Starting phenix.real_space_refine on Mon Jun 9 00:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ueq_64089/06_2025/9ueq_64089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ueq_64089/06_2025/9ueq_64089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ueq_64089/06_2025/9ueq_64089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ueq_64089/06_2025/9ueq_64089.map" model { file = "/net/cci-nas-00/data/ceres_data/9ueq_64089/06_2025/9ueq_64089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ueq_64089/06_2025/9ueq_64089.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 33 5.16 5 C 6308 2.51 5 N 1770 2.21 5 O 1918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10030 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5005 Classifications: {'peptide': 671} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 43, 'TRANS': 627} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 4999 Classifications: {'peptide': 671} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 43, 'TRANS': 627} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {' ZN': 1, 'BTN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.05, per 1000 atoms: 0.70 Number of scatterers: 10030 At special positions: 0 Unit cell: (95.46, 96.32, 122.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 33 16.00 O 1918 8.00 N 1770 7.00 C 6308 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 732 " 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 44.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.915A pdb=" N PHE A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.501A pdb=" N VAL A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 3.576A pdb=" N ARG A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 571 through 579 removed outlier: 3.611A pdb=" N LEU A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 4.025A pdb=" N ARG A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.518A pdb=" N THR A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.595A pdb=" N THR A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 696 removed outlier: 3.726A pdb=" N GLY A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 725 Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.757A pdb=" N ILE A 774 " --> pdb=" O ALA A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 795 through 806 removed outlier: 3.616A pdb=" N TRP A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 removed outlier: 3.663A pdb=" N HIS A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 840 Processing helix chain 'A' and resid 845 through 860 Processing helix chain 'A' and resid 866 through 884 removed outlier: 4.468A pdb=" N LYS A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.697A pdb=" N ALA A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 919 through 924 removed outlier: 4.084A pdb=" N THR A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 947 removed outlier: 4.308A pdb=" N ILE A 945 " --> pdb=" O ALA A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 963 Processing helix chain 'A' and resid 963 through 977 removed outlier: 3.612A pdb=" N THR A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 968 " --> pdb=" O PRO A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 990 Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.587A pdb=" N PHE B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.630A pdb=" N LYS B 488 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 489 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.605A pdb=" N ARG B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.525A pdb=" N SER B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 538' Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 551 through 559 Processing helix chain 'B' and resid 571 through 579 removed outlier: 3.591A pdb=" N VAL B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 595 removed outlier: 3.726A pdb=" N ARG B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 removed outlier: 3.698A pdb=" N ASN B 608 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 631 Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.354A pdb=" N MET B 647 " --> pdb=" O ASN B 643 " (cutoff:3.500A) Proline residue: B 649 - end of helix Processing helix chain 'B' and resid 681 through 696 Processing helix chain 'B' and resid 710 through 723 removed outlier: 3.669A pdb=" N GLN B 715 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG B 716 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.731A pdb=" N TYR B 744 " --> pdb=" O GLN B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 788 through 794 Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.785A pdb=" N TRP B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.723A pdb=" N HIS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 834 Processing helix chain 'B' and resid 835 through 840 removed outlier: 3.558A pdb=" N ALA B 839 " --> pdb=" O GLN B 835 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 840' Processing helix chain 'B' and resid 848 