Starting phenix.real_space_refine on Wed May 14 10:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3v_36862/05_2025/8k3v_36862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3v_36862/05_2025/8k3v_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_36862/05_2025/8k3v_36862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3v_36862/05_2025/8k3v_36862.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3v_36862/05_2025/8k3v_36862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3v_36862/05_2025/8k3v_36862.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11248 Number of models: 1 Model: "" Number of chains: 3 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: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 4} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'UD1': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 12.18, per 1000 atoms: 1.08 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.07 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: 3.49 Time building geometry restraints manager: 4.05 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: 6543 33.01 - 66.02: 243 66.02 - 99.04: 32 99.04 - 132.05: 6 132.05 - 165.06: 2 Dihedral angle restraints: 6826 sinusoidal: 2702 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 6823 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 1127 or resid 1501)) selection = (chain 'B' and (resid 381 through 1127 or resid 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: 6.140 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.110 Process input model: 33.930 Find NCS groups from input model: 0.530 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 17.586 165.061 4158 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (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 TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 PHE 0.020 0.002 PHE B 885 TYR 0.040 0.002 TYR B 696 ARG 0.005 0.001 ARG B 718 Details of bonding type rmsd hydrogen bonds : bond 0.15935 ( 664) hydrogen bonds : angle 7.17806 ( 1902) covalent geometry : bond 0.00790 (11518) covalent geometry : angle 1.06502 (15610) *********************** 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 : 1.335 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: 0.7777 (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: 0.2634 time to fit residues: 74.9449 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 : 1.204 ------------------------------------------------------------------------------- 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 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3853 r_free = 0.3853 target = 0.160014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126200 restraints weight = 12866.756| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.05 r_work: 0.3330 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11518 Z= 0.124 Angle : 0.506 6.120 15610 Z= 0.274 Chirality : 0.040 0.136 1770 Planarity : 0.004 0.045 1900 Dihedral : 10.955 104.491 1732 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.95 % Allowed : 7.36 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1376 helix: 1.85 (0.19), residues: 786 sheet: -0.53 (0.44), residues: 142 loop : -1.20 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 779 HIS 0.003 0.001 HIS A 459 PHE 0.017 0.001 PHE A1052 TYR 0.011 0.001 TYR B 925 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 664) hydrogen bonds : angle 4.47013 ( 1902) covalent geometry : bond 0.00274 (11518) covalent geometry : angle 0.50551 (15610) *********************** 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 157 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.349 Fit side-chains REVERT: A 455 TYR cc_start: 0.8138 (t80) cc_final: 0.7564 (t80) REVERT: A 464 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7535 (mtp180) REVERT: A 471 ASP cc_start: 0.7876 (m-30) cc_final: 0.7526 (m-30) REVERT: A 610 ASP cc_start: 0.7781 (t70) cc_final: 0.7188 (t0) REVERT: A 639 PHE cc_start: 0.8257 (m-80) cc_final: 0.8054 (m-80) REVERT: A 859 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8309 (mppt) REVERT: A 982 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7213 (mp) REVERT: A 989 THR cc_start: 0.6386 (OUTLIER) cc_final: 0.6128 (p) REVERT: A 991 LYS cc_start: 0.3695 (OUTLIER) cc_final: 0.3148 (mttm) REVERT: B 455 TYR cc_start: 0.8188 (t80) cc_final: 0.7629 (t80) REVERT: B 471 ASP cc_start: 0.7930 (m-30) cc_final: 0.7560 (m-30) REVERT: B 529 ASN