Starting phenix.real_space_refine on Mon Sep 14 01:07:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y5m_72513/09_2026/9y5m_72513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y5m_72513/09_2026/9y5m_72513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y5m_72513/09_2026/9y5m_72513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y5m_72513/09_2026/9y5m_72513.map" model { file = "/net/cci-nas-00/data/ceres_data/9y5m_72513/09_2026/9y5m_72513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y5m_72513/09_2026/9y5m_72513.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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 P 12 5.49 5 S 120 5.16 5 C 16705 2.51 5 N 4538 2.21 5 O 5018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26393 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4429 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 542} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4304 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4447 Classifications: {'peptide': 569} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 543} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4307 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 528} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4444 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 543} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4300 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.12, per 1000 atoms: 0.23 Number of scatterers: 26393 At special positions: 0 Unit cell: (135.7, 141.45, 150.65, 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) S 120 16.00 P 12 15.00 O 5018 8.00 N 4538 7.00 C 16705 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: 2.14 Conformation dependent library (CDL) restraints added in 776.4 milliseconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 31 sheets defined 53.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 376 through 408 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.587A pdb=" N ILE A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.836A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.749A pdb=" N ILE A 574 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.699A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.330A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 4.350A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.663A pdb=" N ARG A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 738 through 741 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 922 through 923 No H-bonds generated for 'chain 'A' and resid 922 through 923' Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.746A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 412 through 425 removed outlier: 3.588A pdb=" N ALA B 416 " --> pdb=" O ASP B 412 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 425 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.773A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.641A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 530 through 541 removed outlier: 3.772A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 570 through 581 removed outlier: 4.277A pdb=" N ILE B 574 " --> pdb=" O PRO B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.043A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.650A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 removed outlier: 4.446A pdb=" N ALA B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 738 through 741 Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.788A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 944 " --> pdb=" O ARG B 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 407 removed outlier: 3.894A pdb=" N ARG C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 431 through 448 removed outlier: 3.856A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 570 through 581 removed outlier: 4.213A pdb=" N ILE C 574 " --> pdb=" O PRO C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.989A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 617 removed outlier: 4.489A pdb=" N ALA C 617 " --> pdb=" O PRO C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 682 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.907A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 408 Processing helix chain 'D' and resid 412 through 424 removed outlier: 4.143A pdb=" N ARG D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 removed outlier: 3.525A pdb=" N VAL D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.555A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 530 through 541 removed outlier: 3.759A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 570 through 581 removed outlier: 4.215A pdb=" N ILE D 574 " --> pdb=" O PRO D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 removed outlier: 3.984A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 602 through 611 removed outlier: 3.769A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 4.394A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.803A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 408 removed outlier: 4.210A pdb=" N ARG E 381 