through 860 removed outlier: 4.055A pdb=" N ALA B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 881 Processing helix chain 'B' and resid 886 through 893 Processing helix chain 'B' and resid 902 through 909 Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.589A pdb=" N ARG B 923 " --> pdb=" O PRO B 919 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 919 through 924' Processing helix chain 'B' and resid 940 through 945 removed outlier: 3.531A pdb=" N ILE B 945 " --> pdb=" O ALA B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 949 removed outlier: 3.829A pdb=" N SER B 949 " --> pdb=" O ALA B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 949' Processing helix chain 'B' and resid 951 through 963 Processing helix chain 'B' and resid 963 through 978 Processing helix chain 'B' and resid 984 through 990 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 528 removed outlier: 6.775A pdb=" N VAL A 526 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP A 528 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TRP A 568 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 567 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 603 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY A 569 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 635 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA A 665 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 637 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS A 667 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA A 662 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA A 701 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 664 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LYS A 703 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET A 666 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 754 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 756 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 525 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY A 757 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N THR A 527 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 997 through 1003 removed outlier: 7.112A pdb=" N GLU A 997 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU A1012 " --> pdb=" O GLU A 997 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG A 999 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A1010 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS A1001 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU A1008 " --> pdb=" O LYS A1001 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A1003 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A1013 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N MET A1027 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE A1015 " --> pdb=" O THR A1025 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR A1025 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1061 through 1062 removed outlier: 3.825A pdb=" N VAL A1124 " --> pdb=" O ILE A1062 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1094 through 1099 removed outlier: 7.338A pdb=" N MET A1094 " --> pdb=" O GLU A1090 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A1090 " --> pdb=" O MET A1094 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A1096 " --> pdb=" O THR A1088 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR A1088 " --> pdb=" O ALA A1096 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A1098 " --> pdb=" O ILE A1086 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A1070 " --> pdb=" O ALA A1115 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A1115 " --> pdb=" O VAL A1070 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 525 through 528 removed outlier: 7.086A pdb=" N VAL B 526 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 528 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N TRP B 568 " --> pdb=" O ASP B 528 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 565 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU B 603 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N CYS B 567 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 754 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 731 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 756 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR B 733 " --> pdb=" O ASP B 756 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY B 525 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY B 757 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR B 527 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1000 through 1003 removed outlier: 3.925A pdb=" N LEU B1002 " --> pdb=" O VAL B1006 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL B1006 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1010 through 1015 removed outlier: 5.920A pdb=" N LEU B1012 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B1029 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B1014 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1061 