cc_start: 0.7075 (m-40) cc_final: 0.6857 (m-40) REVERT: B 610 ASP cc_start: 0.7804 (t70) cc_final: 0.7258 (t0) REVERT: B 700 MET cc_start: 0.5737 (tmm) cc_final: 0.5431 (tmm) REVERT: B 859 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8213 (mppt) REVERT: B 982 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7034 (mp) outliers start: 23 outliers final: 11 residues processed: 150 average time/residue: 0.2673 time to fit residues: 55.6522 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 : 1.293 ------------------------------------------------------------------------------- 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 985 THR 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 16 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3811 r_free = 0.3811 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122058 restraints weight = 13155.542| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.12 r_work: 0.3253 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2385 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= 0.168 Angle : 0.522 7.379 15610 Z= 0.282 Chirality : 0.042 0.147 1770 Planarity : 0.004 0.044 1900 Dihedral : 9.425 80.942 1708 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.69 % Allowed : 9.90 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1376 helix: 2.03 (0.19), residues: 786 sheet: -0.50 (0.43), residues: 148 loop : -1.28 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.006 0.001 HIS A 459 PHE 0.020 0.002 PHE B1052 TYR 0.012 0.001 TYR A 925 ARG 0.004 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 664) hydrogen bonds : angle 4.32851 ( 1902) covalent geometry : bond 0.00401 (11518) covalent geometry : angle 0.52197 (15610) *********************** 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 156 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.343 Fit side-chains REVERT: A 455 TYR cc_start: 0.8320 (t80) cc_final: 0.7959 (t80) REVERT: A 471 ASP cc_start: 0.7835 (m-30) cc_final: 0.7391 (m-30) REVERT: A 610 ASP cc_start: 0.7914 (t70) cc_final: 0.7565 (t70) REVERT: A 800 PHE cc_start: 0.7813 (t80) cc_final: 0.7567 (t80) REVERT: A 982 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7218 (mp) REVERT: A 991 LYS cc_start: 0.3997 (OUTLIER) cc_final: 0.3040 (mttm) REVERT: A 1105 VAL cc_start: 0.8082 (t) cc_final: 0.7840 (p) REVERT: B 466 LEU cc_start: 0.8198 (mm) cc_final: 0.7967 (mp) REVERT: B 471 ASP cc_start: 0.7841 (m-30) cc_final: 0.7402 (m-30) REVERT: B 529 ASN cc_start: 0.7436 (m-40) cc_final: 0.7180 (m-40) REVERT: B 610 ASP cc_start: 0.7924 (t70) cc_final: 0.7580 (t70) REVERT: B 641 LYS cc_start: 0.8504 (mttm) cc_final: 0.7832 (mtmt) REVERT: B 700 MET cc_start: 0.5874 (tmm) cc_final: 0.5350 (tmm) REVERT: B 800 PHE cc_start: 0.7813 (t80) cc_final: 0.7563 (t80) REVERT: B 859 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8324 (mppt) REVERT: B 982 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7003 (mp) REVERT: B 1105 VAL cc_start: 0.8041 (t) cc_final: 0.7804 (p) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.2474 time to fit residues: 52.2392 Evaluate side-chains 135 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 395 LEU Chi-restraints excluded: chain B residue 397 ASP 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 123 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3810 r_free = 0.3810 target = 0.155946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122007 restraints weight = 12983.493| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.04 r_work: 0.3270 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2664 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= 0.147 Angle : 0.480 6.114 15610 Z= 0.261 Chirality : 0.040 0.138 1770 Planarity : 0.003 0.042 1900 Dihedral : 9.250 77.529 1703 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 11.08 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1376 helix: 2.20 (0.18), residues: 784 sheet: -0.32 (0.44), residues: 148 loop : -1.30 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1047 HIS 0.004 0.001 HIS A 828 PHE 0.017 0.002 PHE A1052 TYR 0.013 0.001 TYR B 925 ARG 0.002 0.000 ARG A 817 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 664) hydrogen bonds : angle 4.14753 ( 1902) covalent geometry : bond 0.00349 (11518) covalent geometry : angle 0.48037 (15610) *********************** 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 144 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.391 Fit