Starting phenix.real_space_refine on Sat Aug 23 11:16:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3v_36862/08_2025/8k3v_36862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3v_36862/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k3v_36862/08_2025/8k3v_36862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3v_36862/08_2025/8k3v_36862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3v_36862/08_2025/8k3v_36862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3v_36862/08_2025/8k3v_36862.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 7366 2.51 5 N 1802 2.21 5 O 2000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {' MG': 1, 'POV': 2, 'UD1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 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: 5.41, per 1000 atoms: 0.48 Number of scatterers: 11248 At special positions: 0 Unit cell: (132.5, 92.22, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 6 15.00 Mg 2 11.99 O 2000 8.00 N 1802 7.00 C 7366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 519.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 64.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.610A pdb=" N PHE A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.862A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.516A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.550A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.908A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.633A pdb=" N SER A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.831A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.749A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.074A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.736A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.553A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.956A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 removed outlier: 4.529A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 915 " --> pdb=" O PHE A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.549A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.586A pdb=" N ILE A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1127 removed outlier: 4.200A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 410 through 413 removed outlier: 3.610A pdb=" N PHE B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.862A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 478 removed outlier: 3.516A pdb=" N LEU B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.551A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.632A pdb=" N SER B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.831A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.749A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.074A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.565A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.736A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.553A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 894 removed outlier: 3.956A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 932 removed outlier: 4.529A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 915 " --> pdb=" O PHE B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.549A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.586A pdb=" N ILE B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B1005 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B1007 " --> pdb=" O ALA B1003 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B1008 " --> pdb=" O ASN B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1127 removed outlier: 4.200A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.694A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.670A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.693A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.671A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.18 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 1501) selection = (chain 'B' and resid 381 through 1501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1376 helix: 0.99 (0.19), residues: 760 sheet: -1.44 (0.47), residues: 112 loop : -1.77 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 718 TYR 0.040 0.002 TYR B 696 PHE 0.020 0.002 PHE B 885 TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 Details of bonding type rmsd