through 1062 removed outlier: 3.784A pdb=" N VAL B1124 " --> pdb=" O ILE B1062 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG B1108 " --> pdb=" O VAL B1125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 3.579A pdb=" N MET B1094 " --> pdb=" O ALA B1091 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1020 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: 3.21 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3451 1.34 - 1.46: 2150 1.46 - 1.58: 4574 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 10229 Sorted by residual: bond pdb=" N ILE B1098 " pdb=" CA ILE B1098 " ideal model delta sigma weight residual 1.461 1.489 -0.029 1.08e-02 8.57e+03 6.99e+00 bond pdb=" CA PRO B1101 " pdb=" CB PRO B1101 " ideal model delta sigma weight residual 1.533 1.505 0.028 1.42e-02 4.96e+03 3.90e+00 bond pdb=" N THR B1099 " pdb=" CA THR B1099 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.31e-02 5.83e+03 3.77e+00 bond pdb=" N ALA B1100 " pdb=" CA ALA B1100 " ideal model delta sigma weight residual 1.452 1.478 -0.026 1.41e-02 5.03e+03 3.30e+00 bond pdb=" C ILE B1098 " pdb=" O ILE B1098 " ideal model delta sigma weight residual 1.234 1.250 -0.016 9.50e-03 1.11e+04 2.93e+00 ... (remaining 10224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13457 1.53 - 3.07: 378 3.07 - 4.60: 80 4.60 - 6.14: 23 6.14 - 7.67: 11 Bond angle restraints: 13949 Sorted by residual: angle pdb=" N PRO B1101 " pdb=" CA PRO B1101 " pdb=" CB PRO B1101 " ideal model delta sigma weight residual 103.25 109.75 -6.50 1.05e+00 9.07e-01 3.83e+01 angle pdb=" N THR B 541 " pdb=" CA THR B 541 " pdb=" C THR B 541 " ideal model delta sigma weight residual 114.64 107.04 7.60 1.52e+00 4.33e-01 2.50e+01 angle pdb=" N GLU B 848 " pdb=" CA GLU B 848 " pdb=" C GLU B 848 " ideal model delta sigma weight residual 114.56 108.30 6.26 1.27e+00 6.20e-01 2.43e+01 angle pdb=" N ILE B 849 " pdb=" CA ILE B 849 " pdb=" C ILE B 849 " ideal model delta sigma weight residual 111.91 108.33 3.58 8.90e-01 1.26e+00 1.62e+01 angle pdb=" CA GLU A1118 " pdb=" CB GLU A1118 " pdb=" CG GLU A1118 " ideal model delta sigma weight residual 114.10 121.24 -7.14 2.00e+00 2.50e-01 1.27e+01 ... (remaining 13944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 5545 16.10 - 32.21: 468 32.21 - 48.31: 115 48.31 - 64.41: 21 64.41 - 80.51: 12 Dihedral angle restraints: 6161 sinusoidal: 2345 harmonic: 3816 Sorted by residual: dihedral pdb=" CA ALA B 807 " pdb=" C ALA B 807 " pdb=" N PRO B 808 " pdb=" CA PRO B 808 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA PHE B 846 " pdb=" C PHE B 846 " pdb=" N GLU B 847 " pdb=" CA GLU B 847 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA SER A 546 " pdb=" C SER A 546 " pdb=" N GLY A 547 " pdb=" CA GLY A 547 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1307 0.057 - 0.113: 265 0.113 - 0.170: 30 0.170 - 0.227: 4 0.227 - 0.284: 1 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CA PRO B1101 " pdb=" N PRO B1101 " pdb=" C PRO B1101 " pdb=" CB PRO B1101 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB VAL A 866 " pdb=" CA VAL A 866 " pdb=" CG1 VAL A 866 " pdb=" CG2 VAL A 866 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR B 867 " pdb=" N THR B 867 " pdb=" C THR B 867 " pdb=" CB THR B 867 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1604 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN A1202 " -0.026 2.00e-02 2.50e+03 1.01e-01 1.53e+02 pdb=" C4 BTN A1202 " -0.026 2.00e-02 2.50e+03 pdb=" C5 BTN A1202 " 0.152 2.00e-02 2.50e+03 pdb=" N1 BTN A1202 " -0.162 2.00e-02 2.50e+03 pdb=" N2 BTN A1202 " -0.034 2.00e-02 2.50e+03 pdb=" O3 BTN A1202 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 807 " -0.062 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO B 808 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 808 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 808 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 748 " 0.028 2.00e-02 2.50e+03 2.37e-02 1.41e+01 pdb=" CG TRP B 748 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 748 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 748 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 748 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 748 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 748 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 748 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 748 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 748 " 0.002 2.00e-02 2.50e+03 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3066 2.84 - 3.36: 9019 3.36 - 3.87: 15309 3.87 - 4.39: 16927 4.39 - 4.90: 30092 Nonbonded interactions: 74413 Sorted by model distance: nonbonded pdb=" NZ LYS A 703 " pdb="ZN ZN A1201 " model vdw 2.325 2.310 nonbonded pdb=" NZ LYS A1093 " pdb=" O11 BTN A1202 " model vdw 2.332 3.120 nonbonded pdb=" O SER A 965 " pdb=" OE1 GLU A 969 " model vdw 2.426 3.040 nonbonded pdb=" O SER B1112 " pdb=" OD1 ASP B1113 " model vdw 2.466 3.040 nonbonded pdb=" OD1 