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 382 " --> pdb=" O ARG E 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 425 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.932A pdb=" N VAL E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 490 removed outlier: 3.783A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 530 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 570 through 581 removed outlier: 4.212A pdb=" N ILE E 574 " --> pdb=" O PRO E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 595 removed outlier: 3.777A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 592 through 595' Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.304A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 607 " --> pdb=" O PRO E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.118A pdb=" N ALA E 617 " --> pdb=" O PRO E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 653 removed outlier: 3.596A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 738 through 741 Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 853 through 855 No H-bonds generated for 'chain 'E' and resid 853 through 855' Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 905 Processing helix chain 'E' and resid 916 through 921 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.893A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 408 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.625A pdb=" N LEU F 425 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 446 removed outlier: 3.876A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.658A pdb=" N ILE F 468 " --> pdb=" O TRP F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 530 through 541 removed outlier: 3.723A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 570 through 581 removed outlier: 4.194A pdb=" N ILE F 574 " --> pdb=" O PRO F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 595 removed outlier: 3.728A pdb=" N ILE F 595 " --> pdb=" O VAL F 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 592 through 595' Processing helix chain 'F' and resid 602 through 611 removed outlier: 4.079A pdb=" N ALA F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 4.395A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 653 Processing helix chain 'F' and resid 662 through 673 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 742 through 747 Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 906 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.770A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 944 " --> pdb=" O ARG F 940 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.437A pdb=" N ILE A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR A 638 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 589 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 620 Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 691 Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 771 removed outlier: 6.095A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.846A pdb=" N ALA A 878 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA7, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.613A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 519 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA B 639 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 521 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.750A pdb=" N LYS B 690 " --> pdb=" O VAL B 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 799 through 803 removed outlier: 6.172A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS B 839 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET B 766 " --> pdb=" O MET B 879 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB2, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.698A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP C 590 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE C 547 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 587 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR C 638 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA C 639 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE C 521 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB4, first strand: chain 'C' and resid 689 through 691 removed outlier: 6.701A pdb=" N LYS C 690 " --> pdb=" O VAL C 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 799 through 803 removed outlier: 6.149A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET C 766 " --> pdb=" O MET C 879 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB7, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.714A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU D 519 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA D 639 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE D 521 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.725A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 765 through 771 removed outlier: 6.169A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 877 through 879 Processing sheet with id=AC2, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC3, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.746A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 