covalent geometry : bond 0.00790 (11518) covalent geometry : angle 1.06502 (15610) hydrogen bonds : bond 0.15935 ( 664) hydrogen bonds : angle 7.17806 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 0.464 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: 0.1056 time to fit residues: 30.3895 Evaluate side-chains 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 998 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3852 r_free = 0.3852 target = 0.160008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126174 restraints weight = 12932.774| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.06 r_work: 0.3327 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11518 Z= 0.126 Angle : 0.506 6.182 15610 Z= 0.274 Chirality : 0.040 0.136 1770 Planarity : 0.004 0.045 1900 Dihedral : 10.948 104.557 1732 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.95 % Allowed : 7.45 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.23), residues: 1376 helix: 1.84 (0.19), residues: 786 sheet: -0.53 (0.43), residues: 142 loop : -1.21 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.011 0.001 TYR B 925 PHE 0.017 0.001 PHE A1052 TRP 0.011 0.001 TRP A 779 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00278 (11518) covalent geometry : angle 0.50648 (15610) hydrogen bonds : bond 0.04453 ( 664) hydrogen bonds : angle 4.47312 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.413 Fit side-chains REVERT: A 455 TYR cc_start: 0.8141 (t80) cc_final: 0.7516 (t80) REVERT: A 464 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7533 (mtp180) REVERT: A 471 ASP cc_start: 0.7876 (m-30) cc_final: 0.7524 (m-30) REVERT: A 610 ASP cc_start: 0.7788 (t70) cc_final: 0.7195 (t0) REVERT: A 639 PHE cc_start: 0.8239 (m-80) cc_final: 0.8027 (m-80) REVERT: A 859 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8309 (mppt) REVERT: A 982 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7211 (mp) REVERT: A 989 THR cc_start: 0.6398 (OUTLIER) cc_final: 0.6144 (p) REVERT: A 991 LYS cc_start: 0.3704 (OUTLIER) cc_final: 0.3153 (mttm) REVERT: B 455 TYR cc_start: 0.8191 (t80) cc_final: 0.7637 (t80) REVERT: B 471 ASP cc_start: 0.7933 (m-30) cc_final: 0.7562 (m-30) REVERT: B 529 ASN cc_start: 0.7055 (m-40) cc_final: 0.6836 (m-40) REVERT: B 610 ASP cc_start: 0.7808 (t70) cc_final: 0.7263 (t0) REVERT: B 700 MET cc_start: 0.5720 (tmm) cc_final: 0.5418 (tmm) REVERT: B 859 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8214 (mppt) REVERT: B 982 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7035 (mp) outliers start: 23 outliers final: 11 residues processed: 150 average time/residue: 0.1129 time to fit residues: 23.7863 Evaluate side-chains 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 61 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.159860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125906 restraints weight = 13075.286| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.11 r_work: 0.3301 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11518 Z= 0.121 Angle : 0.469 7.671 15610 Z= 0.254 Chirality : 0.039 0.136 1770 Planarity : 0.003 0.044 1900 Dihedral : 9.210 80.089 1708 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.44 % Allowed : 9.31 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.23), residues: 1376 helix: 2.25 (0.19), residues: 786 sheet: -0.33 (0.44), residues: 148 loop : -1.07 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.010 0.001 TYR B 925 PHE 0.018 0.001 PHE B1052 TRP 0.008 0.001 TRP A 779 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00275 (11518) covalent geometry : angle 0.46850 (15610) hydrogen bonds : bond 0.04148 ( 664) hydrogen bonds : angle 4.14344 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.375 Fit side-chains REVERT: A 455 TYR cc_start: 0.8268 (t80) cc_final: 0.7796 (t80) REVERT: A 464 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7430 (mtp180) REVERT: A 471 ASP cc_start: 0.7839 (m-30) cc_final: 0.7483 (m-30) REVERT: A 859 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8282 (mppt) REVERT: A 982 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7189 (mp) REVERT: A 989 THR cc_start: 0.6315 (OUTLIER) cc_final: 0.6079 (p) REVERT: A 991 LYS cc_start: 0.4030 (OUTLIER) cc_final: 0.3123 (mttm) REVERT: A 1105 VAL cc_start: 0.8048 (t) cc_final: 0.7805 (p) REVERT: B 455 TYR cc_start: 