 0.8374 (t80) cc_final: 0.8096 (t80) REVERT: A 471 ASP cc_start: 0.7848 (m-30) cc_final: 0.7369 (m-30) REVERT: A 699 ILE cc_start: 0.4337 (OUTLIER) cc_final: 0.4107 (tp) REVERT: A 758 ARG cc_start: 0.8723 (tmm160) cc_final: 0.8435 (ttt-90) REVERT: A 800 PHE cc_start: 0.7847 (t80) cc_final: 0.7601 (t80) REVERT: A 982 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7227 (mp) REVERT: A 989 THR cc_start: 0.6381 (OUTLIER) cc_final: 0.6149 (p) REVERT: A 991 LYS cc_start: 0.4067 (OUTLIER) cc_final: 0.3331 (ptpt) REVERT: A 1105 VAL cc_start: 0.8077 (t) cc_final: 0.7837 (p) REVERT: B 455 TYR cc_start: 0.8411 (t80) cc_final: 0.8078 (t80) REVERT: B 464 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7655 (mtp180) REVERT: B 471 ASP cc_start: 0.7851 (m-30) cc_final: 0.7424 (m-30) REVERT: B 529 ASN cc_start: 0.7457 (m-40) cc_final: 0.7208 (m-40) REVERT: B 700 MET cc_start: 0.5893 (tmm) cc_final: 0.5287 (tmm) REVERT: B 800 PHE cc_start: 0.7848 (t80) cc_final: 0.7601 (t80) REVERT: B 982 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6976 (mp) REVERT: B 1009 LEU cc_start: 0.6577 (mp) cc_final: 0.6359 (mp) REVERT: B 1105 VAL cc_start: 0.8091 (t) cc_final: 0.7848 (p) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.1033 time to fit residues: 20.6165 Evaluate side-chains 133 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1004 ASN B1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121825 restraints weight = 13078.202| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.07 r_work: 0.3270 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11518 Z= 0.137 Angle : 0.478 7.822 15610 Z= 0.255 Chirality : 0.040 0.135 1770 Planarity : 0.003 0.040 1900 Dihedral : 7.859 73.361 1579 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.28 % Allowed : 10.66 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.23), residues: 1376 helix: 2.40 (0.18), residues: 784 sheet: -0.40 (0.46), residues: 128 loop : -1.27 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 817 TYR 0.019 0.001 TYR A 827 PHE 0.017 0.001 PHE B1052 TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11518) covalent geometry : angle 0.47793 / 0.25 (15610) hydrogen bonds : bond 0.04208 / 2.71 ( 664) hydrogen bonds : angle 4.05170 / 2.85 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.460 Fit side-chains REVERT: A 386 VAL cc_start: 0.8008 (m) cc_final: 0.7725 (t) REVERT: A 455 TYR cc_start: 0.8378 (t80) cc_final: 0.8108 (t80) REVERT: A 471 ASP cc_start: 0.7851 (m-30) cc_final: 0.7385 (m-30) REVERT: A 574 GLN cc_start: 0.7918 (pt0) cc_final: 0.7716 (pt0) REVERT: A 620 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7807 (mtm110) REVERT: A 699 ILE cc_start: 0.4433 (OUTLIER) cc_final: 0.4177 (tp) REVERT: A 758 ARG cc_start: 0.8746 (tmm160) cc_final: 0.8480 (ttt-90) REVERT: A 800 PHE cc_start: 0.7852 (t80) cc_final: 0.7598 (t80) REVERT: A 982 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7280 (mp) REVERT: A 991 LYS cc_start: 0.3936 (OUTLIER) cc_final: 0.3333 (ptpt) REVERT: A 1009 LEU cc_start: 0.6601 (mp) cc_final: 0.6380 (mp) REVERT: A 1105 VAL cc_start: 0.8064 (t) cc_final: 0.7816 (p) REVERT: B 386 VAL cc_start: 0.8020 (m) cc_final: 0.7741 (t) REVERT: B 455 TYR cc_start: 0.8416 (t80) cc_final: 0.8120 (t80) REVERT: B 471 ASP cc_start: 0.7816 (m-30) cc_final: 0.7400 (m-30) REVERT: B 699 ILE cc_start: 0.3818 (OUTLIER) cc_final: 0.3515 (tp) REVERT: B 700 MET cc_start: 0.6015 (tmm) cc_final: 0.5392 (tmm) REVERT: B 800 PHE cc_start: 0.7835 (t80) cc_final: 0.7580 (t80) REVERT: B 938 MET cc_start: 0.6253 (tpt) cc_final: 0.5772 (tpt) REVERT: B 982 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7022 (mp) REVERT: B 1105 VAL cc_start: 0.8069 (t) cc_final: 0.7830 (p) outliers start: 27 outliers final: 16 residues processed: 143 average time/residue: 0.1040 time to fit residues: 21.4153 Evaluate side-chains 136 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 109 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 130 optimal weight: 0.0370 overall best weight: 0.7474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS B1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123986 restraints weight = 13102.698| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.05 r_work: 0.3272 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11518 Z= 0.128 Angle : 0.470 10.597 15610 Z= 0.250 Chirality : 0.040 0.134 1770 Planarity : 0.003 0.038 1900 Dihedral : 7.777 72.956 1579 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.86 % Allowed : 11.68 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1376 helix: 2.52 (0.18), residues: 784 sheet: -0.34 (0.46), residues: 128 loop : -1.28 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 638 TYR 0.020 0.001 TYR A 827 PHE 0.017 0.001 PHE B1052 TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11518) covalent geometry : angle 0.46990 / 0.25 (15610) hydrogen bonds : bond 0.04096 / 2.64 ( 664) hydrogen bonds : angle 3.98483 / 2.80 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.409 Fit side-chains REVERT: A 386 VAL cc_start: 0.8147 (m) cc_final: 0.7829 (t) REVERT: A 455 TYR cc_start: 0.8378 (t80) cc_final: 0.8130 (t80) REVERT: A 471 ASP cc_start: 0.7851 (m-30) cc_final: 0.7383 (m-30) REVERT: A 758 ARG cc_start: 0.8741 (tmm160) cc_final: 0.8479 (ttt-90) REVERT: A 800 PHE cc_start: 0.7822 (t80) cc_final: 0.7593 (t80) REVERT: A 886 MET cc_start: 0.8389 (mtm) cc_final: 0.8108 (mtp) REVERT: A 938 MET cc_start: 0.6146 (tpt) cc_final: 0.5674 (tpt) REVERT: A 982 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7237 (mp) REVERT: A 989 THR cc_start: 0.6418 (OUTLIER) cc_final: 0.6140 (p) REVERT: A 991 LYS cc_start: 0.4094 (OUTLIER) cc_final: 0.3350 (ptpt) REVERT: A 1105 VAL cc_start: 0.8039 (t) cc_final: 0.7802 (p) REVERT: B 386 VAL cc_start: 0.8174 (m) cc_final: 0.7860 (t) REVERT: B 471 ASP cc_start: 0.7828 (m-30) cc_final: 0.7373 (m-30) REVERT: B 527 GLU cc_start: 0.7631 (pt0) cc_final: 0.7425 (pt0) REVERT: B 699 ILE cc_start: 0.3748 (OUTLIER) cc_final: 0.3542 (tp) REVERT: B 700 MET cc_start: 0.5789 (tmm) cc_final: 0.5175 (tmm) REVERT: B 800 PHE cc_start: 0.7823 (t80) cc_final: 0.7599 (t80) REVERT: B 886 MET cc_start: 0.8298 (mtm) cc_final: 0.8080 (mtp) REVERT: B 938 MET cc_start: 0.6172 (tpt) cc_final: 0.5704 (tpt) REVERT: B 982 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7000 (mp) REVERT: B 1009 LEU cc_start: 0.6601 (mp) cc_final: 0.6390 (mp) REVERT: B 1105 VAL cc_start: 0.8075 (t) cc_final: 0.7837 (p) outliers start: 22 outliers final: 12 residues processed: 132 average time/residue: 0.1103 time to fit residues: 20.5833 Evaluate side-chains 129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.0050 