Starting phenix.real_space_refine on Mon Aug 25 02:02:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc1_45431/08_2025/9cc1_45431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc1_45431/08_2025/9cc1_45431.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 { model { file = "/net/cci-nas-00/data/ceres_data/9cc1_45431/08_2025/9cc1_45431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc1_45431/08_2025/9cc1_45431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cc1_45431/08_2025/9cc1_45431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc1_45431/08_2025/9cc1_45431.map" } 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= 0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 119 5.16 5 C 15530 2.51 5 N 4205 2.21 5 O 4651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24523 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4097 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 24, 'TRANS': 500} Chain breaks: 1 Chain: "B" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4095 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4099 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4045 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3977 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3982 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 486} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.87, per 1000 atoms: 0.20 Number of scatterers: 24523 At special positions: 0 Unit cell: (134.946, 131.614, 134.113, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 12 15.00 Mg 6 11.99 O 4651 8.00 N 4205 7.00 C 15530 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 33 sheets defined 51.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 431 through 448 removed outlier: 4.493A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.694A pdb=" N ASP A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.741A pdb=" N VAL A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 3.917A pdb=" N SER A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 592 through 595 removed outlier: 3.747A pdb=" N ILE A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 592 through 595' Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.036A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.523A pdb=" N ASP A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 681 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.656A pdb=" N LEU A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.655A pdb=" N THR A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.985A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 removed outlier: 3.601A pdb=" N PHE B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 4.099A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.633A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 494 through 511 removed outlier: 3.567A pdb=" N ARG B 511 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.802A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 592 through 595 removed outlier: 3.605A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.789A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 4.094A pdb=" N ALA B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.732A pdb=" N ARG B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) 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 704 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 741 through 747 removed outlier: 3.841A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 833 through 838 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 921 Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.972A pdb=" N GLU B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.978A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 431 through 448 removed outlier: 4.133A pdb=" N VAL C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.726A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.891A pdb=" N ALA C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.575A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 704 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 741 through 747 removed outlier: 3.907A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 removed outlier: 3.509A pdb=" N GLN C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 924 through 929 removed outlier: 4.047A pdb=" N GLU C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.914A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 452 through 466 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 528 through 541 removed outlier: 3.527A pdb=" N ALA D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 570 through 581 removed outlier: 4.149A pdb=" N ILE D 574 " --> pdb=" O PRO D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.621A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.575A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 4.727A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 651 removed outlier: 3.525A pdb=" N ASP D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N GLN D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 838 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 921 Processing helix chain 'D' and resid 924 through 928 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.796A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 426 removed outlier: 3.759A pdb=" N LYS E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 452 through 468 Processing helix chain 'E' and resid 481 through 491 Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 528 through 540 removed outlier: 3.645A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 559 removed outlier: 3.549A pdb=" N ILE E 558 " --> pdb=" O VAL E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.611A pdb=" N LYS E 594 " --> pdb=" O GLU E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 646 through 652 Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 682 Processing helix chain 