0.8286 (t80) cc_final: 0.7864 (t80) REVERT: B 464 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7433 (mtp180) REVERT: B 471 ASP cc_start: 0.7850 (m-30) cc_final: 0.7516 (m-30) REVERT: B 529 ASN cc_start: 0.7205 (m-40) cc_final: 0.6979 (m-40) REVERT: B 700 MET cc_start: 0.5946 (tmm) cc_final: 0.5532 (tmm) REVERT: B 859 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8280 (mppt) REVERT: B 982 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6961 (mp) REVERT: B 1105 VAL cc_start: 0.8064 (t) cc_final: 0.7802 (p) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 0.1151 time to fit residues: 24.4761 Evaluate side-chains 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 414 LYS 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 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.158718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124397 restraints weight = 13118.953| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.11 r_work: 0.3286 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11518 Z= 0.126 Angle : 0.466 8.243 15610 Z= 0.251 Chirality : 0.040 0.136 1770 Planarity : 0.003 0.042 1900 Dihedral : 8.960 78.856 1703 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.95 % Allowed : 10.41 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.23), residues: 1376 helix: 2.46 (0.18), residues: 784 sheet: -0.16 (0.44), residues: 148 loop : -1.14 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 787 TYR 0.018 0.001 TYR B 827 PHE 0.015 0.001 PHE B1052 TRP 0.008 0.001 TRP A 779 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00290 (11518) covalent geometry : angle 0.46552 (15610) hydrogen bonds : bond 0.04100 ( 664) hydrogen bonds : angle 4.05260 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.487 Fit side-chains REVERT: A 455 TYR cc_start: 0.8353 (t80) cc_final: 0.7943 (t80) REVERT: A 471 ASP cc_start: 0.7838 (m-30) cc_final: 0.7405 (m-30) REVERT: A 699 ILE cc_start: 0.4293 (OUTLIER) cc_final: 0.4053 (tp) REVERT: A 758 ARG cc_start: 0.8742 (tmm160) cc_final: 0.8466 (ttt-90) REVERT: A 982 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 991 LYS cc_start: 0.4073 (OUTLIER) cc_final: 0.3043 (mttm) REVERT: A 1105 VAL cc_start: 0.8052 (t) cc_final: 0.7809 (p) REVERT: B 455 TYR cc_start: 0.8384 (t80) cc_final: 0.7996 (t80) REVERT: B 464 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7454 (mtp180) REVERT: B 471 ASP cc_start: 0.7847 (m-30) cc_final: 0.7489 (m-30) REVERT: B 700 MET cc_start: 0.5898 (tmm) cc_final: 0.5271 (tmm) REVERT: B 800 PHE cc_start: 0.7817 (t80) cc_final: 0.7615 (t80) REVERT: B 982 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7018 (mp) REVERT: B 1009 LEU cc_start: 0.6532 (mp) cc_final: 0.6291 (mp) REVERT: B 1105 VAL cc_start: 0.8063 (t) cc_final: 0.7820 (p) outliers start: 23 outliers final: 8 residues processed: 147 average time/residue: 0.1135 time to fit residues: 23.5451 Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 699 ILE Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 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 13 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 963 ASN A1004 ASN B1004 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125579 restraints weight = 13032.566| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.04 r_work: 0.3291 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2756 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= 0.123 Angle : 0.454 6.903 15610 Z= 0.246 Chirality : 0.039 0.133 1770 Planarity : 0.003 0.040 1900 Dihedral : 8.740 73.416 1699 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.69 % Allowed : 11.34 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.23), residues: 1376 helix: 2.51 (0.18), residues: 784 sheet: -0.28 (0.47), residues: 128 loop : -1.20 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 436 TYR 0.019 0.001 TYR A 827 PHE 0.017 0.001 PHE A1124 TRP 0.008 0.001 TRP B 779 HIS 0.002 0.001 HIS B 965 Details of bonding type rmsd covalent geometry : bond 0.00284 (11518) covalent geometry : angle 0.45435 (15610) hydrogen bonds : bond 0.04017 ( 664) hydrogen bonds : angle 3.97055 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.486 Fit side-chains REVERT: A 455 TYR cc_start: 0.8378 (t80) cc_final: 0.8055 (t80) REVERT: A 471 ASP cc_start: 0.7822 (m-30) cc_final: 0.7412 (m-30) REVERT: A 