619 through 620 Processing sheet with id=AC5, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.600A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 799 through 803 removed outlier: 6.097A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET E 766 " --> pdb=" O MET E 879 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AC8, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.643A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 619 through 620 Processing sheet with id=AD1, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.711A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 764 through 771 removed outlier: 6.257A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 877 through 879 Processing sheet with id=AD4, first strand: chain 'F' and resid 882 through 883 1302 hydrogen bonds defined for protein. 3819 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: 5.34 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4566 1.32 - 1.44: 6383 1.44 - 1.57: 15692 1.57 - 1.69: 18 1.69 - 1.81: 198 Bond restraints: 26857 Sorted by residual: bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C5 ADP C1001 " pdb=" C6 ADP C1001 " ideal model delta sigma weight residual 1.490 1.401 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C5 ADP B1001 " pdb=" C6 ADP B1001 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O1B ADP B1001 " pdb=" PB ADP B1001 " ideal model delta sigma weight residual 1.510 1.429 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 26852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 36146 3.27 - 6.55: 171 6.55 - 9.82: 19 9.82 - 13.10: 0 13.10 - 16.37: 1 Bond angle restraints: 36337 Sorted by residual: angle pdb=" PA ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PB ADP C1001 " ideal model delta sigma weight residual 120.50 136.87 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" CA GLY B 493 " pdb=" C GLY B 493 " pdb=" O GLY B 493 " ideal model delta sigma weight residual 119.06 113.53 5.53 1.12e+00 7.97e-01 2.44e+01 angle pdb=" CA HIS B 491 " pdb=" C HIS B 491 " pdb=" O HIS B 491 " ideal model delta sigma weight residual 121.40 116.13 5.27 1.13e+00 7.83e-01 2.18e+01 angle pdb=" N ASP B 758 " pdb=" CA ASP B 758 " pdb=" C ASP B 758 " ideal model delta sigma weight residual 111.36 106.47 4.89 1.09e+00 8.42e-01 2.02e+01 angle pdb=" N GLN F 399 " pdb=" CA GLN F 399 " pdb=" C GLN F 399 " ideal model delta sigma weight residual 111.07 106.36 4.71 1.07e+00 8.73e-01 1.94e+01 ... (remaining 36332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 16088 32.52 - 65.04: 292 65.04 - 97.56: 43 97.56 - 130.08: 1 130.08 - 162.59: 1 Dihedral angle restraints: 16425 sinusoidal: 6716 harmonic: 9709 Sorted by residual: dihedral pdb=" O1B ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PB ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sinusoidal sigma weight residual 300.00 137.40 162.59 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O2A ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PA ADP C1001 " pdb=" PB ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 47.94 -107.94 1 2.00e+01 2.50e-03 3.14e+01 dihedral pdb=" C5' ADP C1001 " pdb=" O5' ADP C1001 " pdb=" PA ADP C1001 " pdb=" O2A ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 -156.82 96.83 1 2.00e+01 2.50e-03 2.69e+01 ... (remaining 16422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3553 0.055 - 0.110: 504 0.110 - 0.164: 101 0.164 - 0.219: 5 0.219 - 0.274: 3 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CA LYS A 888 " pdb=" N LYS A 888 " pdb=" C LYS A 888 " pdb=" CB LYS A 888 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA VAL B 759 " pdb=" N VAL B 759 " pdb=" C VAL B 759 " pdb=" CB VAL B 759 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA VAL D 759 " pdb=" N VAL D 759 " pdb=" C VAL D 759 " pdb=" CB VAL D 759 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4163 not shown) Planarity restraints: 4658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 784 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C LEU B 784 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU B 784 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 785 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 482 " 0.203 9.50e-02 1.11e+02 9.09e-02 5.17e+00 pdb=" NE ARG E 482 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG E 482 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 482 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 482 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 667 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C LEU F 667 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU F 667 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA F 668 " 0.013 2.00e-02 2.50e+03 ... (remaining 4655 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2975 2.75 - 3.29: 26202 3.29 - 3.82: 42989 3.82 - 4.36: 54000 4.36 - 4.90: 92414 Nonbonded interactions: 218580 Sorted by model distance: nonbonded pdb=" O ASP A 415 " pdb=" OE1 GLU A 419 " model vdw 2.210 3.040 nonbonded pdb=" O ASP C 415 " pdb=" OE1 GLU C 419 " model vdw 2.213 3.040 