'E' and resid 692 through 702 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 742 through 747 Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 833 through 838 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 938 through 947 removed outlier: 3.898A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 431 through 448 removed outlier: 4.685A pdb=" N VAL F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU F 440 " --> pdb=" O ASP F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 467 Processing helix chain 'F' and resid 479 through 491 removed outlier: 3.769A pdb=" N ALA F 483 " --> pdb=" O ASP F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 528 through 540 removed outlier: 3.709A pdb=" N ALA F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 removed outlier: 4.233A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS F 576 " --> pdb=" O LYS F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 604 through 612 removed outlier: 3.923A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 4.266A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 removed outlier: 3.557A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) 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 704 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 741 through 747 removed outlier: 3.809A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 833 through 838 Processing helix chain 'F' and resid 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 921 Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.585A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.927A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.542A 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: 6.716A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 518 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.238A 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 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.056A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.276A 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: 6.874A 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: 6.002A pdb=" N ILE B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR B 638 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 589 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.178A 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 690 Processing sheet with id=AA9, first strand: chain 'B' and resid 765 through 769 removed outlier: 5.832A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 877 through 879 removed outlier: 6.771A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB3, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.041A pdb=" N ILE C 587 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR C 638 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 589 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR C 522 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 619 through 620 Processing sheet with id=AB5, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.784A pdb=" N LYS C 690 " --> pdb=" O VAL C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 764 through 769 removed outlier: 5.978A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 877 through 879 Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 883 Processing sheet with id=AB9, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.829A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 587 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR D 638 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE D 589 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 619 through 620 Processing sheet with id=AC2, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.871A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 764 through 771 removed outlier: 6.084A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 877 through 879 Processing sheet with id=AC5, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC6, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.810A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 519 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA E 639 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 619 through 620 Processing sheet with id=AC8, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.609A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 764 through 771 removed outlier: 6.020A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 877 through 879 Processing sheet with id=AD2, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AD3, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.854A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU F 519 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA F 639 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE F 521 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE F 518 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 764 through 771 removed outlier: 6.127A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 877 through 879 removed outlier: 6.905A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 882 through 883 1113 hydrogen bonds defined for protein. 