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1004 ASN B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125648 restraints weight = 13047.529| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.05 r_work: 0.3295 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11518 Z= 0.106 Angle : 0.442 8.246 15610 Z= 0.236 Chirality : 0.039 0.128 1770 Planarity : 0.003 0.036 1900 Dihedral : 7.506 71.040 1579 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.52 % Allowed : 12.52 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.23), residues: 1376 helix: 2.70 (0.18), residues: 784 sheet: -0.16 (0.46), residues: 128 loop : -1.24 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 638 TYR 0.018 0.001 TYR B 827 PHE 0.015 0.001 PHE B1052 TRP 0.007 0.001 TRP A 779 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11518) covalent geometry : angle 0.44216 / 0.24 (15610) hydrogen bonds : bond 0.03689 / 2.38 ( 664) hydrogen bonds : angle 3.85975 / 2.71 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.398 Fit side-chains REVERT: A 386 VAL cc_start: 0.8244 (m) cc_final: 0.7927 (t) REVERT: A 455 TYR cc_start: 0.8379 (t80) cc_final: 0.8164 (t80) REVERT: A 471 ASP cc_start: 0.7819 (m-30) cc_final: 0.7364 (m-30) REVERT: A 758 ARG cc_start: 0.8728 (tmm160) cc_final: 0.8485 (ttt-90) REVERT: A 800 PHE cc_start: 0.7822 (t80) cc_final: 0.7582 (t80) REVERT: A 982 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7226 (mp) REVERT: A 989 THR cc_start: 0.6441 (OUTLIER) cc_final: 0.6181 (p) REVERT: A 991 LYS cc_start: 0.3861 (OUTLIER) cc_final: 0.3096 (ptpt) REVERT: A 1105 VAL cc_start: 0.8027 (t) cc_final: 0.7793 (p) REVERT: B 386 VAL cc_start: 0.8265 (m) cc_final: 0.7963 (t) REVERT: B 471 ASP cc_start: 0.7808 (m-30) cc_final: 0.7352 (m-30) REVERT: B 527 GLU cc_start: 0.7660 (pt0) cc_final: 0.7449 (pt0) REVERT: B 699 ILE cc_start: 0.3711 (OUTLIER) cc_final: 0.3484 (tp) REVERT: B 700 MET cc_start: 0.5731 (tmm) cc_final: 0.5091 (tmm) REVERT: B 800 PHE cc_start: 0.7822 (t80) cc_final: 0.7582 (t80) REVERT: B 886 MET cc_start: 0.8260 (mtm) cc_final: 0.8053 (mtp) REVERT: B 982 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6939 (mp) REVERT: B 1105 VAL cc_start: 0.8041 (t) cc_final: 0.7798 (p) outliers start: 18 outliers final: 10 residues processed: 129 average time/residue: 0.1099 time to fit residues: 20.1933 Evaluate side-chains 130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121916 restraints weight = 13078.270| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.06 r_work: 0.3246 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11518 Z= 0.172 Angle : 0.516 9.163 15610 Z= 0.273 Chirality : 0.041 0.141 1770 Planarity : 0.003 0.032 1900 Dihedral : 7.976 74.806 1579 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.18 % Allowed : 12.77 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.23), residues: 1376 helix: 2.47 (0.18), residues: 784 sheet: -0.20 (0.46), residues: 128 loop : -1.37 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 638 TYR 0.017 0.001 TYR B 827 PHE 0.020 0.002 PHE A1052 TRP 0.008 0.001 TRP B1047 HIS 0.006 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (11518) covalent geometry : angle 0.51588 / 0.27 (15610) hydrogen bonds : bond 0.04620 / 2.98 ( 664) hydrogen bonds : angle 4.10693 / 2.88 