nonbonded pdb=" O LEU B 610 " pdb=" ND2 ASN B 616 " model vdw 2.233 3.120 nonbonded pdb=" OD2 ASP D 554 " pdb=" OH TYR E 565 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 757 " pdb=" OG1 THR B 886 " model vdw 2.242 3.040 ... (remaining 218575 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 391 through 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 598 or (resid 599 and (name N or name CA or \ name C or name O or name CB )) or resid 600 through 649 or (resid 650 and (name \ N or name CA or name C or name O or name CB )) or resid 651 through 689 or (res \ id 690 and (name N or name CA or name C or name O or name CB )) or resid 691 thr \ ough 789 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 1001)) selection = (chain 'B' and ((resid 391 through 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 649 or (resid 650 and (name N or name CA or \ name C or name O or name CB )) or resid 651 through 685 or (resid 686 and (name \ N or name CA or name C or name O or name CB )) or resid 687 through 789 or (res \ id 796 and (name N or name CA or name C or name O or name CB )) or resid 797 thr \ ough 947 or resid 1001)) selection = (chain 'C' and ((resid 391 through 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 598 or (resid 599 and (name N or name CA or \ name C or name O or name CB )) or resid 600 through 689 or (resid 690 and (name \ N or name CA or name C or name O or name CB )) or resid 691 through 789 or (res \ id 796 and (name N or name CA or name C or name O or name CB )) or resid 797 thr \ ough 947 or resid 1001)) selection = (chain 'D' and ((resid 391 through 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 649 or (resid 650 and (name N or name CA or \ name C or name O or name CB )) or resid 651 through 685 or (resid 686 and (name \ N or name CA or name C or name O or name CB )) or resid 687 through 947 or resi \ d 1001)) selection = (chain 'E' and ((resid 391 through 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 598 or (resid 599 and (name N or name CA or \ name C or name O or name CB )) or resid 600 through 649 or (resid 650 and (name \ N or name CA or name C or name O or name CB )) or resid 651 through 689 or (res \ id 690 and (name N or name CA or name C or name O or name CB )) or resid 691 thr \ ough 789 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 947 or resid 1001)) selection = (chain 'F' and ((resid 391 through 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 649 or (resid 650 and (name N or name CA or \ name C or name O or name CB )) or resid 651 through 685 or (resid 686 and (name \ N or name CA or name C or name O or name CB )) or resid 687 through 947 or resi \ d 1001)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.970 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 : 0.004 0.114 26857 Z= 0.203 Angle : 0.593 16.370 36337 Z= 0.322 Chirality : 0.042 0.274 4166 Planarity : 0.004 0.091 4658 Dihedral : 13.361 162.594 10171 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.11 % Allowed : 0.28 % Favored : 99.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3341 helix: 1.87 (0.13), residues: 1556 sheet: 0.49 (0.24), residues: 424 loop : 0.01 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 482 TYR 0.019 0.001 TYR C 834 PHE 0.010 0.001 PHE E 504 TRP 0.008 0.001 TRP C 470 HIS 0.010 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 (26857) covalent geometry : angle 0.59343 / 0.32 (36337) hydrogen bonds : bond 0.14253 / 9.75 ( 1302) hydrogen bonds : angle 6.60297 / 4.67 ( 3819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 HIS cc_start: 0.7556 (t-170) cc_final: 0.7328 (t70) REVERT: A 397 GLN cc_start: 0.8175 (mt0) cc_final: 0.7943 (mt0) REVERT: A 647 GLU cc_start: 0.7238 (tp30) cc_final: 0.7024 (tp30) REVERT: A 833 ASP cc_start: 0.7563 (t0) cc_final: 0.7289 (t0) REVERT: B 492 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.5525 (p90) REVERT: D 417 ILE cc_start: 0.8565 (mm) cc_final: 0.8263 (mm) REVERT: E 397 GLN cc_start: 0.8224 (mt0) cc_final: 0.7789 (mp10) REVERT: E 420 LYS cc_start: 0.8395 (ttpt) cc_final: 0.7843 (ttpt) outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.8070 time to fit residues: 222.0198 Evaluate side-chains 175 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 492 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 GLN B 702 GLN D 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092733 restraints weight = 39150.420| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.90 r_work: 0.3065 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26857 Z= 0.130 Angle : 0.556 8.180 36337 Z= 0.280 Chirality : 0.041 0.149 4166 Planarity : 0.004 0.041 4658 Dihedral : 6.629 126.616 3705 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.77 % Allowed : 5.41 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.14), residues: 3341 helix: 2.03 (0.13), residues: 1577 sheet: 0.68 (0.24), residues: 424 loop : 0.01 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 652 TYR 0.036 0.001 TYR A 599 PHE 0.012 0.001 PHE E 504 TRP 0.008 0.001 TRP D 464 HIS 0.005 0.001 HIS E 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (26857) covalent