3222 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: 4.15 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4152 1.32 - 1.44: 6062 1.44 - 1.56: 14533 1.56 - 1.69: 18 1.69 - 1.81: 196 Bond restraints: 24961 Sorted by residual: bond pdb=" C PRO F 524 " pdb=" O PRO F 524 " ideal model delta sigma weight residual 1.240 1.193 0.048 1.12e-02 7.97e+03 1.80e+01 bond pdb=" C GLU B 781 " pdb=" O GLU B 781 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" CA SER B 799 " pdb=" CB SER B 799 " ideal model delta sigma weight residual 1.534 1.471 0.063 1.76e-02 3.23e+03 1.26e+01 bond pdb=" C ASN B 584 " pdb=" N PRO B 585 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.33e-02 5.65e+03 1.05e+01 bond pdb=" CA SER A 508 " pdb=" CB SER A 508 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.71e-02 3.42e+03 1.02e+01 ... (remaining 24956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 33115 1.97 - 3.94: 560 3.94 - 5.91: 115 5.91 - 7.88: 13 7.88 - 9.85: 2 Bond angle restraints: 33805 Sorted by residual: angle pdb=" N PHE A 504 " pdb=" CA PHE A 504 " pdb=" C PHE A 504 " ideal model delta sigma weight residual 112.45 105.62 6.83 1.39e+00 5.18e-01 2.41e+01 angle pdb=" N GLY B 798 " pdb=" CA GLY B 798 " pdb=" C GLY B 798 " ideal model delta sigma weight residual 112.58 106.12 6.46 1.58e+00 4.01e-01 1.67e+01 angle pdb=" C ASP E 833 " pdb=" CA ASP E 833 " pdb=" CB ASP E 833 " ideal model delta sigma weight residual 110.09 103.28 6.81 1.67e+00 3.59e-01 1.66e+01 angle pdb=" CA PHE A 504 " pdb=" CB PHE A 504 " pdb=" CG PHE A 504 " ideal model delta sigma weight residual 113.80 117.81 -4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C GLU A 503 " pdb=" CA GLU A 503 " pdb=" CB GLU A 503 " ideal model delta sigma weight residual 110.01 102.95 7.06 1.80e+00 3.09e-01 1.54e+01 ... (remaining 33800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.71: 14639 25.71 - 51.42: 493 51.42 - 77.13: 51 77.13 - 102.83: 11 102.83 - 128.54: 3 Dihedral angle restraints: 15197 sinusoidal: 6154 harmonic: 9043 Sorted by residual: dihedral pdb=" C5' ADP C1002 " pdb=" O5' ADP C1002 " pdb=" PA ADP C1002 " pdb=" O2A ADP C1002 " ideal model delta sinusoidal sigma weight residual 300.00 171.46 128.54 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP C1002 " pdb=" O3A ADP C1002 " pdb=" PB ADP C1002 " pdb=" PA ADP C1002 " ideal model delta sinusoidal sigma weight residual -60.00 61.51 -121.52 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" CA TRP F 464 " pdb=" C TRP F 464 " pdb=" N LEU F 465 " pdb=" CA LEU F 465 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 15194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3341 0.063 - 0.126: 514 0.126 - 0.188: 31 0.188 - 0.251: 5 0.251 - 0.314: 2 Chirality restraints: 3893 Sorted by residual: chirality pdb=" CA ASP D 797 " pdb=" N ASP D 797 " pdb=" C ASP D 797 " pdb=" CB ASP D 797 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA GLU A 503 " pdb=" N GLU A 503 " pdb=" C GLU A 503 " pdb=" CB GLU A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP E 833 " pdb=" N ASP E 833 " pdb=" C ASP E 833 " pdb=" CB ASP E 833 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3890 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 645 " 0.066 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO F 646 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 646 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 646 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 464 " -0.032 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP F 464 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP F 464 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP F 464 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 464 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 464 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 464 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 464 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 464 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 464 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 612 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO F 613 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 613 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 613 " -0.026 5.00e-02 4.00e+02 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 197 2.59 - 3.17: 20360 3.17 - 3.75: 38359 3.75 - 4.32: 54938 4.32 - 4.90: 90328 Nonbonded interactions: 204182 Sorted by model distance: nonbonded pdb="MG MG B1001 " pdb=" O1B ADP B1002 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR C 530 " pdb="MG MG C1001 " model vdw 2.041 2.170 nonbonded pdb=" O1B ADP E1000 " pdb="MG MG E1001 " model vdw 2.068 2.170 nonbonded pdb=" O3B ADP F1000 " pdb="MG MG F1001 " model vdw 2.074 2.170 nonbonded pdb=" OG1 THR A 530 " pdb="MG MG A1001 " model vdw 2.076 2.170 ... (remaining 204177 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 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 through 450 or (resid 451 and (name N or name C \ A or name C or name O or name CB )) or resid 452 through 550 or resid 556 throug \ h 562 or (resid 563 and (name N or name CA or name C or name O or name CB )) or \ resid 564 through 596 or resid 603 through 631 or (resid 632 and (name N or name \ CA or name C or name O or name CB )) or resid 633 through 644 or (resid 645 and \ (name N or name CA or name C or name O or name CB )) or resid 646 through 649 o \ r (resid 650 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 51 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'B' and ((resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 through 450 or (resid 451 and (name N or name C \ A or name C or name O or name CB )) or resid 452 through 550 or resid 556 throug \ h 562 or (resid 563 and (name N or name CA or name C or name O or name CB )) or \ resid 564 through 596 or resid 603 through 631 or (resid 632 and (name N or name \ CA or name C or name O or name CB )) or resid 633 through 644 or (resid 645 and \ (name N or name CA or name C or name O or name CB )) or resid 646 through 649 o \ r (resid 650 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 51 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'C' and ((resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 through 450 or (resid 451 and (name N or name C \ A or name C or name O or name CB )) or resid 452 through 550 or resid 556 throug \ h 562 or (resid 563 and (name N or name CA or name C or name O or name CB )) or \ resid 564 through 596 or resid 603 through 631 or (resid 632 and (name N or name \ CA or name C or name O or name CB )) or resid 633 through 644 or (resid 645 and \ (name N or name CA or name C or name O or name CB )) or resid 646 through 649 o \ r (resid 650 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 51 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'D' and ((resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 through 550 or resid 556 through 562 or (resid \ 563 and (name N or name CA or name C or name O or name CB )) or resid 564 throug \ h 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) or \ resid 633 through 644 or (resid 645 and (name N or name CA or name C or name O o \ r name CB )) or resid 646 through 649 or (resid 650 and (name N or name CA or na \ me 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)) selection = (chain 'E' and (resid 422 through 450 or (resid 451 and (name N or name CA or na \ me C or name O or name CB )) or resid 452 through 550 or resid 556 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 through 644 or (resid 645 and (name N or name CA or name C or name O or name \ CB )) or resid 646 through 689 or (resid 690 and (name N or name CA or name C or \ name O or name CB )) or resid 691 through 788 or resid 796 through 947)) selection = (chain 'F' and ((resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 through 450 or (resid 451 and (name N or name C \ A or name C or name O or name CB )) or resid 452 through 562 or (resid 563 and ( \ name N or name CA or name C or name O or name CB )) or resid 564 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 689 or (resid 690 and (name N or name CA or name C or n \ ame O or name CB )) or resid 691 through 788 or resid 796 through 947)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 0.030 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.220 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.040 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24961 Z= 0.182 Angle : 0.648 9.849 33805 Z= 0.367 Chirality : 0.044 0.314 3893 Planarity : 0.004 0.098 4320 Dihedral : 12.734 128.542 9369 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.54 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.55 % 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 aren not related in a simple way. whole: 0.65 (0.15), residues: 3091 helix: 1.06 (0.14), residues: 1361 sheet: 0.57 (0.27), residues: 353 loop : -0.13 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 705 TYR 0.018 0.001 TYR F 522 PHE 0.026 0.001 PHE F 547 TRP 0.063 0.002 TRP F 464 HIS 0.003 0.001 HIS F 433 Details of bonding type rmsd covalent geometry : bond 0.00320 (24961) covalent geometry : angle 0.64753 (33805) hydrogen bonds : bond 0.15258 ( 1113) hydrogen bonds : angle 7.12618 ( 3222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 466 THR cc_start: 0.8545 (m) cc_final: 0.8293 (p) REVERT: E 464 TRP cc_start: 0.7154 (m100) cc_final: 0.6879 (m100) REVERT: E 579 LYS cc_start: 0.8093 (pttt) cc_final: 0.7893 (ptmt) REVERT: E 673 TYR cc_start: 0.8247 (m-80) cc_final: 0.7970 (m-80) REVERT: F 608 LEU cc_start: 0.7455 (mt) cc_final: 0.7173 (mt) outliers start: 2 outliers final: 3 residues processed: 403 average time/residue: 0.6907 time to fit residues: 312.9707 Evaluate side-chains 215 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain C residue 833 ASP Chi-restraints excluded: chain E residue 643 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 GLN A 618 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 664 GLN D 711 ASN E 477 ASN E 515 GLN E 575 GLN E 827 GLN F 477 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101741 restraints weight = 33376.119| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.95 r_work: 0.3112 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24961 Z= 0.127 Angle : 0.602 8.753 33805 Z= 0.298 Chirality : 0.042 0.169 3893 Planarity : 0.005 0.067 4320 Dihedral : 6.609 128.137 3457 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.74 % Allowed : 8.24 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3091 helix: 1.30 (0.14), residues: 1387 sheet: 0.51 (0.25), residues: 404 loop : -0.04 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 710 TYR 0.019 0.001 TYR F 461 PHE 0.035 0.002 PHE A 455 TRP 0.053 0.002 TRP F 464 HIS 0.004 0.001 HIS A 843 Details of bonding type rmsd covalent geometry : bond 0.00295 (24961) covalent geometry : angle 0.60191 (33805) hydrogen bonds : bond 0.03702 ( 1113) hydrogen bonds : angle 5.21279 ( 3222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.7147 (ttp-110) REVERT: A 482 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6831 (ttp-110) REVERT: A 569 MET cc_start: 0.8164 (mtm) cc_final: 0.7892 (mtm) REVERT: A 614 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: B 422 ARG cc_start: 0.8739 (mmt180) cc_final: 0.8323 (tpp-160) REVERT: B 482 ARG cc_start: 0.7830 (tmt170) cc_final: 0.7472 (tmt170) REVERT: B 754 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: C 466 THR cc_start: 0.8650 (m) cc_final: 0.8364 (p) REVERT: D 477 ASN cc_start: 0.8327 (p0) cc_final: 0.8045 (p0) REVERT: D 756 MET cc_start: 0.8588 (ttm) cc_final: 0.8091 (ttm) REVERT: E 545 PHE cc_start: 0.7857 (t80) cc_final: 0.7636 (t80) REVERT: E 579 LYS cc_start: 0.8220 (pttt) cc_final: 0.7831 (ptmt) REVERT: F 583 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: F 595 ILE cc_start: 0.7786 (tp) cc_final: 0.7524 (pp) REVERT: F 608 LEU cc_start: 0.6825 (mt) cc_final: 0.6527 (mt) REVERT: F 618 ASN cc_start: 0.7901 (t0) cc_final: 0.7613 (m-40) REVERT: F 630 LEU cc_start: 0.8373 (mt) cc_final: 0.8065 (mp) outliers start: 46 outliers final: 10 residues processed: 261 average time/residue: 0.6382 time to fit residues: 189.2061 Evaluate side-chains 210 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ARG Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 754 GLU Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain D residue 594 LYS Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 701 LYS Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 583 GLU Chi-restraints excluded: chain F residue 637 