699 ILE cc_start: 0.4281 (OUTLIER) cc_final: 0.4019 (tp) REVERT: A 758 ARG cc_start: 0.8745 (tmm160) cc_final: 0.8477 (ttt-90) REVERT: A 982 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 991 LYS cc_start: 0.3995 (OUTLIER) cc_final: 0.3033 (mttm) REVERT: A 1009 LEU cc_start: 0.6330 (mp) cc_final: 0.6094 (mp) REVERT: A 1105 VAL cc_start: 0.8065 (t) cc_final: 0.7821 (p) REVERT: B 455 TYR cc_start: 0.8430 (t80) cc_final: 0.8100 (t80) REVERT: B 464 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7415 (mtp-110) REVERT: B 471 ASP cc_start: 0.7833 (m-30) cc_final: 0.7428 (m-30) REVERT: B 699 ILE cc_start: 0.3970 (OUTLIER) cc_final: 0.3696 (tp) REVERT: B 700 MET cc_start: 0.6016 (tmm) cc_final: 0.5424 (tmm) REVERT: B 800 PHE cc_start: 0.7841 (t80) cc_final: 0.7608 (t80) REVERT: B 982 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7020 (mp) REVERT: B 1105 VAL cc_start: 0.8070 (t) cc_final: 0.7832 (p) outliers start: 20 outliers final: 11 residues processed: 134 average time/residue: 0.1097 time to fit residues: 20.8610 Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 699 ILE Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS B1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118002 restraints weight = 13111.316| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.08 r_work: 0.3205 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11518 Z= 0.231 Angle : 0.568 9.026 15610 Z= 0.303 Chirality : 0.043 0.152 1770 Planarity : 0.004 0.039 1900 Dihedral : 9.445 80.958 1699 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.69 % Allowed : 12.18 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.23), residues: 1376 helix: 2.10 (0.18), residues: 784 sheet: -0.37 (0.44), residues: 148 loop : -1.46 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 436 TYR 0.021 0.002 TYR A 827 PHE 0.021 0.002 PHE B1052 TRP 0.008 0.001 TRP A1047 HIS 0.007 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00564 (11518) covalent geometry : angle 0.56797 (15610) hydrogen bonds : bond 0.05314 ( 664) hydrogen bonds : angle 4.33411 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.417 Fit side-chains REVERT: A 386 VAL cc_start: 0.8179 (m) cc_final: 0.7869 (t) REVERT: A 455 TYR cc_start: 0.8437 (t80) cc_final: 0.8190 (t80) REVERT: A 471 ASP cc_start: 0.7853 (m-30) cc_final: 0.7365 (m-30) REVERT: A 620 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7763 (mtm180) REVERT: A 982 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7215 (mp) REVERT: A 989 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.6247 (p) REVERT: A 991 LYS cc_start: 0.4339 (OUTLIER) cc_final: 0.3278 (ptpt) REVERT: A 1105 VAL cc_start: 0.8093 (t) cc_final: 0.7871 (p) REVERT: B 386 VAL cc_start: 0.8219 (m) cc_final: 0.7925 (t) REVERT: B 471 ASP cc_start: 0.7867 (m-30) cc_final: 0.7379 (m-30) REVERT: B 641 LYS cc_start: 0.8531 (mttm) cc_final: 0.7881 (mtmt) REVERT: B 700 MET cc_start: 0.5813 (tmm) cc_final: 0.5199 (tmm) REVERT: B 982 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7013 (mp) REVERT: B 1105 VAL cc_start: 0.8105 (t) cc_final: 0.7877 (p) outliers start: 20 outliers final: 11 residues processed: 129 average time/residue: 0.1164 time to fit residues: 20.9464 Evaluate side-chains 123 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 133 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.158001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124590 restraints weight = 13014.287| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.04 r_work: 0.3275 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11518 Z= 0.116 Angle : 0.455 8.153 15610 Z= 0.245 Chirality : 0.039 0.129 1770 Planarity : 0.003 0.037 1900 Dihedral : 8.868 71.725 1699 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.52 % Allowed : 12.01 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.23), residues: 1376 helix: 2.50 (0.18), residues: 784 sheet: -0.32 (0.46), residues: 128 loop : -1.36 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 464 TYR 0.022 0.001 TYR A 827 PHE 0.015 0.001 PHE B1052 TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00266 (11518) covalent geometry : angle 0.45461 (15610) hydrogen bonds : bond 0.03955 ( 664) hydrogen bonds : angle 3.97949 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.443 Fit side-chains REVERT: A 386 VAL cc_start: 0.8196 (m) cc_final: 