geometry : angle 0.55551 / 0.28 (36337) hydrogen bonds : bond 0.03951 / 2.67 ( 1302) hydrogen bonds : angle 5.06246 / 3.59 ( 3819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8364 (mt0) cc_final: 0.8001 (mt0) REVERT: A 402 ILE cc_start: 0.8029 (mp) cc_final: 0.7768 (mp) REVERT: A 494 MET cc_start: 0.8871 (mtp) cc_final: 0.8651 (mtp) REVERT: A 647 GLU cc_start: 0.7983 (tp30) cc_final: 0.7469 (tp30) REVERT: A 833 ASP cc_start: 0.8404 (t0) cc_final: 0.7989 (t0) REVERT: C 402 ILE cc_start: 0.8022 (mp) cc_final: 0.7764 (mp) REVERT: D 417 ILE cc_start: 0.8161 (mm) cc_final: 0.7886 (mm) REVERT: D 756 MET cc_start: 0.8254 (mtp) cc_final: 0.7991 (ttm) REVERT: E 397 GLN cc_start: 0.8489 (mt0) cc_final: 0.7935 (mp10) REVERT: E 413 ASP cc_start: 0.7540 (p0) cc_final: 0.7141 (p0) REVERT: E 423 GLU cc_start: 0.8295 (pp20) cc_final: 0.8060 (pp20) outliers start: 22 outliers final: 14 residues processed: 204 average time/residue: 0.7375 time to fit residues: 173.5460 Evaluate side-chains 182 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 643 ASP Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 62 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 chunk 234 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 GLN E 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092010 restraints weight = 39232.947| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.90 r_work: 0.3037 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26857 Z= 0.134 Angle : 0.532 8.837 36337 Z= 0.264 Chirality : 0.040 0.155 4166 Planarity : 0.004 0.045 4658 Dihedral : 6.386 132.231 3703 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.95 % Allowed : 6.88 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.14), residues: 3341 helix: 2.06 (0.13), residues: 1576 sheet: 0.68 (0.24), residues: 430 loop : -0.11 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 650 TYR 0.016 0.001 TYR A 939 PHE 0.013 0.001 PHE E 504 TRP 0.008 0.001 TRP D 464 HIS 0.004 0.001 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (26857) covalent geometry : angle 0.53166 / 0.26 (36337) hydrogen bonds : bond 0.03632 / 2.45 ( 1302) hydrogen bonds : angle 4.74774 / 3.37 ( 3819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8429 (mt0) cc_final: 0.8033 (mt0) REVERT: A 402 ILE cc_start: 0.7971 (mp) cc_final: 0.7733 (mm) REVERT: A 647 GLU cc_start: 0.8073 (tp30) cc_final: 0.7498 (tp30) REVERT: B 403 ILE cc_start: 0.8851 (mt) cc_final: 0.8533 (tt) REVERT: C 402 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7653 (mp) REVERT: C 826 MET cc_start: 0.7795 (ttp) cc_final: 0.7504 (ttp) REVERT: D 417 ILE cc_start: 0.8152 (mm) cc_final: 0.7880 (mm) REVERT: E 423 GLU cc_start: 0.8288 (pp20) cc_final: 0.8048 (pp20) REVERT: E 482 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7926 (ttp80) outliers start: 27 outliers final: 17 residues processed: 201 average time/residue: 0.7439 time to fit residues: 171.7034 Evaluate side-chains 189 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 173 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 303 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 306 optimal weight: 0.9980 chunk 159 optimal weight: 0.3980 chunk 180 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 391 HIS E 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093375 restraints weight = 39168.027| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.90 r_work: 0.3076 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26857 Z= 0.102 Angle : 0.503 8.734 36337 Z= 0.248 Chirality : 0.039 0.153 4166 Planarity : 0.004 0.043 4658 Dihedral : 6.077 132.326 3701 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.30 % Allowed : 7.97 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3341 helix: 2.17 (0.13), residues: 1583 sheet: 0.77 (0.24), residues: 430 loop : -0.06 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 650 TYR 0.014 0.001 TYR A 939 PHE 0.010 0.001 PHE D 820 TRP 0.008 0.001 TRP D 464 HIS 0.011 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (26857) covalent geometry : angle 0.50322 / 0.25 (36337) hydrogen bonds : bond 0.03164 / 2.13 ( 1302) hydrogen bonds : angle 4.51073 / 3.20 ( 3819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8450 (mt0) cc_final: 0.8001 (mt0) REVERT: A 402 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7702 (mm) REVERT: A 647 GLU cc_start: 0.8058 (tp30) cc_final: 0.7506 (tp30) REVERT: B 450 ASN cc_start: 0.7734 (p0) cc_final: 0.7335 (m-40) REVERT: C 402 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7681 (mm) REVERT: C 411 LYS cc_start: 0.8236 (tppp) cc_final: 0.7799 (ttpt) REVERT: C 494 MET cc_start: 0.8552 (mtp) cc_final: 0.8092 (mtt) REVERT: C 773 MET cc_start: 0.9220 (mmm) cc_final: 0.8894 (mmp) REVERT: C 826 MET cc_start: 0.7758 (ttp) cc_final: 0.7471 (ttp) REVERT: D 417 ILE cc_start: 0.8220 (mm) cc_final: 0.7943 (mm) REVERT: D 432 LYS cc_start: 0.8732 (tptm) cc_final: 0.8500 (tptm) REVERT: E 393 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8425 (pttm) REVERT: E 397 GLN cc_start: 0.8429 (mt0) cc_final: 0.7831 (mt0) REVERT: E 423 GLU cc_start: 0.8301 (pp20) cc_final: 0.8093 (pp20) REVERT: E 482 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7942 (ttp80) REVERT: E 647 GLU cc_start: 0.7899 (tp30) cc_final: 0.7388 (tp30) outliers start: 37 outliers final: 15 residues processed: 201 average time/residue: 0.7349 time to fit residues: 169.5865 Evaluate side-chains 185 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 90 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 262 optimal weight: 0.0060 chunk 264 optimal weight: 0.7980 chunk 261 optimal weight: 0.0980 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093771 restraints weight = 39170.476| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.94 r_work: 0.3075 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26857 Z= 0.111 Angle : 0.503 8.776 36337 Z= 0.248 Chirality : 0.040 0.147 4166 Planarity : 0.004 0.044 4658 Dihedral : 5.935 121.767 3701 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.26 % Allowed : 8.67 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.14), residues: 3341 helix: 2.21 (0.13), residues: 1583 sheet: 0.84 (0.24), residues: 418 loop : -0.06 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 650 TYR 0.015 0.001 TYR A 939 PHE 0.011 0.001 PHE E 504 TRP 0.006 0.001 TRP D 464 HIS 0.004 0.001 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (26857) covalent geometry : angle 0.50291 / 0.25 (36337) hydrogen bonds : bond 0.03157 / 2.12 ( 1302) hydrogen bonds : angle 4.42319 / 3.14 ( 3819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8509 (mt0) cc_final: 0.8056 (mt0) REVERT: A 402 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7854 (mm) REVERT: A 441 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8433 (tp30) REVERT: A 647 GLU cc_start: 0.8057 (tp30) cc_final: 0.7510 (tp30) REVERT: B 450 ASN cc_start: 0.7752 (p0) cc_final: 0.7384 (m-40) REVERT: C 402 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7757 (mp) REVERT: C 411 LYS cc_start: 0.8240 (tppp) cc_final: 0.7830 (ttpt) REVERT: C 773 MET cc_start: 0.9176 (mmm) cc_final: 0.8841 (mmp) REVERT: C 826 MET cc_start: 0.7689 (ttp) cc_final: 0.7422 (ttp) REVERT: D 417 ILE cc_start: 0.8309 (mm) cc_final: 0.8024 (mm) REVERT: E 391 HIS cc_start: 0.7582 (t-90) cc_final: 0.7295 (t-170) REVERT: E 393 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8498 (pttm) REVERT: E 397 GLN cc_start: 0.8511 (mt0) cc_final: 0.7926 (mt0) REVERT: E 402 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7772 (mp) REVERT: E 419 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: E 647 GLU cc_start: 0.7895 (tp30) cc_final: 0.7409 (tp30) outliers start: 36 outliers final: 15 residues processed: 199 average time/residue: 0.7452 time to fit residues: 171.0317 Evaluate side-chains 194 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 161 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 278 optimal weight: 0.3980 chunk 285 optimal weight: 0.8980 chunk 302 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.085121 restraints weight = 39774.692| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.69 r_work: 0.2891 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26857 Z= 0.111 Angle : 0.504 8.787 36337 Z= 0.248 Chirality : 0.040 0.172 4166 Planarity : 0.004 0.044 4658 Dihedral : 5.850 112.531 3701 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.44 % Allowed : 9.38 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.14), residues: 3341 helix: 2.25 (0.13), residues: 1582 sheet: 0.88 (0.24), residues: 418 loop : -0.05 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 482 TYR 0.015 0.001 TYR A 939 PHE 0.011 0.001 PHE E 504 TRP 0.006 0.001 TRP D 464 HIS 0.004 0.001 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (26857) covalent geometry : angle 0.50415 / 0.25 (36337) hydrogen bonds : bond 0.03128 / 2.11 ( 1302) hydrogen bonds : angle 4.36989 / 3.10 ( 3819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8510 (mt0) cc_final: 0.8090 (mt0) REVERT: A 402 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7922 (mm) REVERT: A 441 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (tp30) REVERT: A 647 GLU cc_start: 0.8050 (tp30) cc_final: 0.7565 (tp30) REVERT: B 450 ASN cc_start: 0.7811 (p0) cc_final: 0.7458 (m-40) REVERT: C 402 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7882 (mm) REVERT: C 411 LYS cc_start: 0.8237 (tppp) cc_final: 0.7898 (ttpt) REVERT: C 773 MET cc_start: 0.9167 (mmm) cc_final: 0.8725 (mmp) REVERT: C 826 MET cc_start: 0.7648 (ttp) cc_final: 0.7441 (ttp) REVERT: D 417 ILE cc_start: 0.8338 (mm) cc_final: 0.8016 (mm) REVERT: E 397 GLN cc_start: 0.8555 (mt0) cc_final: 0.7954 (mt0) REVERT: E 402 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7867 (mp) REVERT: E 419 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6941 (mp0) outliers start: 41 outliers final: 17 residues processed: 197 average time/residue: 0.7353 time to fit residues: 167.4160 Evaluate side-chains 193 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 214 optimal weight: 0.8980 chunk 322 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 47 optimal weight: 0.0170 chunk 229 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.084850 restraints