Starting phenix.real_space_refine on Wed Sep 17 17:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ueq_64089/09_2025/9ueq_64089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ueq_64089/09_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_64089/09_2025/9ueq_64089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ueq_64089/09_2025/9ueq_64089.map" model { file = "/net/cci-nas-00/data/ceres_data/9ueq_64089/09_2025/9ueq_64089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ueq_64089/09_2025/9ueq_64089.cif" } resolution = 3.2 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 2} 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: 2.30, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 312.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.41 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: 1.66 Time building geometry restraints manager: 1.09 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- 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 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: -1.64 (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 ARG 0.013 0.001 ARG B1035 TYR 0.015 0.001 TYR A 680 PHE 0.010 0.001 PHE B 846 TRP 0.064 0.003 TRP B 748 HIS 0.005 0.001 HIS A 973 Details of bonding type rmsd covalent geometry : bond 0.00298 (10229) covalent geometry : angle 0.66351 (13949) hydrogen bonds : bond 0.20023 ( 360) hydrogen bonds : angle 7.29392 ( 1020) metal coordination : bond 0.00367 ( 1) *********************** 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 : 0.360 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: 0.1290 time to fit residues: 23.5298 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076927 restraints weight = 22920.104| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.60 r_work: 0.3068 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10230 Z= 0.193 Angle : 0.665 7.539 13949 Z= 0.341 Chirality : 0.047 0.188 1607 Planarity : 0.006 0.086 1850 Dihedral : 5.033 46.587 1487 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.47 % Favored : 92.23 % Rotamer: Outliers : 0.98 % Allowed : 8.14 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1338 helix: -0.00 (0.24), residues: 533 sheet: 0.06 (0.46), residues: 130 loop : -2.22 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1056 TYR 0.019 0.001 TYR A 684 PHE 0.019 0.002 PHE A1066 TRP 0.051 0.002 TRP B 748 HIS 0.008 0.002 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00462 (10229) covalent geometry : angle 0.66529 (13949) hydrogen bonds : bond 0.05113 ( 360) hydrogen bonds : angle 5.17764 ( 1020) metal coordination : bond 0.00389 ( 1) *********************** 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 64 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7907 (t0) cc_final: 0.7506 (t0) REVERT: A 548 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 1040 ARG cc_start: 0.8979 (ttm170) cc_final: 0.8571 (tpt170) REVERT: B 847 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7745 (pp20) REVERT: B 910 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: B 1027 MET cc_start: 0.8315 (mtm) cc_final: 0.7563 (mtm) REVERT: B 1092 MET cc_start: 0.5861 (tpp) cc_final: 0.5614 (tpp) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.1109 time to fit residues: 9.4463 Evaluate side-chains 55 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 910 GLU Chi-restraints excluded: chain B residue 1117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 133 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.077164 restraints weight = 22803.817| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.58 r_work: 0.3070 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2336 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= 0.133 Angle : 0.588 7.356 13949 Z= 0.298 Chirality : 0.044 0.172 1607 Planarity : 0.005 0.079 1850 Dihedral : 4.663 38.356 1487 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.77 % Favored : 91.93 % Rotamer: Outliers : 1.67 % Allowed : 9.90 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.39 (0.23), residues: 1338 helix: 0.25 (0.24), residues: 528 sheet: 0.14 (0.46), residues: 130 loop : -2.18 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 896 TYR 0.015 0.001 TYR A 684 PHE 0.013 0.001 PHE A1066 TRP 0.036 0.002 TRP B 748 HIS 0.007 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00317 (10229) covalent geometry : angle 0.58763 (13949) hydrogen bonds : bond 0.03962 ( 360) hydrogen bonds : angle 4.70267 ( 1020) metal coordination : bond 0.00035 ( 1) *********************** 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 69 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7952 (t0) cc_final: 0.7433 (t0) REVERT: A 1001 LYS cc_start: 0.7979 (tptt) cc_final: 0.7547 (tptt) REVERT: A 1040 ARG cc_start: 0.8990 (ttm170) cc_final: 0.8635 (tpt170) REVERT: B 910 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8303 (pt0) REVERT: B 1023 MET cc_start: 0.7220 (tpp) cc_final: 0.6584 (mmm) REVERT: B 1027 MET cc_start: 0.8309 (mtm) cc_final: 0.7630 (mtm) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.1092 time to fit residues: 10.3074 Evaluate side-chains 57 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 1121 ASP Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 