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 215 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 294 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN B 827 GLN C 477 ASN E 477 ASN E 827 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103650 restraints weight = 33321.422| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.71 r_work: 0.3160 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24961 Z= 0.163 Angle : 0.602 8.771 33805 Z= 0.297 Chirality : 0.043 0.189 3893 Planarity : 0.005 0.063 4320 Dihedral : 6.507 125.198 3449 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.00 % Allowed : 10.35 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.15), residues: 3091 helix: 1.37 (0.14), residues: 1382 sheet: 0.50 (0.26), residues: 384 loop : -0.25 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 459 TYR 0.016 0.002 TYR B 939 PHE 0.027 0.002 PHE E 547 TRP 0.046 0.002 TRP F 464 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00395 (24961) covalent geometry : angle 0.60230 (33805) hydrogen bonds : bond 0.03775 ( 1113) hydrogen bonds : angle 4.93388 ( 3222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: A 655 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8153 (mpt) REVERT: A 773 MET cc_start: 0.8333 (mmm) cc_final: 0.8116 (mmm) REVERT: B 482 ARG cc_start: 0.7898 (tmt170) cc_final: 0.7561 (tmt170) REVERT: B 754 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: C 509 GLN cc_start: 0.8513 (tt0) cc_final: 0.8300 (mt0) REVERT: C 833 ASP cc_start: 0.7498 (t0) cc_final: 0.7288 (t0) REVERT: D 477 ASN cc_start: 0.8409 (p0) cc_final: 0.8012 (p0) REVERT: D 756 MET cc_start: 0.8846 (ttm) cc_final: 0.8372 (ttm) REVERT: D 922 ASP cc_start: 0.8034 (t0) cc_final: 0.7821 (t0) REVERT: E 579 LYS cc_start: 0.8292 (pttt) cc_final: 0.7948 (ptmt) REVERT: E 766 MET cc_start: 0.8523 (ttt) cc_final: 0.8321 (ttp) REVERT: F 462 LEU cc_start: 0.8200 (mm) cc_final: 0.7864 (mm) REVERT: F 595 ILE cc_start: 0.7909 (tp) cc_final: 0.7598 (pp) REVERT: F 608 LEU cc_start: 0.7099 (mt) cc_final: 0.6738 (mt) REVERT: F 618 ASN cc_start: 0.7907 (t0) cc_final: 0.7641 (m-40) REVERT: F 630 LEU cc_start: 0.8496 (mt) cc_final: 0.8252 (mp) outliers start: 53 outliers final: 16 residues processed: 257 average time/residue: 0.6369 time to fit residues: 186.6229 Evaluate side-chains 216 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 754 GLU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 LYS Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 754 GLU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 517 LYS Chi-restraints excluded: chain F residue 637 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 31 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 264 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 233 optimal weight: 0.0470 chunk 306 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 711 ASN E 477 ASN E 575 GLN E 827 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106765 restraints weight = 32703.236| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.72 r_work: 0.3206 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24961 Z= 0.113 Angle : 0.560 8.469 33805 Z= 0.273 Chirality : 0.041 0.150 3893 Planarity : 0.004 0.053 4320 Dihedral : 6.327 125.461 3449 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.78 % Allowed : 11.33 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3091 helix: 1.60 (0.14), residues: 1385 sheet: 0.56 (0.25), residues: 399 loop : -0.18 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 459 TYR 0.013 0.001 TYR B 939 PHE 0.041 0.001 PHE A 455 TRP 0.036 0.002 TRP F 464 HIS 0.003 0.001 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00261 (24961) covalent geometry : angle 0.55985 (33805) hydrogen bonds : bond 0.03143 ( 1113) hydrogen bonds : angle 4.70445 ( 3222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: A 655 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8082 (mpt) REVERT: B 482 ARG cc_start: 0.7884 (tmt170) cc_final: 0.7474 (tmt170) REVERT: C 833 ASP cc_start: 0.7380 (t0) cc_final: 0.7162 (t0) REVERT: D 756 MET cc_start: 0.8822 (ttm) cc_final: 0.8364 (ttm) REVERT: D 922 ASP cc_start: 0.8010 (t0) cc_final: 0.7808 (t0) REVERT: E 477 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8307 (p0) REVERT: E 579 LYS cc_start: 0.8273 (pttt) cc_final: 0.7930 (ptmt) REVERT: E 783 SER cc_start: 0.8695 (p) cc_final: 0.8418 (t) REVERT: F 435 MET cc_start: 0.7837 (mmm) cc_final: 0.7363 (mmt) REVERT: F 462 LEU cc_start: 0.8194 (mm) cc_final: 0.7896 (mm) REVERT: F 595 ILE cc_start: 0.7930 (tp) cc_final: 0.7682 (pp) REVERT: F 608 LEU cc_start: 0.7068 (mt) cc_final: 0.6717 (mt) REVERT: F 618 ASN cc_start: 0.7892 (t0) cc_final: 0.7627 (m-40) REVERT: F 630 LEU cc_start: 0.8469 (mt) cc_final: 0.8251 (mp) REVERT: F 922 ASP cc_start: 0.8280 (t0) cc_final: 0.8060 (t0) outliers start: 47 outliers final: 9 residues processed: 254 average time/residue: 0.6409 time to fit residues: 185.0907 Evaluate side-chains 213 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 754 GLU Chi-restraints excluded: chain F residue 637 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS E 575 GLN E 827 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109706 restraints weight = 32263.679| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.80 r_work: 0.3310 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24961 Z= 0.149 Angle : 0.587 9.215 33805 Z= 0.286 Chirality : 0.042 0.172 3893 Planarity : 0.004 0.058 4320 Dihedral : 6.394 124.214 3449 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.78 % Allowed : 12.58 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.15), residues: 3091 helix: 1.57 (0.14), residues: 1385 sheet: 0.58 (0.26), residues: 384 loop : -0.27 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 459 TYR 0.016 0.001 TYR B 939 PHE 0.028 0.002 PHE E 547 TRP 0.035 0.002 TRP F 464 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00361 (24961) covalent geometry : angle 0.58740 (33805) hydrogen bonds : bond 0.03376 ( 1113) hydrogen bonds : angle 4.70954 ( 3222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 559 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7554 (mtmt) REVERT: A 614 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: A 655 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8053 (mpt) REVERT: A 937 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: B 482 ARG cc_start: 0.7931 (tmt170) cc_final: 0.7699 (tmt170) REVERT: C 655 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (mmt) REVERT: D 756 MET cc_start: 0.8857 (ttm) cc_final: 0.8433 (ttm) REVERT: D 922 ASP cc_start: 0.8050 (t0) cc_final: 0.7796 (t0) REVERT: E 579 LYS cc_start: 0.8307 (pttt) cc_final: 0.7950 (ptmt) REVERT: E 632 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8141 (mttm) REVERT: E 783 SER cc_start: 0.8732 (p) cc_final: 0.8504 (t) REVERT: F 435 MET cc_start: 0.7603 (mmm) cc_final: 0.7087 (mmt) REVERT: F 462 LEU cc_start: 0.8211 (mm) cc_final: 0.7900 (mm) REVERT: F 595 ILE cc_start: 0.7958 (tp) cc_final: 0.7677 (pp) REVERT: F 608 LEU cc_start: 0.7031 (mt) cc_final: 0.6656 (mt) REVERT: F 618 ASN cc_start: 0.7990 (t0) cc_final: 0.7702 (m-40) REVERT: F 922 ASP cc_start: 0.8317 (t0) cc_final: 0.8065 (t0) outliers start: 47 outliers final: 15 residues processed: 234 average time/residue: 0.6435 time to fit residues: 171.4045 Evaluate side-chains 217 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 594 LYS Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 655 MET Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 632 LYS Chi-restraints excluded: chain E residue 754 GLU Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 658 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 176 optimal weight: 0.0010 chunk 307 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN F 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110909 restraints weight = 31847.765| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.69 r_work: 0.3352 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24961 Z= 0.127 Angle : 0.573 8.907 33805 Z= 0.279 Chirality : 0.041 0.167 3893 Planarity : 0.004 0.058 4320 Dihedral : 6.330 124.032 3449 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.04 % Allowed : 12.96 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3091 helix: 1.67 (0.14), residues: 1383 sheet: 0.57 (0.26), residues: 389 loop : -0.25 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 459 TYR 0.014 0.001 TYR B 939 PHE 0.035 0.002 PHE A 455 TRP 0.034 0.002 TRP F 464 HIS 0.004 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00305 (24961) covalent geometry : angle 0.57263 (33805) hydrogen bonds : bond 0.03191 ( 1113) hydrogen bonds : angle 4.64361 ( 3222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 559 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7806 (ttmt) REVERT: A 614 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: A 655 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8001 (mpt) REVERT: A 937 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: B 482 ARG cc_start: 0.7923 (tmt170) cc_final: 0.7588 (tmt170) REVERT: B 918 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7803 (mmmm) REVERT: D 756 MET cc_start: 0.8868 (ttm) cc_final: 0.8475 (ttm) REVERT: D 922 ASP cc_start: 0.8021 (t0) cc_final: 0.7786 (t0) REVERT: E 579 LYS cc_start: 0.8285 (pttt) cc_final: 0.7937 (ptmt) REVERT: E 632 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8157 (mttm) REVERT: E 718 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8373 (ttmt) REVERT: E 783 SER cc_start: 0.8761 (p) cc_final: 0.8552 (t) REVERT: E 907 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8262 (t) REVERT: F 435 MET cc_start: 0.7432 (mmm) cc_final: 0.6930 (mmt) REVERT: F 462 LEU cc_start: 0.8214 (mm) cc_final: 0.7910 (mm) REVERT: F 575 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: F 595 ILE cc_start: 0.7907 (tp) cc_final: 0.7640 (pp) REVERT: F 608 LEU cc_start: 0.7064 (mt) cc_final: 0.6688 (mt) REVERT: F 922 ASP cc_start: 0.8349 (t0) cc_final: 0.8104 (t0) outliers start: 54 outliers final: 16 residues processed: 245 average time/residue: 0.6529 time to fit residues: 182.0662 Evaluate side-chains 219 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 632 LYS Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain E residue 754 GLU Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 517 LYS Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 637 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 119 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 267 optimal weight: 0.9980 chunk 157 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN E 477 ASN E 575 GLN E 827 GLN F 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106674 restraints weight = 32800.699| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.70 r_work: 0.3209 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24961 Z= 0.147 Angle : 0.599 10.837 33805 Z= 0.290 Chirality : 0.042 0.195 3893 Planarity : 0.004 0.060 4320 Dihedral : 6.369 123.439 3449 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.00 % Allowed : 13.