weight = 39655.676| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.70 r_work: 0.2883 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26857 Z= 0.108 Angle : 0.499 8.822 36337 Z= 0.246 Chirality : 0.039 0.151 4166 Planarity : 0.004 0.044 4658 Dihedral : 5.764 101.925 3701 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.19 % Allowed : 9.94 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.14), residues: 3341 helix: 2.29 (0.13), residues: 1582 sheet: 0.92 (0.24), residues: 418 loop : -0.03 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 482 TYR 0.015 0.001 TYR A 939 PHE 0.011 0.001 PHE E 504 TRP 0.007 0.001 TRP D 464 HIS 0.004 0.001 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (26857) covalent geometry : angle 0.49946 / 0.25 (36337) hydrogen bonds : bond 0.03041 / 2.05 ( 1302) hydrogen bonds : angle 4.32103 / 3.07 ( 3819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8535 (mt0) cc_final: 0.8100 (mt0) REVERT: A 402 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7866 (mm) REVERT: A 441 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8547 (tp30) REVERT: A 647 GLU cc_start: 0.8063 (tp30) cc_final: 0.7542 (tp30) REVERT: B 450 ASN cc_start: 0.7776 (p0) cc_final: 0.7428 (m-40) REVERT: B 494 MET cc_start: 0.8702 (mtt) cc_final: 0.8429 (mtp) REVERT: C 402 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7900 (mm) REVERT: C 411 LYS cc_start: 0.8255 (tppp) cc_final: 0.7904 (ttpt) REVERT: C 773 MET cc_start: 0.9189 (mmm) cc_final: 0.8761 (mmp) REVERT: C 826 MET cc_start: 0.7625 (ttp) cc_final: 0.7382 (ttp) REVERT: D 417 ILE cc_start: 0.8303 (mm) cc_final: 0.7997 (mm) REVERT: D 647 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7320 (mm-30) REVERT: D 650 ARG cc_start: 0.8618 (ttm170) cc_final: 0.8311 (ttm110) REVERT: D 756 MET cc_start: 0.8542 (ttm) cc_final: 0.8243 (ttm) REVERT: E 391 HIS cc_start: 0.7643 (t-90) cc_final: 0.7389 (t-170) REVERT: E 397 GLN cc_start: 0.8546 (mt0) cc_final: 0.7939 (mt0) REVERT: E 402 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7839 (mp) REVERT: F 445 LEU cc_start: 0.8499 (tp) cc_final: 0.8233 (tt) outliers start: 34 outliers final: 17 residues processed: 201 average time/residue: 0.7440 time to fit residues: 172.6287 Evaluate side-chains 198 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 61 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 263 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.084711 restraints weight = 39803.577| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.72 r_work: 0.2886 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26857 Z= 0.116 Angle : 0.510 8.873 36337 Z= 0.250 Chirality : 0.040 0.201 4166 Planarity : 0.004 0.044 4658 Dihedral : 5.758 96.828 3701 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.95 % Allowed : 10.64 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.14), residues: 3341 helix: 2.27 (0.13), residues: 1583 sheet: 0.92 (0.24), residues: 418 loop : -0.04 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 650 TYR 0.015 0.001 TYR A 939 PHE 0.012 0.001 PHE E 504 TRP 0.006 0.001 TRP C 470 HIS 0.005 0.001 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26857) covalent geometry : angle 0.50988 / 0.25 (36337) hydrogen bonds : bond 0.03113 / 2.09 ( 1302) hydrogen bonds : angle 4.31396 / 3.06 ( 3819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8534 (mt0) cc_final: 0.8052 (mt0) REVERT: A 402 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7869 (mm) REVERT: A 441 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8535 (tp30) REVERT: A 647 GLU cc_start: 0.8072 (tp30) cc_final: 0.7585 (tp30) REVERT: B 450 ASN cc_start: 0.7797 (p0) cc_final: 0.7462 (m-40) REVERT: B 494 MET cc_start: 0.8665 (mtt) cc_final: 0.8406 (mtp) REVERT: C 402 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 411 LYS cc_start: 0.8300 (tppp) cc_final: 0.8006 (ttpt) REVERT: C 773 MET cc_start: 0.9167 (mmm) cc_final: 0.8732 (mmp) REVERT: D 417 ILE cc_start: 0.8324 (mm) cc_final: 0.8006 (mm) REVERT: D 647 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 756 MET cc_start: 0.8561 (ttm) cc_final: 0.8238 (ttm) REVERT: E 391 HIS cc_start: 0.7520 (t-90) cc_final: 0.7282 (t-170) REVERT: E 397 GLN cc_start: 0.8543 (mt0) cc_final: 0.7949 (mt0) REVERT: E 402 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7865 (mp) REVERT: F 810 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8734 (tpp) outliers start: 27 outliers final: 17 residues processed: 194 average time/residue: 0.7220 time to fit residues: 161.6103 Evaluate side-chains 198 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 174 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 149 optimal weight: 0.0050 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.085018 restraints weight = 39820.127| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.69 r_work: 0.2892 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26857 Z= 0.112 Angle : 0.509 8.792 36337 Z= 0.251 Chirality : 0.040 0.143 4166 Planarity : 0.004 0.044 4658 Dihedral : 5.739 94.133 3701 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.95 % Allowed : 10.96 