ASP A 639 " pdb=" N ALA A 640 " model vdw 2.474 3.120 ... (remaining 74408 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 457 through 1039 or (resid 1040 and (name N or name CA or \ name C or name O or name CB )) or resid 1041 through 1100 or (resid 1101 and (na \ me N or name CA or name C or name O or name CB )) or resid 1102 through 1106 or \ (resid 1107 through 1108 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1109 through 1127)) selection = (chain 'B' and (resid 457 through 494 or (resid 495 through 497 and (name N or n \ ame CA or name C or name O or name CB )) or resid 498 through 515 or (resid 516 \ and (name N or name CA or name C or name O or name CB )) or resid 517 through 11 \ 27)) } 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: 97.700 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10230 Z= 0.142 Angle : 0.664 7.670 13949 Z= 0.351 Chirality : 0.046 0.284 1607 Planarity : 0.006 0.101 1850 Dihedral : 13.442 80.515 3721 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.22 % Favored : 91.63 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % 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: -1.64 (0.23), residues: 1338 helix: -0.09 (0.24), residues: 515 sheet: 0.30 (0.44), residues: 140 loop : -2.26 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B 748 HIS 0.005 0.001 HIS A 973 PHE 0.010 0.001 PHE B 846 TYR 0.015 0.001 TYR A 680 ARG 0.013 0.001 ARG B1035 Details of bonding type rmsd hydrogen bonds : bond 0.20023 ( 360) hydrogen bonds : angle 7.29392 ( 1020) metal coordination : bond 0.00367 ( 1) covalent geometry : bond 0.00298 (10229) covalent geometry : angle 0.66351 (13949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1084 GLN cc_start: 0.7097 (tt0) cc_final: 0.6737 (tp-100) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.3114 time to fit residues: 57.4260 Evaluate side-chains 58 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN A 740 GLN B 642 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.105452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080536 restraints weight = 22487.327| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.56 r_work: 0.3141 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10230 Z= 0.127 Angle : 0.611 7.179 13949 Z= 0.310 Chirality : 0.045 0.181 1607 Planarity : 0.005 0.081 1850 Dihedral : 4.882 50.355 1487 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.55 % Favored : 92.15 % Rotamer: Outliers : 0.88 % Allowed : 6.86 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1338 helix: 0.15 (0.24), residues: 530 sheet: 0.24 (0.44), residues: 140 loop : -2.20 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 748 HIS 0.010 0.001 HIS B 732 PHE 0.016 0.001 PHE A1066 TYR 0.016 0.001 TYR A 684 ARG 0.006 0.001 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 360) hydrogen bonds : angle 5.04869 ( 1020) metal coordination : bond 0.00194 ( 1) covalent geometry : bond 0.00294 (10229) covalent geometry : angle 0.61073 (13949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7837 (t0) cc_final: 0.7365 (t0) REVERT: A 901 GLU cc_start: 0.7177 (tp30) cc_final: 0.6841 (tp30) REVERT: A 934 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8306 (tpp80) REVERT: A 1001 LYS cc_start: 0.7944 (tptt) cc_final: 0.7670 (tptt) REVERT: A 1040 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8597 (tpt170) REVERT: B 847 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7720 (pp20) REVERT: B 1027 MET cc_start: 0.8309 (mtm) cc_final: 0.7553 (mtm) REVERT: B 1092 MET cc_start: 0.5818 (tpp) cc_final: 0.5567 (tpp) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.2290 time to fit residues: 23.0894 Evaluate side-chains 59 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1066 PHE Chi-restraints excluded: chain B residue 568 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN B 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077321 restraints weight = 22890.604| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.55 r_work: 0.3065 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10230 Z= 0.145 Angle : 0.604 7.602 13949 Z= 0.306 Chirality : 0.045 0.172 1607 Planarity : 0.005 0.077 1850 Dihedral : 4.661 37.072 1487 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.15 % Favored : 91.55 % Rotamer: Outliers : 1.67 % Allowed : 9.41 % Favored : 88.92 % 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: -1.29 (0.23), residues: 1338 helix: 0.35 (0.24), residues: 527 sheet: 0.13 (0.46), residues: 130 loop : -2.12 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 748 HIS 0.007 0.001 HIS B 732 PHE 0.014 0.001 PHE A1066 TYR 0.017 0.001 TYR A 684 ARG 0.007 0.000 ARG B1042 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 360) hydrogen bonds : angle 4.65584 ( 1020) metal coordination : bond 0.00137 ( 1) covalent geometry : bond 0.00344 (10229) covalent geometry : angle 0.60371 (13949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7949 (t0) cc_final: 0.7406 (t0) REVERT: A 548 