994 GLN 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 131 optimal weight: 9.9990 chunk 25 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 4 optimal weight: 0.0060 chunk 36 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080267 restraints weight = 23035.225| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.63 r_work: 0.3130 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10230 Z= 0.093 Angle : 0.534 7.223 13949 Z= 0.269 Chirality : 0.042 0.165 1607 Planarity : 0.005 0.069 1850 Dihedral : 4.258 31.943 1487 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.40 % Favored : 92.38 % Rotamer: Outliers : 1.47 % Allowed : 10.39 % Favored : 88.14 % 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: -1.04 (0.24), residues: 1338 helix: 0.56 (0.24), residues: 524 sheet: 0.36 (0.45), residues: 140 loop : -2.02 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 896 TYR 0.013 0.001 TYR A 684 PHE 0.011 0.001 PHE A1066 TRP 0.023 0.001 TRP B 748 HIS 0.007 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00209 (10229) covalent geometry : angle 0.53375 (13949) hydrogen bonds : bond 0.02710 ( 360) hydrogen bonds : angle 4.39322 ( 1020) metal coordination : bond 0.00001 ( 1) *********************** 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 71 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7903 (t0) cc_final: 0.7286 (t0) REVERT: A 934 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8338 (mmm160) REVERT: A 1001 LYS cc_start: 0.7854 (tptt) cc_final: 0.7631 (tptt) REVERT: A 1040 ARG cc_start: 0.8993 (ttm170) cc_final: 0.8646 (tpt170) REVERT: B 800 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8017 (tp30) REVERT: B 910 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: B 1023 MET cc_start: 0.7502 (tpp) cc_final: 0.6809 (mmm) REVERT: B 1027 MET cc_start: 0.8259 (mtm) cc_final: 0.7685 (mtm) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1095 time to fit residues: 10.8089 Evaluate side-chains 60 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 969 GLU Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1066 PHE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 994 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 85 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.103152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078156 restraints weight = 22908.958| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.60 r_work: 0.3096 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10230 Z= 0.108 Angle : 0.543 8.016 13949 Z= 0.272 Chirality : 0.043 0.164 1607 Planarity : 0.005 0.068 1850 Dihedral : 4.191 27.240 1487 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 1.76 % Allowed : 11.67 % Favored : 86.57 % 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: -0.97 (0.24), residues: 1338 helix: 0.68 (0.25), residues: 524 sheet: 0.29 (0.47), residues: 130 loop : -1.99 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1042 TYR 0.014 0.001 TYR A 684 PHE 0.012 0.001 PHE A1066 TRP 0.024 0.001 TRP B 748 HIS 0.007 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00256 (10229) covalent geometry : angle 0.54323 (13949) hydrogen bonds : bond 0.03146 ( 360) hydrogen bonds : angle 4.34140 ( 1020) metal coordination : bond 0.00029 ( 1) *********************** 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 64 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7945 (t0) cc_final: 0.7306 (t0) REVERT: A 1001 LYS cc_start: 0.7789 (tptt) cc_final: 0.7533 (tptt) REVERT: A 1040 ARG cc_start: 0.9015 (ttm170) cc_final: 0.8647 (tpt170) REVERT: B 910 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: B 1023 MET cc_start: 0.7467 (tpp) cc_final: 0.6852 (mmm) REVERT: B 1027 MET cc_start: 0.8210 (mtm) cc_final: 0.7602 (mtm) outliers start: 18 outliers final: 13 residues processed: 60 average time/residue: 0.1058 time to fit residues: 9.2418 Evaluate side-chains 58 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 731 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 1048 VAL 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 888 ASP Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 994 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 0.0030 chunk 46 optimal weight: 0.0270 chunk 129 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 0.5248 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.105862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081241 restraints weight = 22522.692| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.39 r_work: 0.3165 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2774 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= 0.097 Angle : 0.534 8.427 13949 Z= 0.268 Chirality : 0.043 0.177 1607 Planarity : 0.004 0.066 1850 Dihedral : 4.095 28.018 1487 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.77 % Favored : 92.00 % Rotamer: Outliers : 2.16 % Allowed : 11.57 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.89 (0.24), residues: 1338 helix: 0.71 (0.24), residues: 531 sheet: 0.37 (0.47), residues: 130 loop : -1.93 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1042 TYR 0.013 0.001 TYR A 684 PHE 0.006 0.001 PHE A 635 TRP 0.022 0.001 TRP B 748 HIS 0.006 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00226 (10229) covalent geometry : angle 0.53360 (13949) hydrogen bonds : bond 0.02840 ( 360) hydrogen bonds : angle 4.21042 ( 1020) metal coordination : bond 0.00024 ( 1) *********************** 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 70 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7911 (t0) cc_final: 0.7260 (t0) REVERT: A 1001 LYS cc_start: 0.7937 (tptt) cc_final: 0.7652 (tptt) REVERT: A 1040 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8632 (tpt170) REVERT: B 910 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: B 1023 MET cc_start: 0.7644 (tpp) cc_final: 0.6996 (mmm) REVERT: B 1027 MET cc_start: 0.8382 (mtm) cc_final: 0.7716 (mtm) outliers start: 22 outliers final: 15 residues processed: 66 average time/residue: 0.0955 time to fit residues: 9.5040 Evaluate side-chains 62 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 1121 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 568 TRP 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 1039 VAL Chi-restraints excluded: chain B residue 1088 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 0.0270 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- 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 = 0.103113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077875 restraints weight = 23125.244| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.46 r_work: 0.3106 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10230 Z= 0.143 Angle : 0.584 9.021 13949 Z= 0.293 Chirality : 0.044 0.171 1607 Planarity : 0.005 0.068 1850 Dihedral : 4.249 28.889 1487 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.45 % Favored : 91.33 % Rotamer: Outliers : 2.06 % Allowed : 12.35 % 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 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: -0.95 (0.24), residues: 1338 helix: 0.67 (0.24), residues: 526 sheet: 0.26 (0.47), residues: 130 loop : -1.94 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 934 TYR 0.015 0.001 TYR A 684 PHE 0.007 0.001 PHE A 635 TRP 0.027 0.001 TRP B 748 HIS 0.006 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00343 (10229) covalent geometry : angle 0.58429 (13949) hydrogen bonds : bond 0.03869 ( 360) hydrogen bonds : angle 4.37393 ( 1020) metal coordination : bond 0.00092 ( 1) *********************** 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 67 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.8069 (t0) cc_final: 0.7438 (t0) REVERT: A 1001 LYS cc_start: 0.7958 (tptt) cc_final: 0.7665 (tptt) REVERT: A 1040 ARG cc_start: 0.8942 (ttm170) cc_final: 0.8730 (tpt170) REVERT: B 910 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: B 1023 MET cc_start: 0.7635 (tpp) cc_final: 0.7091 (mmm) REVERT: B 1027 MET cc_start: 0.8387 (mtm) cc_final: 0.7713 (mtm) outliers start: 21 outliers final: 16 residues processed: 64 average time/residue: 0.1035 time to fit residues: 9.6519 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 : 0.396 ------------------------------------------------------------------------------- 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 731 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 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 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 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 71 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 118 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 0.0030 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.104719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080497 restraints weight = 22735.204| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.42 r_work: 0.3147 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2979 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= 0.098 Angle : 0.539 9.838 13949 Z= 0.271 Chirality : 0.043 0.168 1607 Planarity : 0.005 0.070 1850 Dihedral : 4.097 29.846 1487 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.77 % Favored : 92.00 % Rotamer: Outliers : 2.25 % Allowed : 11.86 % 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 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: -0.81 (0.24), residues: 1338 helix: 0.81 (0.24), residues: 526 sheet: 0.31 (0.47), residues: 130 loop : -1.88 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 934 TYR 0.013 0.001 TYR A 684 PHE 0.006 0.001 PHE A 635 TRP 0.021 0.001 TRP B 748 HIS 0.006 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00228 (10229) covalent geometry : angle 0.53938 (13949) hydrogen bonds : bond 0.02913 ( 360) hydrogen bonds : angle 4.20042 ( 1020) metal coordination : bond 0.00005 ( 1) *********************** 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 72 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.7990 (t0) cc_final: 0.7354 (t0) REVERT: A 1001 LYS cc_start: 0.7939 (tptt) cc_final: 0.7629 (tptt) REVERT: A 1040 ARG cc_start: 0.8947 (ttm170) cc_final: 0.8626 (tpt170) REVERT: A 1118 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: B 910 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: B 997 GLU cc_start: 0.8203 (pm20) cc_final: 0.7639 (tm-30) REVERT: B 1023 MET cc_start: 0.7661 (tpp) cc_final: 0.7008 (mmm) REVERT: B 1027 MET cc_start: 0.8368 (mtm) cc_final: 0.7676 (mtm) outliers start: 23 outliers final: 18 residues processed: 67 average time/residue: 0.0988 time to fit residues: 9.6006 Evaluate side-chains 67 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 846 PHE 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 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 28 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.103651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079114 restraints weight = 23068.285| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.48 r_work: 0.3111 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10230 Z= 0.124 Angle : 0.565 9.414 13949 Z= 0.284 Chirality : 0.044 0.170 1607 Planarity : 0.005 0.070 1850 Dihedral : 4.164 29.814 1487 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 2.06 % Allowed : 12.45 % Favored : 85.49 % 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: -0.78 (0.24), residues: 1338 helix: 0.81 (0.24), residues: 527 sheet: 0.24 (0.45), residues: 140 loop : -1.85 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 934 TYR 0.014 0.001 TYR A 684 PHE 0.007 0.001 PHE A 635 TRP 0.024 0.001 TRP B 748 HIS 0.006 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00298 (10229) covalent geometry : angle 0.56490 (13949) hydrogen bonds : bond 0.03473 ( 360) hydrogen bonds : angle 4.27192 ( 1020) metal coordination : bond 0.00055 ( 1) *********************** 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 65 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.8101 (t0) cc_final: 0.7497 (t0) REVERT: A 1040 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8706 (tpt170) REVERT: A 1118 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: B 910 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: B 997 GLU cc_start: 0.8305 (pm20) cc_final: 0.7710 (tm-30) REVERT: B 1023 MET cc_start: 0.7676 (tpp) cc_final: 0.7111 (mmm) REVERT: B 1027 MET cc_start: 0.8378 (mtm) cc_final: 0.7670 (mtm) outliers start: 21 outliers final: 17 residues processed: 63 average time/residue: 0.1008 time to fit residues: 9.4181 Evaluate side-chains 61 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 1039 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 131 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.101852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077365 restraints weight = 22556.558| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.33 r_work: 0.3076 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10230 Z= 0.158 Angle : 0.608 9.311 13949 Z= 0.308 Chirality : 0.045 0.176 1607 Planarity : 0.005 0.072 1850 Dihedral : 4.432 30.203 1487 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.37 % Favored : 91.41 % Rotamer: Outliers : 1.96 % Allowed : 12.35 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1338 helix: 0.71 (0.24), residues: 524 sheet: 0.06 (0.45), residues: 140 loop : -1.93 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 934 TYR 0.015 0.001 TYR A 684 PHE 0.009 0.001 PHE A1066 TRP 0.027 0.001 TRP B 748 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00380 (10229) covalent geometry : angle 0.60796 (13949) hydrogen bonds : bond 0.04236 ( 360) hydrogen bonds : angle 4.47287 ( 1020) metal coordination : bond 0.00163 ( 1) ********************** 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 60 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 ASP cc_start: 0.8139 (t0) cc_final: 0.7592 (t0) REVERT: A 1040 ARG cc_start: 0.8994 (ttm170) cc_final: 0.8737 (tpt170) REVERT: A 1118 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: B 1023 MET cc_start: 0.7710 (tpp) cc_final: 0.7132 (mmm) REVERT: B 1027 MET cc_start: 0.8443 (mtm) cc_final: 0.7697 (mtm) outliers start: 20 outliers final: 17 residues processed: 58 average time/residue: 0.1069 time to fit residues: 9.1203 Evaluate side-chains 55 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 731 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 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 = 0.3686 r_free = 0.3686 target = 0.103324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078978 restraints weight = 22772.885| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.35 r_work: 0.3106 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10230 Z= 0.117 Angle : 0.579 9.658 13949 Z= 0.292 Chirality : 0.044 0.186 1607 Planarity : 0.005 0.070 1850 Dihedral : 4.256 30.268 1487 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.00 % Favored : 91.78 % Rotamer: Outliers : 1.86 % Allowed : 12.84 % 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 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: -0.79 (0.24), residues: 1338 helix: 0.81 (0.24), residues: 526 sheet: 0.13 (0.44), residues: 148 loop : -1.85 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 934 TYR 0.014 0.001 TYR A 684 PHE 0.007 0.001 PHE A1066 TRP 0.023 0.001 TRP B 748 HIS 0.006 0.001 HIS B 732 Details of bonding type rmsd covalent geometry : bond 0.00280 (10229) covalent geometry : angle 0.57887 (13949) hydrogen bonds : bond 0.03356 ( 360) hydrogen bonds : angle 4.34353 ( 1020) metal coordination : bond 0.00041 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.75 seconds wall clock time: 39 minutes 56.15 seconds (2396.15 seconds total)