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.375 Fit side-chains REVERT: A 386 VAL cc_start: 0.8238 (m) cc_final: 0.8001 (t) REVERT: A 471 ASP cc_start: 0.7836 (m-30) cc_final: 0.7363 (m-30) REVERT: A 982 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7272 (mp) REVERT: A 989 THR cc_start: 0.6440 (OUTLIER) cc_final: 0.6172 (p) REVERT: A 991 LYS cc_start: 0.3879 (OUTLIER) cc_final: 0.2978 (ptpt) REVERT: A 1105 VAL cc_start: 0.8044 (t) cc_final: 0.7811 (p) REVERT: B 386 VAL cc_start: 0.8244 (m) cc_final: 0.8002 (t) REVERT: B 471 ASP cc_start: 0.7822 (m-30) cc_final: 0.7345 (m-30) REVERT: B 527 GLU cc_start: 0.7663 (pt0) cc_final: 0.7440 (pt0) REVERT: B 699 ILE cc_start: 0.3734 (OUTLIER) cc_final: 0.3500 (tp) REVERT: B 700 MET cc_start: 0.5841 (tmm) cc_final: 0.5153 (tmm) REVERT: B 982 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6966 (mp) REVERT: B 1105 VAL cc_start: 0.8069 (t) cc_final: 0.7832 (p) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.1074 time to fit residues: 18.9181 Evaluate side-chains 122 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 0.0170 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126467 restraints weight = 12907.197| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.04 r_work: 0.3305 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11518 Z= 0.102 Angle : 0.447 9.925 15610 Z= 0.236 Chirality : 0.039 0.155 1770 Planarity : 0.003 0.031 1900 Dihedral : 7.477 67.298 1579 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.27 % Allowed : 12.69 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.23), residues: 1376 helix: 2.75 (0.18), residues: 784 sheet: -0.02 (0.46), residues: 128 loop : -1.25 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 638 TYR 0.017 0.001 TYR A 827 PHE 0.014 0.001 PHE A1052 TRP 0.007 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11518) covalent geometry : angle 0.44730 / 0.24 (15610) hydrogen bonds : bond 0.03555 / 2.30 ( 664) hydrogen bonds : angle 3.86831 / 2.71 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.440 Fit side-chains REVERT: A 386 VAL cc_start: 0.8260 (m) cc_final: 0.8011 (t) REVERT: A 471 ASP cc_start: 0.7850 (m-30) cc_final: 0.7386 (m-30) REVERT: A 529 ASN cc_start: 0.7616 (m-40) cc_final: 0.7328 (m-40) REVERT: A 800 PHE cc_start: 0.7823 (t80) cc_final: 0.7604 (t80) REVERT: A 938 MET cc_start: 0.6015 (tpt) cc_final: 0.5686 (mmm) REVERT: A 982 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 989 THR cc_start: 0.6430 (OUTLIER) cc_final: 0.6186 (p) REVERT: A 991 LYS cc_start: 0.3968 (OUTLIER) cc_final: 0.3143 (ptpt) REVERT: A 1105 VAL cc_start: 0.8010 (t) cc_final: 0.7755 (p) REVERT: B 386 VAL cc_start: 0.8303 (m) cc_final: 0.8061 (t) REVERT: B 416 MET cc_start: 0.8167 (tmm) cc_final: 0.7959 (tmm) REVERT: B 417 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7336 (ttm170) REVERT: B 471 ASP cc_start: 0.7846 (m-30) cc_final: 0.7382 (m-30) REVERT: B 527 GLU cc_start: 0.7593 (pt0) cc_final: 0.7372 (pt0) REVERT: B 699 ILE cc_start: 0.3707 (OUTLIER) cc_final: 0.3470 (tp) REVERT: B 700 MET cc_start: 0.5965 (tmm) cc_final: 0.5253 (tmm) REVERT: B 800 PHE cc_start: 0.7819 (t80) cc_final: 0.7578 (t80) REVERT: B 938 MET cc_start: 0.6037 (tpt) cc_final: 0.5715 (mmm) REVERT: B 982 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.6992 (mp) REVERT: B 1105 VAL cc_start: 0.8034 (t) cc_final: 0.7777 (p) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 0.1096 time to fit residues: 20.4429 Evaluate side-chains 123 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121402 restraints weight = 13036.262| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.06 r_work: 0.3268 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11518 Z= 0.146 Angle : 0.502 11.961 15610 Z= 0.262 Chirality : 0.040 0.144 1770 Planarity : 0.003 0.031 1900 Dihedral : 7.764 71.327 1579 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.18 % Allowed : 13.54 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1376 helix: 2.63 (0.18), residues: 784 sheet: -0.01 (0.46), residues: 128 loop : -1.33 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 638 TYR 0.020 0.001 TYR B 827 PHE 0.019 0.002 PHE B1052 TRP 0.008 0.001 TRP B1047 HIS 0.005 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11518) covalent geometry : angle 0.50156 / 0.26 (15610) hydrogen bonds : bond 0.04278 / 2.76 ( 664) hydrogen bonds : angle 4.04313 / 2.82 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.421 Fit side-chains REVERT: A 464 ARG cc_start: 0.7707 (mtp180) cc_final: 0.7360 (mtp-110) REVERT: A 471 ASP cc_start: 0.7834 (m-30) cc_final: 0.7418 (m-30) REVERT: A 529 ASN cc_start: 0.7690 (m-40) cc_final: 0.7392 (m-40) REVERT: A 982 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7249 (mp) REVERT: A 989 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.6151 (p) REVERT: A 991 LYS cc_start: 0.3615 (OUTLIER) cc_final: 0.2892 (ptpt) REVERT: A 1105 VAL cc_start: 0.8032 (t) cc_final: 0.7780 (p) REVERT: B 416 MET cc_start: 0.8337 (tmm) cc_final: 0.8029 (tmm) REVERT: B 464 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7352 (mtp180) REVERT: B 471 ASP cc_start: 0.7819 (m-30) cc_final: 0.7401 (m-30) REVERT: B 527 GLU cc_start: 0.7641 (pt0) cc_final: 0.7412 (pt0) REVERT: B 699 ILE cc_start: 0.3733 (OUTLIER) cc_final: 0.3473 (tp) REVERT: B 700 MET cc_start: 0.5960 (tmm) cc_final: 0.5222 (tmm) REVERT: B 982 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7019 (mp) REVERT: B 1105 VAL cc_start: 0.8065 (t) cc_final: 0.7814 (p) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.1116 time to fit residues: 19.9145 Evaluate side-chains 124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127451 restraints weight = 13100.288| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.06 r_work: 0.3314 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11518 Z= 0.096 Angle : 0.449 11.110 15610 Z= 0.235 Chirality : 0.039 0.150 1770 Planarity : 0.003 0.031 1900 Dihedral : 7.321 66.507 1579 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.35 % Allowed : 13.79 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.23), residues: 1376 helix: 2.86 (0.18), residues: 786 sheet: 0.21 (0.46), residues: 128 loop : -1.32 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 638 TYR 0.018 0.001 TYR B 827 PHE 0.014 0.001 PHE B1052 TRP 0.008 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (11518) covalent geometry : angle 0.44900 / 0.23 (15610) hydrogen bonds : bond 0.03451 / 2.23 ( 664) hydrogen bonds : angle 3.84030 / 2.68 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.91 seconds wall clock time: 48 minutes 48.68 seconds (2928.68 seconds total)