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8190 (pp) REVERT: A 1001 LYS cc_start: 0.7911 (tptt) cc_final: 0.7610 (tptt) REVERT: A 1040 ARG cc_start: 0.8961 (ttm170) cc_final: 0.8629 (tpt170) REVERT: B 586 GLU cc_start: 0.7961 (mp0) cc_final: 0.7746 (mp0) REVERT: B 997 GLU cc_start: 0.8450 (pm20) cc_final: 0.7709 (tm-30) REVERT: B 1023 MET cc_start: 0.7235 (tpp) cc_final: 0.6609 (mmm) REVERT: B 1027 MET cc_start: 0.8270 (mtm) cc_final: 0.7579 (mtm) outliers start: 17 outliers final: 12 residues processed: 63 average time/residue: 0.2449 time to fit residues: 22.5022 Evaluate side-chains 56 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1066 PHE Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 95 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.103801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.078760 restraints weight = 22692.946| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.59 r_work: 0.3101 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10230 Z= 0.106 Angle : 0.552 8.779 13949 Z= 0.278 Chirality : 0.043 0.175 1607 Planarity : 0.005 0.073 1850 Dihedral : 4.396 32.360 1487 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.47 % Favored : 92.30 % Rotamer: Outliers : 1.18 % Allowed : 10.59 % Favored : 88.24 % 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: -1.11 (0.23), residues: 1338 helix: 0.54 (0.24), residues: 527 sheet: 0.21 (0.46), residues: 130 loop : -2.05 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 748 HIS 0.007 0.001 HIS B 732 PHE 0.012 0.001 PHE A1066 TYR 0.014 0.001 TYR A 684 ARG 0.003 0.000 ARG B1042 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 360) hydrogen bonds : angle 4.44343 ( 1020) metal coordination : bond 0.00044 ( 1) covalent geometry : bond 0.00250 (10229) covalent geometry : angle 0.55198 (13949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7895 (t0) cc_final: 0.7275 (t0) REVERT: A 1001 LYS cc_start: 0.7858 (tptt) cc_final: 0.7657 (tptt) REVERT: A 1040 ARG cc_start: 0.8985 (ttm170) cc_final: 0.8654 (tpt170) REVERT: B 586 GLU cc_start: 0.7996 (mp0) cc_final: 0.7725 (mp0) REVERT: B 997 GLU cc_start: 0.8455 (pm20) cc_final: 0.8238 (pm20) REVERT: B 1023 MET cc_start: 0.7462 (tpp) cc_final: 0.6713 (mmm) REVERT: B 1027 MET cc_start: 0.8259 (mtm) cc_final: 0.7663 (mtm) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.2343 time to fit residues: 20.5097 Evaluate side-chains 56 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1066 PHE Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.103313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078286 restraints weight = 22680.963| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.58 r_work: 0.3089 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10230 Z= 0.111 Angle : 0.546 7.518 13949 Z= 0.275 Chirality : 0.043 0.168 1607 Planarity : 0.005 0.069 1850 Dihedral : 4.257 27.748 1487 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 1.96 % Allowed : 11.67 % Favored : 86.37 % 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: -1.01 (0.24), residues: 1338 helix: 0.67 (0.25), residues: 524 sheet: 0.21 (0.46), residues: 130 loop : -2.01 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 748 HIS 0.007 0.001 HIS B 732 PHE 0.012 0.001 PHE A1066 TYR 0.015 0.001 TYR A 684 ARG 0.005 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 360) hydrogen bonds : angle 4.39302 ( 1020) metal coordination : bond 0.00087 ( 1) covalent geometry : bond 0.00262 (10229) covalent geometry : angle 0.54640 (13949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7949 (t0) cc_final: 0.7314 (t0) REVERT: A 934 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8337 (mmm160) REVERT: A 1001 LYS cc_start: 0.7840 (tptt) cc_final: 0.7600 (tptt) REVERT: A 1040 ARG cc_start: 0.9017 (ttm170) cc_final: 0.8652 (tpt170) REVERT: A 1118 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: B 800 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8074 (tp30) REVERT: B 863 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7647 (pp) REVERT: B 1023 MET cc_start: 0.7491 (tpp) cc_final: 0.6863 (mmm) REVERT: B 1027 MET cc_start: 0.8245 (mtm) cc_final: 0.7616 (mtm) outliers start: 20 outliers final: 15 residues processed: 61 average time/residue: 0.2078 time to fit residues: 19.3381 Evaluate side-chains 59 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1031 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079058 restraints weight = 22826.878| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.48 r_work: 0.3116 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10230 Z= 0.125 Angle : 0.556 9.159 13949 Z= 0.282 Chirality : 0.044 0.169 1607 Planarity : 0.005 0.070 1850 Dihedral : 4.304 28.383 1487 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.70 % Favored : 92.08 % Rotamer: Outliers : 2.06 % Allowed : 12.06 % Favored : 85.88 % 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: -1.01 (0.24), residues: 1338 helix: 0.67 (0.24), residues: 524 sheet: 0.21 (0.47), residues: 