0.7880 (t) REVERT: A 471 ASP cc_start: 0.7839 (m-30) cc_final: 0.7369 (m-30) REVERT: A 982 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 989 THR cc_start: 0.6520 (OUTLIER) cc_final: 0.6235 (p) REVERT: A 991 LYS cc_start: 0.3921 (OUTLIER) cc_final: 0.3052 (ptpt) REVERT: A 1105 VAL cc_start: 0.8056 (t) cc_final: 0.7815 (p) REVERT: B 386 VAL cc_start: 0.8239 (m) cc_final: 0.7921 (t) REVERT: B 464 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7640 (mtp180) REVERT: B 471 ASP cc_start: 0.7837 (m-30) cc_final: 0.7380 (m-30) REVERT: B 700 MET cc_start: 0.6057 (tmm) cc_final: 0.5254 (tmm) REVERT: B 800 PHE cc_start: 0.7839 (t80) cc_final: 0.7574 (t80) REVERT: B 982 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7019 (mp) REVERT: B 1105 VAL cc_start: 0.8077 (t) cc_final: 0.7840 (p) outliers start: 18 outliers final: 11 residues processed: 125 average time/residue: 0.1143 time to fit residues: 20.3417 Evaluate side-chains 122 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU 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 448 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.153169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118639 restraints weight = 13121.807| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.10 r_work: 0.3218 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11518 Z= 0.222 Angle : 0.558 7.691 15610 Z= 0.296 Chirality : 0.043 0.147 1770 Planarity : 0.004 0.033 1900 Dihedral : 9.266 77.326 1699 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.61 % Allowed : 12.01 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.23), residues: 1376 helix: 2.18 (0.18), residues: 784 sheet: -0.27 (0.43), residues: 148 loop : -1.57 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 638 TYR 0.026 0.002 TYR B 455 PHE 0.021 0.002 PHE B1052 TRP 0.008 0.001 TRP B1047 HIS 0.007 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00542 (11518) covalent geometry : angle 0.55800 (15610) hydrogen bonds : bond 0.05188 ( 664) hydrogen bonds : angle 4.30558 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.448 Fit side-chains REVERT: A 386 VAL cc_start: 0.8220 (m) cc_final: 0.7942 (t) REVERT: A 471 ASP cc_start: 0.7838 (m-30) cc_final: 0.7348 (m-30) REVERT: A 527 GLU cc_start: 0.7655 (pt0) cc_final: 0.7454 (pt0) REVERT: A 827 TYR cc_start: 0.8101 (m-80) cc_final: 0.7828 (m-80) REVERT: A 982 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7240 (mp) REVERT: A 989 THR cc_start: 0.6441 (OUTLIER) cc_final: 0.6122 (p) REVERT: A 991 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.2593 (ptpt) REVERT: A 1105 VAL cc_start: 0.8057 (t) cc_final: 0.7828 (p) REVERT: B 386 VAL cc_start: 0.8229 (m) cc_final: 0.8003 (t) REVERT: B 471 ASP cc_start: 0.7848 (m-30) cc_final: 0.7354 (m-30) REVERT: B 700 MET cc_start: 0.6054 (tmm) cc_final: 0.5251 (tmm) REVERT: B 827 TYR cc_start: 0.8099 (m-80) cc_final: 0.7832 (m-80) REVERT: B 982 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6947 (mp) REVERT: B 1105 VAL cc_start: 0.8085 (t) cc_final: 0.7850 (p) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.1101 time to fit residues: 19.8821 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU 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 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 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 34 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.155995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121962 restraints weight = 12866.770| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.06 r_work: 0.3269 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11518 Z= 0.117 Angle : 0.464 7.292 15610 Z= 0.248 Chirality : 0.039 0.130 1770 Planarity : 0.003 0.032 1900 Dihedral : 8.855 71.802 1699 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.27 % Allowed : 12.