side-chains REVERT: A 455 TYR cc_start: 0.8411 (t80) cc_final: 0.8076 (t80) REVERT: A 471 ASP cc_start: 0.7830 (m-30) cc_final: 0.7366 (m-30) REVERT: A 574 GLN cc_start: 0.7892 (pt0) cc_final: 0.7639 (pt0) REVERT: A 620 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7786 (mtm110) REVERT: A 758 ARG cc_start: 0.8798 (tmm160) cc_final: 0.8524 (ttt-90) REVERT: A 800 PHE cc_start: 0.7857 (t80) cc_final: 0.7600 (t80) REVERT: A 982 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7226 (mp) REVERT: A 991 LYS cc_start: 0.4123 (OUTLIER) cc_final: 0.3353 (ptpt) REVERT: A 1105 VAL cc_start: 0.8090 (t) cc_final: 0.7844 (p) REVERT: B 455 TYR cc_start: 0.8420 (t80) cc_final: 0.8112 (t80) REVERT: B 471 ASP cc_start: 0.7836 (m-30) cc_final: 0.7363 (m-30) REVERT: B 574 GLN cc_start: 0.7994 (pt0) cc_final: 0.7767 (pt0) REVERT: B 578 LYS cc_start: 0.7860 (tttt) cc_final: 0.7628 (ttpp) REVERT: B 700 MET cc_start: 0.5873 (tmm) cc_final: 0.5261 (tmm) REVERT: B 800 PHE cc_start: 0.7848 (t80) cc_final: 0.7591 (t80) REVERT: B 982 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6945 (mp) REVERT: B 1009 LEU cc_start: 0.6615 (mp) cc_final: 0.6390 (mp) REVERT: B 1105 VAL cc_start: 0.8108 (t) cc_final: 0.7867 (p) outliers start: 20 outliers final: 9 residues processed: 139 average time/residue: 0.2601 time to fit residues: 52.0416 Evaluate side-chains 130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 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 1042 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 135 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A1004 ASN B 472 ASN B1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118139 restraints weight = 13014.890| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.05 r_work: 0.3219 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11518 Z= 0.207 Angle : 0.542 6.194 15610 Z= 0.291 Chirality : 0.042 0.149 1770 Planarity : 0.004 0.040 1900 Dihedral : 9.380 79.672 1699 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.95 % Allowed : 11.51 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1376 helix: 2.01 (0.18), residues: 784 sheet: -0.44 (0.43), residues: 148 loop : -1.49 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.005 0.001 HIS A 828 PHE 0.020 0.002 PHE B1052 TYR 0.014 0.002 TYR A 925 ARG 0.002 0.001 ARG B 718 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 664) hydrogen bonds : angle 4.33950 ( 1902) covalent geometry : bond 0.00505 (11518) covalent geometry : angle 0.54205 (15610) *********************** 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 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.231 Fit side-chains REVERT: A 386 VAL cc_start: 0.8142 (m) cc_final: 0.7848 (t) REVERT: A 391 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7017 (pt) REVERT: A 471 ASP cc_start: 0.7851 (m-30) cc_final: 0.7372 (m-30) REVERT: A 574 GLN cc_start: 0.8079 (pt0) cc_final: 0.7866 (pt0) REVERT: A 620 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7698 (mtm180) REVERT: A 700 MET cc_start: 0.5636 (tmm) cc_final: 0.5419 (tmm) REVERT: A 982 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7266 (mp) REVERT: A 989 THR cc_start: 0.6559 (OUTLIER) cc_final: 0.6267 (p) REVERT: A 991 LYS cc_start: 0.3958 (OUTLIER) cc_final: 0.2927 (ptpt) REVERT: A 1105 VAL cc_start: 0.8090 (t) cc_final: 0.7864 (p) REVERT: B 386 VAL cc_start: 0.8184 (m) cc_final: 0.7893 (t) REVERT: B 471 ASP cc_start: 0.7845 (m-30) cc_final: 0.7367 (m-30) REVERT: B 578 LYS cc_start: 0.7823 (tttt) cc_final: 0.7565 (ttpp) REVERT: B 700 MET cc_start: 0.5932 (tmm) cc_final: 0.5310 (tmm) REVERT: B 827 TYR cc_start: 0.8057 (m-80) cc_final: 0.7683 (m-80) REVERT: B 982 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7024 (mp) REVERT: B 1105 VAL cc_start: 0.8106 (t) cc_final: 0.7883 (p) outliers start: 23 outliers final: 13 residues processed: 134 average time/residue: 0.2417 time to fit residues: 46.1304 Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 434 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 397 ASP 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 982 ILE 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 84 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124477 restraints weight = 13050.780| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.06 r_work: 0.3282 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11518 Z= 0.109 Angle : 0.446 6.037 15610 Z= 0.242 Chirality : 0.039 0.130 1770 Planarity : 