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.14), residues: 3341 helix: 2.30 (0.13), residues: 1583 sheet: 0.92 (0.24), residues: 418 loop : -0.04 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 650 TYR 0.015 0.001 TYR A 939 PHE 0.011 0.001 PHE E 504 TRP 0.006 0.001 TRP D 464 HIS 0.005 0.001 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (26857) covalent geometry : angle 0.50853 / 0.25 (36337) hydrogen bonds : bond 0.03062 / 2.06 ( 1302) hydrogen bonds : angle 4.30094 / 3.06 ( 3819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8539 (mt0) cc_final: 0.8261 (mt0) REVERT: A 402 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7886 (mm) REVERT: A 409 LEU cc_start: 0.8051 (mt) cc_final: 0.7811 (mm) REVERT: A 441 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: A 647 GLU cc_start: 0.8102 (tp30) cc_final: 0.7628 (tp30) REVERT: B 450 ASN cc_start: 0.7796 (p0) cc_final: 0.7454 (m-40) REVERT: C 393 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8514 (mtmm) REVERT: C 402 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8022 (mm) REVERT: C 411 LYS cc_start: 0.8320 (tppp) cc_final: 0.8033 (ttpt) REVERT: C 773 MET cc_start: 0.9137 (mmm) cc_final: 0.8702 (mmp) REVERT: D 756 MET cc_start: 0.8570 (ttm) cc_final: 0.8258 (ttm) REVERT: E 397 GLN cc_start: 0.8549 (mt0) cc_final: 0.7951 (mt0) REVERT: E 402 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7882 (mp) REVERT: F 810 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8716 (tpp) outliers start: 27 outliers final: 18 residues processed: 198 average time/residue: 0.7255 time to fit residues: 166.5189 Evaluate side-chains 197 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 120 optimal weight: 2.9990 chunk 262 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 chunk 105 optimal weight: 0.0050 chunk 118 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085988 restraints weight = 39750.333| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.64 r_work: 0.2912 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26857 Z= 0.096 Angle : 0.505 9.749 36337 Z= 0.248 Chirality : 0.039 0.207 4166 Planarity : 0.004 0.044 4658 Dihedral : 5.651 92.178 3701 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.81 % Allowed : 11.38 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.14), residues: 3341 helix: 2.36 (0.13), residues: 1584 sheet: 0.94 (0.24), residues: 418 loop : -0.00 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 482 TYR 0.012 0.001 TYR A 939 PHE 0.010 0.001 PHE E 545 TRP 0.008 0.001 TRP F 464 HIS 0.005 0.001 HIS E 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (26857) covalent geometry : angle 0.50480 / 0.25 (36337) hydrogen bonds : bond 0.02896 / 1.95 ( 1302) hydrogen bonds : angle 4.23893 / 3.01 ( 3819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8542 (mt0) cc_final: 0.8261 (mt0) REVERT: A 402 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 441 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: A 647 GLU cc_start: 0.8058 (tp30) cc_final: 0.7553 (tp30) REVERT: B 450 ASN cc_start: 0.7745 (p0) cc_final: 0.7404 (m-40) REVERT: C 393 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8536 (mtmm) REVERT: C 402 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7956 (mm) REVERT: C 411 LYS cc_start: 0.8291 (tppp) cc_final: 0.7945 (ttpt) REVERT: C 620 LEU cc_start: 0.9207 (tp) cc_final: 0.8979 (mt) REVERT: C 773 MET cc_start: 0.9130 (mmm) cc_final: 0.8743 (mmp) REVERT: D 756 MET cc_start: 0.8509 (ttm) cc_final: 0.8099 (ttm) REVERT: E 397 GLN cc_start: 0.8516 (mt0) cc_final: 0.7920 (mt0) REVERT: E 402 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7838 (mp) REVERT: E 419 GLU cc_start: 0.8157 (pt0) cc_final: 0.7798 (pp20) REVERT: F 810 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8701 (tpp) outliers start: 23 outliers final: 15 residues processed: 195 average time/residue: 0.7275 time to fit residues: 163.8395 Evaluate side-chains 195 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 810 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 219 optimal weight: 0.8980 chunk 298 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085449 restraints weight = 39557.458| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.68 r_work: 0.2898 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26857 Z= 0.109 Angle : 0.510 8.492 36337 Z= 0.251 Chirality : 0.040 0.139 4166 Planarity : 0.004 0.043 4658 Dihedral : 5.674 93.501 3701 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 11.41 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.14), residues: 3341 helix: 2.33 (0.13), residues: 1584 sheet: 0.95 (0.24), residues: 418 loop : -0.02 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 482 TYR 0.014 0.001 TYR A 939 PHE 0.011 0.001 PHE E 504 TRP 0.006 0.001 TRP D 464 HIS 0.003 0.001 HIS E 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (26857) covalent geometry : angle 0.51017 / 0.25 (36337) hydrogen bonds : bond 0.02978 / 2.01 ( 1302) hydrogen bonds : angle 4.23585 / 3.01 ( 3819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7586.23 seconds wall clock time: 130 minutes 34.33 seconds (7834.33 seconds total)