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.23), residues: 1376 helix: 2.53 (0.18), residues: 784 sheet: -0.25 (0.46), residues: 128 loop : -1.44 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 638 TYR 0.021 0.001 TYR B 455 PHE 0.016 0.001 PHE B1052 TRP 0.009 0.001 TRP A1047 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00267 (11518) covalent geometry : angle 0.46434 (15610) hydrogen bonds : bond 0.03984 ( 664) hydrogen bonds : angle 4.01743 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.319 Fit side-chains REVERT: A 386 VAL cc_start: 0.8266 (m) cc_final: 0.8003 (t) REVERT: A 471 ASP cc_start: 0.7836 (m-30) cc_final: 0.7372 (m-30) REVERT: A 527 GLU cc_start: 0.7711 (pt0) cc_final: 0.7496 (pt0) REVERT: A 529 ASN cc_start: 0.7676 (m-40) cc_final: 0.7346 (m-40) REVERT: A 827 TYR cc_start: 0.7929 (m-80) cc_final: 0.7715 (m-80) REVERT: A 982 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7178 (mp) REVERT: A 989 THR cc_start: 0.6345 (OUTLIER) cc_final: 0.6049 (p) REVERT: A 991 LYS cc_start: 0.3347 (OUTLIER) cc_final: 0.2634 (ptpt) REVERT: A 1105 VAL cc_start: 0.8022 (t) cc_final: 0.7769 (p) REVERT: B 386 VAL cc_start: 0.8304 (m) cc_final: 0.8058 (t) REVERT: B 471 ASP cc_start: 0.7842 (m-30) cc_final: 0.7374 (m-30) REVERT: B 700 MET cc_start: 0.6131 (tmm) cc_final: 0.5687 (tmm) REVERT: B 800 PHE cc_start: 0.7829 (t80) cc_final: 0.7552 (t80) REVERT: B 827 TYR cc_start: 0.7923 (m-80) cc_final: 0.7712 (m-80) REVERT: B 982 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7021 (mp) REVERT: B 1105 VAL cc_start: 0.8025 (t) cc_final: 0.7772 (p) outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.1126 time to fit residues: 18.8324 Evaluate side-chains 122 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 448 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.150703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116347 restraints weight = 13122.050| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.06 r_work: 0.3204 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3277 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= 0.272 Angle : 0.605 8.853 15610 Z= 0.318 Chirality : 0.045 0.156 1770 Planarity : 0.004 0.038 1900 Dihedral : 9.377 76.673 1699 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.27 % Allowed : 12.69 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.22), residues: 1376 helix: 2.05 (0.18), residues: 784 sheet: -0.39 (0.43), residues: 148 loop : -1.73 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 638 TYR 0.028 0.002 TYR B 455 PHE 0.021 0.002 PHE B1052 TRP 0.009 0.001 TRP B1047 HIS 0.006 0.002 HIS B 828 Details of bonding type rmsd covalent geometry : bond 0.00674 (11518) covalent geometry : angle 0.60477 (15610) hydrogen bonds : bond 0.05521 ( 664) hydrogen bonds : angle 4.42815 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.409 Fit side-chains REVERT: A 471 ASP cc_start: 0.7856 (m-30) cc_final: 0.7379 (m-30) REVERT: A 527 GLU cc_start: 0.7781 (pt0) cc_final: 0.7570 (pt0) REVERT: A 827 TYR cc_start: 0.8095 (m-80) cc_final: 0.7844 (m-80) REVERT: A 982 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7308 (mp) REVERT: A 989 THR cc_start: 0.6312 (OUTLIER) cc_final: 0.6092 (p) REVERT: A 991 LYS cc_start: 0.3129 (OUTLIER) cc_final: 0.2398 (ptpt) REVERT: A 1105 VAL cc_start: 0.8080 (t) cc_final: 0.7842 (p) REVERT: B 471 ASP cc_start: 0.7868 (m-30) cc_final: 0.7389 (m-30) REVERT: B 700 MET cc_start: 0.6017 (tmm) cc_final: 0.5551 (tmm) REVERT: B 827 TYR cc_start: 0.8100 (m-80) cc_final: 0.7853 (m-80) REVERT: B 982 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.6972 (mp) REVERT: B 1105 VAL cc_start: 0.8090 (t) cc_final: 0.7855 (p) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 0.1132 time to fit residues: 20.0479 Evaluate side-chains 124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.156165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122232 restraints weight = 13029.167| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.05 r_work: 0.3277 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11518 Z= 0.118 Angle : 0.468 8.244 15610 Z= 0.250 Chirality : 0.039 0.139 1770 Planarity : 0.003 0.032 1900 Dihedral : 8.853 71.714 1699 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.18 % Allowed : 13.20 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.23), residues: 1376 helix: 2.52 (0.18), residues: 784 sheet: -0.34 (0.45), residues: 128 loop : -1.54 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 638 TYR 0.021 0.001 TYR B 455 PHE 0.016 0.001 PHE B1052 TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00268 (11518) covalent geometry : angle 0.46816 (15610) hydrogen bonds : bond 0.03930 ( 664) hydrogen bonds : angle 4.01421 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.26 seconds wall clock time: 47 minutes 22.23 seconds (2842.23 seconds total)