0.003 0.038 1900 Dihedral : 8.869 72.532 1699 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.35 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1376 helix: 2.48 (0.18), residues: 784 sheet: -0.36 (0.46), residues: 128 loop : -1.34 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 779 HIS 0.004 0.001 HIS B 828 PHE 0.014 0.001 PHE A1052 TYR 0.022 0.001 TYR A 827 ARG 0.003 0.000 ARG B 464 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 664) hydrogen bonds : angle 3.98394 ( 1902) covalent geometry : bond 0.00243 (11518) covalent geometry : angle 0.44575 (15610) *********************** 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 134 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.304 Fit side-chains REVERT: A 386 VAL cc_start: 0.8213 (m) cc_final: 0.7888 (t) REVERT: A 471 ASP cc_start: 0.7840 (m-30) cc_final: 0.7367 (m-30) REVERT: A 574 GLN cc_start: 0.7864 (pt0) cc_final: 0.7578 (tt0) REVERT: A 758 ARG cc_start: 0.8755 (tmm160) cc_final: 0.8521 (ttt-90) REVERT: A 800 PHE cc_start: 0.7830 (t80) cc_final: 0.7560 (t80) REVERT: A 938 MET cc_start: 0.6117 (tpt) cc_final: 0.5654 (tpt) REVERT: A 982 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7244 (mp) REVERT: A 989 THR cc_start: 0.6395 (OUTLIER) cc_final: 0.6119 (p) REVERT: A 991 LYS cc_start: 0.4003 (OUTLIER) cc_final: 0.3208 (ptpt) REVERT: A 1105 VAL cc_start: 0.8084 (t) cc_final: 0.7835 (p) REVERT: B 386 VAL cc_start: 0.8211 (m) cc_final: 0.7914 (t) REVERT: B 416 MET cc_start: 0.8426 (tmm) cc_final: 0.7940 (tmm) REVERT: B 471 ASP cc_start: 0.7827 (m-30) cc_final: 0.7357 (m-30) REVERT: B 527 GLU cc_start: 0.7563 (pt0) cc_final: 0.7351 (pt0) REVERT: B 574 GLN cc_start: 0.7825 (pt0) cc_final: 0.7606 (tt0) REVERT: B 578 LYS cc_start: 0.7835 (tttt) cc_final: 0.7556 (ttpp) REVERT: B 700 MET cc_start: 0.6039 (tmm) cc_final: 0.5586 (tmm) REVERT: B 800 PHE cc_start: 0.7832 (t80) cc_final: 0.7564 (t80) REVERT: B 938 MET cc_start: 0.6150 (tpt) cc_final: 0.5699 (tpt) REVERT: B 982 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6919 (mp) REVERT: B 1009 LEU cc_start: 0.6599 (mp) cc_final: 0.6377 (mp) REVERT: B 1105 VAL cc_start: 0.8103 (t) cc_final: 0.7858 (p) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.2475 time to fit residues: 45.8011 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 : 1.296 ------------------------------------------------------------------------------- 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 673 VAL 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 539 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL 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 119 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125082 restraints weight = 13052.344| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.04 r_work: 0.3280 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3157 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= 0.116 Angle : 0.456 8.765 15610 Z= 0.245 Chirality : 0.039 0.131 1770 Planarity : 0.003 0.037 1900 Dihedral : 8.748 72.278 1699 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.61 % Allowed : 12.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1376 helix: 2.57 (0.18), residues: 784 sheet: -0.25 (0.46), residues: 128 loop : -1.30 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS B 828 PHE 0.017 0.001 PHE B1052 TYR 0.022 0.001 TYR B 455 ARG 0.002 0.000 ARG B 464 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 664) hydrogen bonds : angle 3.96162 ( 1902) covalent geometry : bond 0.00264 (11518) covalent geometry : angle 0.45574 (15610) *********************** 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 130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.219 Fit side-chains REVERT: A 386 VAL cc_start: 0.8252 (m) cc_final: 0.7934 (t) REVERT: A 471 ASP cc_start: 0.7847 (m-30) cc_final: 0.7383 (m-30) REVERT: A 700 MET cc_start: 0.5502 (tmm) cc_final: 0.5270 (tmm) REVERT: A 758 ARG cc_start: 0.8741 (tmm160) cc_final: 0.8491 (ttt-90) REVERT: A 800 PHE cc_start: 0.7842 (t80) cc_final: 0.7608 (t80) REVERT: A 938 MET cc_start: 0.6147 (tpt) cc_final: 0.5675 (tpt) REVERT: A 982 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7260 (mp) REVERT: A 989 THR cc_start: 0.6412 (OUTLIER) cc_final: 0.6140 (p) REVERT: A 991 LYS cc_start: 0.3777 (OUTLIER) cc_final: 0.3025 (ptpt) REVERT: A 1105 VAL cc_start: 0.8040 (t) cc_final: 0.7798 (p) REVERT: B 386 VAL cc_start: 0.8214 (m) cc_final: 0.7914 (t) REVERT: B 471 ASP