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3091 helix: 1.62 (0.14), residues: 1384 sheet: 0.55 (0.26), residues: 388 loop : -0.28 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 459 TYR 0.015 0.001 TYR B 939 PHE 0.030 0.002 PHE E 547 TRP 0.032 0.002 TRP F 464 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00356 (24961) covalent geometry : angle 0.59896 (33805) hydrogen bonds : bond 0.03294 ( 1113) hydrogen bonds : angle 4.65214 ( 3222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7851 (mm) REVERT: A 559 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7571 (mtmt) REVERT: A 614 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7035 (pm20) REVERT: A 937 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: B 423 GLU cc_start: 0.8547 (tp30) cc_final: 0.8232 (tp30) REVERT: B 482 ARG cc_start: 0.7886 (tmt170) cc_final: 0.7565 (tmt170) REVERT: B 655 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7695 (mpt) REVERT: B 918 LYS cc_start: 0.8333 (mmpt) cc_final: 0.7863 (mmmm) REVERT: D 546 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8425 (ttt-90) REVERT: D 756 MET cc_start: 0.8859 (ttm) cc_final: 0.8466 (ttm) REVERT: D 922 ASP cc_start: 0.8006 (t0) cc_final: 0.7783 (t0) REVERT: E 579 LYS cc_start: 0.8269 (pttt) cc_final: 0.7914 (ptmt) REVERT: E 907 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8229 (t) REVERT: F 435 MET cc_start: 0.7450 (mmm) cc_final: 0.6924 (mmt) REVERT: F 462 LEU cc_start: 0.8197 (mm) cc_final: 0.7907 (mm) REVERT: F 595 ILE cc_start: 0.7894 (tp) cc_final: 0.7652 (pp) REVERT: F 608 LEU cc_start: 0.7094 (mt) cc_final: 0.6712 (mt) REVERT: F 922 ASP cc_start: 0.8322 (t0) cc_final: 0.8108 (t0) outliers start: 53 outliers final: 23 residues processed: 236 average time/residue: 0.6724 time to fit residues: 180.4262 Evaluate side-chains 218 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 LYS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 658 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 146 optimal weight: 0.8980 chunk 310 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 155 optimal weight: 0.0470 chunk 88 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 575 GLN E 827 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110061 restraints weight = 32059.108| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.82 r_work: 0.3318 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24961 Z= 0.147 Angle : 0.604 11.160 33805 Z= 0.294 Chirality : 0.042 0.175 3893 Planarity : 0.004 0.061 4320 Dihedral : 6.395 123.126 3449 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.51 % Allowed : 14.47 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.15), residues: 3091 helix: 1.64 (0.14), residues: 1381 sheet: 0.50 (0.25), residues: 398 loop : -0.29 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 459 TYR 0.015 0.001 TYR B 939 PHE 0.029 0.002 PHE E 547 TRP 0.038 0.002 TRP F 464 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00358 (24961) covalent geometry : angle 0.60445 (33805) hydrogen bonds : bond 0.03316 ( 1113) hydrogen bonds : angle 4.66993 ( 3222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8188 (mt-10) REVERT: A 468 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 559 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7840 (ttmt) REVERT: A 614 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: A 937 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: B 426 LYS cc_start: 0.9001 (mptt) cc_final: 0.8787 (mptt) REVERT: B 482 ARG cc_start: 0.7953 (tmt170) cc_final: 0.7629 (tmt170) REVERT: B 655 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7715 (mpt) REVERT: B 796 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7170 (pptt) REVERT: B 918 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7874 (mmmm) REVERT: D 756 MET cc_start: 0.8906 (ttm) cc_final: 0.8506 (ttm) REVERT: D 922 ASP cc_start: 0.8081 (t0) cc_final: 0.7880 (t0) REVERT: E 579 LYS cc_start: 0.8257 (pttt) cc_final: 0.7905 (ptmt) REVERT: E 907 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8221 (t) REVERT: F 435 MET cc_start: 0.7443 (mmm) cc_final: 0.6911 (mmt) REVERT: F 595 ILE cc_start: 0.7912 (tp) cc_final: 0.7675 (pp) REVERT: F 608 LEU cc_start: 0.7040 (mt) cc_final: 0.6645 (mt) REVERT: F 922 ASP cc_start: 0.8388 (t0) cc_final: 0.8150 (t0) outliers start: 40 outliers final: 22 residues processed: 221 average time/residue: 0.6292 time to fit residues: 158.7514 Evaluate side-chains 222 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 637 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 162 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 575 GLN ** E 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109856 restraints weight = 31836.377| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.78 r_work: 0.3323 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24961 Z= 0.150 Angle : 0.610 12.267 33805 Z= 0.296 Chirality : 0.042 0.173 3893 Planarity : 0.004 0.061 4320 Dihedral : 6.406 122.951 3449 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.62 % Allowed : 14.51 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3091 helix: 1.63 (0.14), residues: 1381 sheet: 0.48 (0.25), residues: 398 loop : -0.33 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 459 TYR 0.015 0.001 TYR B 939 PHE 0.028 0.002 PHE B 547 TRP 0.036 0.002 TRP F 464 HIS 0.003 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00365 (24961) covalent geometry : angle 0.61014 (33805) hydrogen bonds : bond 0.03336 ( 1113) hydrogen bonds : angle 4.68453 ( 3222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.8356 (tttp) cc_final: 0.8132 (tttm) REVERT: A 468 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7909 (mm) REVERT: A 559 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7858 (ttmt) REVERT: A 614 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: A 937 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: B 423 GLU cc_start: 0.8543 (tp30) cc_final: 0.8286 (tp30) REVERT: B 482 ARG cc_start: 0.7940 (tmt170) cc_final: 0.7623 (tmt170) REVERT: B 655 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7713 (mpt) REVERT: B 918 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7879 (mmmm) REVERT: D 756 MET cc_start: 0.8900 (ttm) cc_final: 0.8509 (ttm) REVERT: E 579 LYS cc_start: 0.8277 (pttt) cc_final: 0.7919 (ptmt) REVERT: E 632 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (mttm) REVERT: E 907 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8211 (t) REVERT: F 435 MET cc_start: 0.7390 (mmm) cc_final: 0.6846 (mmt) REVERT: F 462 LEU cc_start: 0.8050 (mm) cc_final: 0.7766 (mm) REVERT: F 569 MET cc_start: 0.6658 (mmm) cc_final: 0.5099 (tmm) REVERT: F 578 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8212 (mtmt) REVERT: F 608 LEU cc_start: 0.7040 (mt) cc_final: 0.6640 (mt) REVERT: F 922 ASP cc_start: 0.8357 (t0) cc_final: 0.8123 (t0) REVERT: F 929 GLU cc_start: 0.6930 (pm20) cc_final: 0.6677 (pm20) outliers start: 43 outliers final: 26 residues processed: 229 average time/residue: 0.6315 time to fit residues: 165.2999 Evaluate side-chains 225 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 632 LYS Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 658 VAL Chi-restraints excluded: chain F residue 777 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 63 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 827 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110148 restraints weight = 31776.491| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.70 r_work: 0.3339 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24961 Z= 0.135 Angle : 0.616 13.245 33805 Z= 0.299 Chirality : 0.042 0.176 3893 Planarity : 0.004 0.061 4320 Dihedral : 6.364 122.853 3449 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.59 % Allowed : 14.77 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3091 helix: 1.67 (0.14), residues: 1382 sheet: 0.48 (0.25), residues: 398 loop : -0.31 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 459 TYR 0.014 0.001 TYR B 939 PHE 0.031 0.002 PHE E 547 TRP 0.044 0.002 TRP F 464 HIS 0.004 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00325 (24961) covalent geometry : angle 0.61640 (33805) hydrogen bonds : bond 0.03244 ( 1113) hydrogen bonds : angle 4.64813 ( 3222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8125 (mt-10) REVERT: A 468 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7853 (mm) REVERT: A 559 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7522 (mtmt) REVERT: A 614 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: A 937 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8091 (mm-30) REVERT: B 423 GLU cc_start: 0.8541 (tp30) cc_final: 0.8272 (tp30) REVERT: B 482 ARG cc_start: 0.7915 (tmt170) cc_final: 0.7590 (tmt170) REVERT: B 655 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7710 (mpt) REVERT: B 796 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7067 (pptt) REVERT: B 918 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7854 (mmmm) REVERT: D 756 MET cc_start: 0.8861 (ttm) cc_final: 0.8483 (ttm) REVERT: E 579 LYS cc_start: 0.8248 (pttt) cc_final: 0.7894 (ptmt) REVERT: E 632 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8230 (mttm) REVERT: E 907 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (t) REVERT: F 435 MET cc_start: 0.7373 (mmm) cc_final: 0.6840 (mmt) REVERT: F 462 LEU cc_start: 0.8018 (mm) cc_final: 0.7746 (mm) REVERT: F 569 MET cc_start: 0.6596 (mmm) cc_final: 0.4983 (tmm) REVERT: F 578 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8246 (mtmt) REVERT: F 608 LEU cc_start: 0.6929 (mt) cc_final: 0.6533 (mt) REVERT: F 922 ASP cc_start: 0.8344 (t0) cc_final: 0.8094 (t0) REVERT: F 929 GLU cc_start: 0.6954 (pm20) cc_final: 0.6693 (pm20) outliers start: 42 outliers final: 29 residues processed: 225 average time/residue: 0.6094 time to fit residues: 157.0694 Evaluate side-chains 227 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 833 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 632 LYS Chi-restraints excluded: chain E residue 735 VAL Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 827 GLN Chi-restraints excluded: chain E residue 907 VAL Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 658 VAL Chi-restraints excluded: chain F residue 777 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.0878 > 50: distance: 52 - 138: 36.871 distance: 55 - 149: 28.700 distance: 74 - 92: 19.195 distance: 81 - 101: 13.394 distance: 85 - 112: 21.775 distance: 89 - 92: 19.670 distance: 92 - 93: 16.953 distance: 93 - 94: 14.842 distance: 93 - 96: 13.524 distance: 94 - 95: 24.949 distance: 94 - 101: 19.560 distance: 96 - 97: 23.970 distance: 97 - 98: 25.564 distance: 98 - 99: 10.985 distance: 99 - 100: 14.447 distance: 101 - 102: 10.134 distance: 102 - 103: 13.927 distance: 102 - 105: 16.841 distance: 103 - 104: 11.233 distance: 103 - 112: 19.587 distance: 105 - 106: 6.603 distance: 106 - 107: 5.809 distance: 107 - 108: 7.468 distance: 108 - 109: 5.226 distance: 109 - 110: 7.697 distance: 109 - 111: 10.289 distance: 112 - 113: 40.496 distance: 113 - 114: 20.312 distance: 113 - 116: 46.534 distance: 114 - 115: 43.652 distance: 114 - 117: 52.865 distance: 117 - 118: 40.726 distance: 118 - 119: 47.997 distance: 119 - 120: 61.377 distance: 119 - 121: 41.962 distance: 121 - 122: 23.624 distance: 122 - 123: 38.003 distance: 122 - 125: 32.954 distance: 123 - 124: 50.460 distance: 123 - 128: 40.229 distance: 125 - 126: 31.595 distance: 125 - 127: 61.356 distance: 128 - 129: 17.585 distance: 129 - 130: 25.817 distance: 129 - 132: 33.627 distance: 130 - 131: 26.025 distance: 130 - 135: 17.798 distance: 132 - 133: 32.616 distance: 132 - 134: 38.474 distance: 135 - 136: 26.836 distance: 136 - 137: 40.202 distance: 136 - 139: 26.488 distance: 137 - 138: 29.882 distance: 137 - 141: 10.499 distance: 139 - 140: 54.212 distance: 141 - 142: 54.277 distance: 141 - 203: 33.066 distance: 142 - 143: 16.756 distance: 142 - 145: 24.275 distance: 143 - 144: 54.326 distance: 143 - 149: 17.303 distance: 144 - 215: 28.242 distance: 145 - 146: 49.197 distance: 145 - 147: 32.985 distance: 146 - 148: 39.925 distance: 149 - 150: 21.976 distance: 150 - 151: 54.496 distance: 150 - 153: 9.579 distance: 151 - 152: 56.394 distance: 151 - 156: 33.501 distance: 153 - 154: 51.763 distance: 153 - 155: 29.750 distance: 156 - 157: 35.678 distance: 156 - 218: 30.271 distance: 157 - 158: 55.898 distance: 157 - 160: 42.080 distance: 158 - 159: 52.244 distance: 158 - 164: 28.271 distance: 159 - 233: 30.209 distance: 160 - 161: 34.252 distance: 161 - 162: 27.944 distance: 161 - 163: 26.487