130 loop : -2.02 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 748 HIS 0.006 0.001 HIS B 732 PHE 0.007 0.001 PHE A 635 TYR 0.015 0.001 TYR A 684 ARG 0.003 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 360) hydrogen bonds : angle 4.37711 ( 1020) metal coordination : bond 0.00104 ( 1) covalent geometry : bond 0.00298 (10229) covalent geometry : angle 0.55588 (13949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.8038 (t0) cc_final: 0.7410 (t0) REVERT: A 548 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 1001 LYS cc_start: 0.7978 (tptt) cc_final: 0.7706 (tptt) REVERT: A 1040 ARG cc_start: 0.8942 (ttm170) cc_final: 0.8641 (tpt170) REVERT: B 863 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7901 (pp) REVERT: B 910 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: B 1023 MET cc_start: 0.7674 (tpp) cc_final: 0.7184 (mmm) REVERT: B 1027 MET cc_start: 0.8417 (mtm) cc_final: 0.7748 (mtm) outliers start: 21 outliers final: 16 residues processed: 57 average time/residue: 0.2154 time to fit residues: 18.9555 Evaluate side-chains 58 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.103936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079732 restraints weight = 22758.881| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.37 r_work: 0.3131 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10230 Z= 0.113 Angle : 0.548 9.326 13949 Z= 0.276 Chirality : 0.043 0.167 1607 Planarity : 0.005 0.068 1850 Dihedral : 4.199 29.205 1487 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.92 % Favored : 91.85 % Rotamer: Outliers : 2.25 % Allowed : 12.16 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1338 helix: 0.72 (0.24), residues: 526 sheet: 0.26 (0.47), residues: 130 loop : -1.95 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 748 HIS 0.006 0.001 HIS B 732 PHE 0.009 0.001 PHE A1066 TYR 0.014 0.001 TYR A 684 ARG 0.004 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 360) hydrogen bonds : angle 4.28810 ( 1020) metal coordination : bond 0.00023 ( 1) covalent geometry : bond 0.00270 (10229) covalent geometry : angle 0.54771 (13949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 ASN cc_start: 0.8114 (t0) cc_final: 0.7850 (t0) REVERT: A 493 ASP cc_start: 0.8054 (t0) cc_final: 0.7452 (t0) REVERT: A 934 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8337 (mmm160) REVERT: A 1001 LYS cc_start: 0.7979 (tptt) cc_final: 0.7677 (tptt) REVERT: A 1118 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: B 863 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7936 (pp) REVERT: B 1023 MET cc_start: 0.7648 (tpp) cc_final: 0.7127 (mmm) REVERT: B 1027 MET cc_start: 0.8425 (mtm) cc_final: 0.7722 (mtm) REVERT: B 1039 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8540 (t) outliers start: 23 outliers final: 17 residues processed: 61 average time/residue: 0.2219 time to fit residues: 20.4236 Evaluate side-chains 61 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.103152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078752 restraints weight = 23155.409| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.47 r_work: 0.3104 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10230 Z= 0.122 Angle : 0.553 9.786 13949 Z= 0.279 Chirality : 0.044 0.169 1607 Planarity : 0.005 0.069 1850 Dihedral : 4.221 29.512 1487 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.92 % Favored : 91.85 % Rotamer: Outliers : 2.35 % Allowed : 12.06 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1338 helix: 0.75 (0.24), residues: 525 sheet: 0.22 (0.47), residues: 130 loop : -1.94 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 748 HIS 0.006 0.001 HIS B 732 PHE 0.007 0.001 PHE A 635 TYR 0.015 0.001 TYR A 684 ARG 0.003 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 360) hydrogen bonds : angle 4.31646 ( 1020) metal coordination : bond 0.00088 ( 1) covalent geometry : bond 0.00292 (10229) covalent geometry : angle 0.55321 (13949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 ASN cc_start: 0.8128 (t0) cc_final: 0.7861 (t0) REVERT: A 493 ASP cc_start: 0.8112 (t0) cc_final: 0.7512 (t0) REVERT: A 700 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 846 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: A 934 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8448 (mmm160) REVERT: A 1118 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: B 863 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 1023 MET cc_start: 0.7687 (tpp) cc_final: 0.7111 (mmm) REVERT: B 1027 MET cc_start: 0.8417 (mtm) cc_final: 0.7713 (mtm) REVERT: B 1039 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8498 (t) outliers start: 24 outliers final: 17 residues processed: 61 average time/residue: 0.1955 time to fit residues: 18.7672 Evaluate side-chains 62 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.102826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078436 restraints weight = 22978.746| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.46 r_work: 0.3115 