cc_start: 0.7833 (m-30) cc_final: 0.7370 (m-30) REVERT: B 527 GLU cc_start: 0.7575 (pt0) cc_final: 0.7349 (pt0) REVERT: B 578 LYS cc_start: 0.7928 (tttt) cc_final: 0.7639 (ttpp) REVERT: B 700 MET cc_start: 0.6065 (tmm) cc_final: 0.5659 (tmm) REVERT: B 800 PHE cc_start: 0.7841 (t80) cc_final: 0.7607 (t80) REVERT: B 938 MET cc_start: 0.6174 (tpt) cc_final: 0.5712 (tpt) REVERT: B 982 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6933 (mp) REVERT: B 1105 VAL cc_start: 0.8050 (t) cc_final: 0.7812 (p) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.2601 time to fit residues: 46.8669 Evaluate side-chains 123 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 610 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL 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 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 672 THR 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 55 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116703 restraints weight = 13217.132| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.05 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11518 Z= 0.271 Angle : 0.603 9.050 15610 Z= 0.318 Chirality : 0.045 0.155 1770 Planarity : 0.004 0.037 1900 Dihedral : 9.391 77.938 1699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 12.44 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1376 helix: 2.03 (0.18), residues: 784 sheet: -0.34 (0.43), residues: 148 loop : -1.63 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1047 HIS 0.008 0.002 HIS A 828 PHE 0.022 0.002 PHE B1052 TYR 0.028 0.002 TYR B 455 ARG 0.003 0.001 ARG B 464 Details of bonding type rmsd hydrogen bonds : bond 0.05584 ( 664) hydrogen bonds : angle 4.45213 ( 1902) covalent geometry : bond 0.00667 (11518) covalent geometry : angle 0.60342 (15610) *********************** 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 129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.222 Fit side-chains REVERT: A 386 VAL cc_start: 0.8350 (m) cc_final: 0.8145 (t) REVERT: A 391 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7022 (pt) REVERT: A 471 ASP cc_start: 0.7861 (m-30) cc_final: 0.7398 (m-30) REVERT: A 700 MET cc_start: 0.5514 (tmm) cc_final: 0.5238 (tmm) REVERT: A 982 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7245 (mp) REVERT: A 989 THR cc_start: 0.6386 (OUTLIER) cc_final: 0.6160 (p) REVERT: A 991 LYS cc_start: 0.3732 (OUTLIER) cc_final: 0.2689 (ptpt) REVERT: A 1105 VAL cc_start: 0.8121 (t) cc_final: 0.7889 (p) REVERT: B 386 VAL cc_start: 0.8363 (m) cc_final: 0.8162 (t) REVERT: B 471 ASP cc_start: 0.7867 (m-30) cc_final: 0.7385 (m-30) REVERT: B 527 GLU cc_start: 0.7632 (pt0) cc_final: 0.7399 (pt0) REVERT: B 700 MET cc_start: 0.6050 (tmm) cc_final: 0.5582 (tmm) REVERT: B 982 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6989 (mp) REVERT: B 1105 VAL cc_start: 0.8132 (t) cc_final: 0.7902 (p) outliers start: 20 outliers final: 11 residues processed: 125 average time/residue: 0.2450 time to fit residues: 43.3801 Evaluate side-chains 119 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE 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 673 VAL 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 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL 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 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121629 restraints weight = 13045.734| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.07 r_work: 0.3267 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11518 Z= 0.120 Angle : 0.463 7.867 15610 Z= 0.248 Chirality : 0.039 0.133 1770 Planarity : 0.003 0.036 1900 Dihedral : 8.864 71.815 1699 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 13.03 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1376 helix: 2.59 (0.18), residues: 772 sheet: -0.30 (0.45), residues: 128 loop : -1.44 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1047 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE A1052 TYR 0.020 0.001 TYR B 455 ARG 0.002 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 664) hydrogen bonds : angle 4.04236 ( 1902) covalent geometry : bond 0.00275 (11518) covalent geometry : angle 0.46294 (15610) *********************** 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 128 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.256 Fit side-chains REVERT: A 386 VAL cc_start: 0.8321 (m) cc_final: 0.8099 (t) REVERT: A 471 ASP cc_start: 0.7845 (m-30) cc_final: 0.7400 (m-30) REVERT: A 700 MET cc_start: 0.5324 (tmm) cc_final: 0.5029 (tmm) REVERT: A 982 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7200 (mp) REVERT: A 991 LYS cc_start: 0.3358 (OUTLIER) cc_final: 0.2641 (ptpt) REVERT: A 1105 VAL cc_start: 0.8045 (t) cc_final: 0.7798 (p) REVERT: B 471 ASP cc_start: 0.7831 (m-30) cc_final: 0.7366 (m-30) REVERT: B 527 GLU cc_start: 0.7633 (pt0) cc_final: 0.7404 (pt0) REVERT: B 700 MET cc_start: 0.6008 (tmm) cc_final: 0.5563 (tmm) REVERT: B 800 PHE cc_start: 0.7835 (t80) cc_final: 0.7556 (t80) REVERT: B 938 MET cc_start: 0.6182 (tpt) cc_final: 0.5756 (tpt) REVERT: B 982 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7051 (mp) REVERT: B 1105 VAL cc_start: 0.8048 (t) cc_final: 0.7796 (p) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 0.2563 time to fit residues: 45.2709 Evaluate side-chains 124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 446 THR 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 673 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 446 THR 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 673 VAL 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 72 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 0.0050 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118279 restraints weight = 13034.612| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.05 r_work: 0.3225 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11518 Z= 0.204 Angle : 0.545 9.289 15610 Z= 0.287 Chirality : 0.042 0.144 1770 Planarity : 0.004 0.036 1900 Dihedral : 9.095 75.075 1698 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.86 % Allowed : 12.77 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1376 helix: 2.35 (0.18), residues: 772 sheet: -0.18 (0.44), residues: 148 loop : -1.56 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 779 HIS 0.006 0.001 HIS A 828 PHE 0.021 0.002 PHE B1052 TYR 0.026 0.002 TYR A 455 ARG 0.004 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 664) hydrogen bonds : angle 4.26341 ( 1902) covalent geometry : bond 0.00499 (11518) covalent geometry : angle 0.54487 (15610) ********************** 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 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.307 Fit side-chains REVERT: A 446 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 471 ASP cc_start: 0.7843 (m-30) cc_final: 0.7387 (m-30) REVERT: A 700 MET cc_start: 0.5354 (tmm) cc_final: 0.5070 (tmm) REVERT: A 982 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7291 (mp) REVERT: A 991 LYS cc_start: 0.3330 (OUTLIER) cc_final: 0.2550 (ptpt) REVERT: A 1105 VAL cc_start: 0.8084 (t) cc_final: 0.7850 (p) REVERT: B 446 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 471 ASP cc_start: 0.7824 (m-30) cc_final: 0.7344 (m-30) REVERT: B 527 GLU cc_start: 0.7670 (pt0) cc_final: 0.7436 (pt0) REVERT: B 700 MET cc_start: 0.5945 (tmm) cc_final: 0.5491 (tmm) REVERT: B 982 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7020 (mp) REVERT: B 1105 VAL cc_start: 0.8092 (t) cc_final: 0.7861 (p) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.2528 time to fit residues: 45.4005 Evaluate side-chains 129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 448 LEU 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 673 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 448 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 673 VAL Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1089 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121044 restraints weight = 12902.782| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.05 r_work: 0.3258 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11518 Z= 0.134 Angle : 0.482 8.757 15610 Z= 0.255 Chirality : 0.040 0.139 1770 Planarity : 0.003 0.036 1900 Dihedral : 8.851 72.607 1698 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.69 % Allowed : 13.20 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1376 helix: 2.58 (0.18), residues: 772 sheet: -0.21 (0.46), residues: 128 loop : -1.47 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.005 0.001 HIS A 828 PHE 0.017 0.001 PHE A1052 TYR 0.022 0.001 TYR B 455 ARG 0.002 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 664) hydrogen bonds : angle 4.07649 ( 1902) covalent geometry : bond 0.00314 (11518) covalent geometry : angle 0.48154 (15610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5914.56 seconds wall clock time: 103 minutes 32.13 seconds (6212.13 seconds total)