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10230 Z= 0.123 Angle : 0.567 11.595 13949 Z= 0.284 Chirality : 0.044 0.168 1607 Planarity : 0.005 0.068 1850 Dihedral : 4.225 29.878 1487 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.85 % Favored : 91.93 % Rotamer: Outliers : 2.35 % Allowed : 12.25 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.24), residues: 1338 helix: 0.78 (0.24), residues: 526 sheet: 0.25 (0.47), residues: 130 loop : -1.90 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 748 HIS 0.006 0.001 HIS B 732 PHE 0.007 0.001 PHE A 635 TYR 0.015 0.001 TYR A 684 ARG 0.004 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 360) hydrogen bonds : angle 4.29290 ( 1020) metal coordination : bond 0.00083 ( 1) covalent geometry : bond 0.00295 (10229) covalent geometry : angle 0.56678 (13949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 ASN cc_start: 0.8141 (t0) cc_final: 0.7871 (t0) REVERT: A 493 ASP cc_start: 0.8073 (t0) cc_final: 0.7498 (t0) REVERT: A 700 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 846 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: A 934 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8380 (mmm160) REVERT: A 1118 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7531 (pt0) REVERT: B 586 GLU cc_start: 0.8054 (mp0) cc_final: 0.7810 (mp0) REVERT: B 863 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7948 (pp) REVERT: B 1023 MET cc_start: 0.7728 (tpp) cc_final: 0.7151 (mmm) REVERT: B 1027 MET cc_start: 0.8412 (mtm) cc_final: 0.7662 (mtm) outliers start: 24 outliers final: 17 residues processed: 63 average time/residue: 0.2000 time to fit residues: 19.3326 Evaluate side-chains 63 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.103503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079261 restraints weight = 23117.294| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.46 r_work: 0.3103 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10230 Z= 0.112 Angle : 0.555 10.114 13949 Z= 0.278 Chirality : 0.043 0.166 1607 Planarity : 0.005 0.068 1850 Dihedral : 4.157 29.908 1487 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.55 % Favored : 92.23 % Rotamer: Outliers : 2.06 % Allowed : 12.65 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1338 helix: 0.85 (0.24), residues: 526 sheet: 0.32 (0.45), residues: 138 loop : -1.84 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 748 HIS 0.006 0.001 HIS B 732 PHE 0.006 0.001 PHE A 635 TYR 0.014 0.001 TYR A 684 ARG 0.003 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 360) hydrogen bonds : angle 4.23804 ( 1020) metal coordination : bond 0.00063 ( 1) covalent geometry : bond 0.00269 (10229) covalent geometry : angle 0.55527 (13949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 ASN cc_start: 0.8140 (t0) cc_final: 0.7866 (t0) REVERT: A 493 ASP cc_start: 0.8115 (t0) cc_final: 0.7530 (t0) REVERT: A 700 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 846 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: A 934 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8464 (mmm160) REVERT: A 1023 MET cc_start: 0.7478 (tpp) cc_final: 0.6923 (tpp) REVERT: A 1118 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: B 586 GLU cc_start: 0.8061 (mp0) cc_final: 0.7827 (mp0) REVERT: B 863 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7935 (pp) REVERT: B 1023 MET cc_start: 0.7738 (tpp) cc_final: 0.7140 (mmm) REVERT: B 1027 MET cc_start: 0.8383 (mtm) cc_final: 0.7671 (mtm) outliers start: 21 outliers final: 17 residues processed: 60 average time/residue: 0.1947 time to fit residues: 18.2332 Evaluate side-chains 62 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1075 CYS Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 994 GLN Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 94 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.106344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080952 restraints weight = 22609.749| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.56 r_work: 0.3137 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10230 Z= 0.093 Angle : 0.535 10.050 13949 Z= 0.267 Chirality : 0.043 0.177 1607 Planarity : 0.004 0.066 1850 Dihedral : 3.978 30.820 1487 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.77 % Favored : 92.00 % Rotamer: Outliers : 1.86 % Allowed : 13.04 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1338 helix: 0.92 (0.24), residues: 533 sheet: 0.46 (0.45), residues: 138 loop : -1.78 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 748 HIS 0.006 0.001 HIS B 732 PHE 0.006 0.001 PHE A 635 TYR 0.013 0.001 TYR A 684 ARG 0.003 0.000 ARG B 999 Details of bonding type rmsd hydrogen bonds : bond 0.02621 ( 360) hydrogen bonds : angle 4.11228 ( 1020) metal coordination : bond 0.00018 ( 1) covalent geometry : bond 0.00215 (10229) covalent geometry : angle 0.53525 (13949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.47 seconds wall clock time: 78 minutes 55.41 seconds (4735.41 seconds total)