Starting phenix.real_space_refine on Sat Jun 21 05:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc1_45431/06_2025/9cc1_45431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc1_45431/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cc1_45431/06_2025/9cc1_45431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc1_45431/06_2025/9cc1_45431.map" model { file = "/net/cci-nas-00/data/ceres_data/9cc1_45431/06_2025/9cc1_45431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc1_45431/06_2025/9cc1_45431.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG:plan': 3} 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: 16.13, per 1000 atoms: 0.66 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: 5.78 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.86 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: 8.95 Time building geometry restraints manager: 6.91 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: 4.680 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: 0.990 Check model and map are aligned: 0.200 Set scattering table: 0.200 Process input model: 55.900 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.120 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (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 TRP 0.063 0.002 TRP F 464 HIS 0.003 0.001 HIS F 433 PHE 0.026 0.001 PHE F 547 TYR 0.018 0.001 TYR F 522 ARG 0.004 0.000 ARG D 705 Details of bonding type rmsd hydrogen bonds : bond 0.15258 ( 1113) hydrogen bonds : angle 7.12618 ( 3222) covalent geometry : bond 0.00320 (24961) covalent geometry : angle 0.64753 (33805) *********************** 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 : 2.606 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: 1.8052 time to fit residues: 822.0589 Evaluate side-chains 214 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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 262 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 282 optimal weight: 0.0870 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 C 477 ASN D 664 GLN D 711 ASN E 477 ASN E 575 GLN E 827 GLN F 477 ASN ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098784 restraints weight = 33258.746| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.96 r_work: 0.3053 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24961 Z= 0.208 Angle : 0.662 9.225 33805 Z= 0.330 Chirality : 0.045 0.208 3893 Planarity : 0.005 0.069 4320 Dihedral : 6.868 126.189 3457 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.08 % Allowed : 8.16 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3091 helix: 1.09 (0.14), residues: 1380 sheet: 0.45 (0.26), residues: 395 loop : -0.28 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 464 HIS 0.005 0.001 HIS A 843 PHE 0.036 0.002 PHE A 455 TYR 0.019 0.002 TYR F 461 ARG 0.005 0.001 ARG C 755 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 1113) hydrogen bonds : angle 5.29924 ( 3222) covalent geometry : bond 0.00508 (24961) covalent geometry : angle 0.66177 (33805) *********************** 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 284 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 482 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6914 (tmm160) REVERT: A 614 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: B 422 ARG cc_start: 0.8734 (mmt180) cc_final: 0.8357 (tpp-160) REVERT: B 482 ARG cc_start: 0.7872 (tmt170) cc_final: 0.7506 (tmt170) REVERT: B 754 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: C 466 THR cc_start: 0.8678 (m) cc_final: 0.8421 (p) REVERT: C 686 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: D 477 ASN cc_start: 0.8398 (p0) cc_final: 0.8125 (p0) REVERT: D 756 MET cc_start: 0.8739 (ttm) cc_final: 0.8259 (ttm) REVERT: D 922 ASP cc_start: 0.8136 (t0) cc_final: 0.7843 (t0) REVERT: E 579 LYS cc_start: 0.8280 (pttt) cc_final: 0.7911 (ptmt) REVERT: F 595 ILE cc_start: 0.7813 (tp) cc_final: 0.7528 (pp) REVERT: F 608 LEU cc_start: 0.6828 (mt) cc_final: 0.6525 (mt) REVERT: F 618 ASN cc_start: 0.7830 (t0) cc_final: 0.7592 (m-40) REVERT: F 630 LEU cc_start: 0.8400 (mt) cc_final: 0.8080 (mp) outliers start: 55 outliers final: 15 residues processed: 266 average time/residue: 1.5869 time to fit residues: 481.9557 Evaluate side-chains 212 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 3.157 ------------------------------------------------------------------------------- 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 685 ASP 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 642 THR Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 833 ASP Chi-restraints excluded: chain D residue 475 ASN 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 F residue 465 LEU 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 99 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 295 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 827 GLN ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107438 restraints weight = 32604.302| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.70 r_work: 0.3217 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1861 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= 0.131 Angle : 0.583 8.754 33805 Z= 0.287 Chirality : 0.042 0.164 3893 Planarity : 0.004 0.056 4320 Dihedral : 6.488 125.378 3451 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.78 % Allowed : 10.62 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3091 helix: 1.34 (0.14), residues: 1383 sheet: 0.38 (0.25), residues: 402 loop : -0.26 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 464 HIS 0.003 0.001 HIS C 843 PHE 0.027 0.001 PHE E 547 TYR 0.014 0.001 TYR B 939 ARG 0.006 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1113) hydrogen bonds : angle 4.98390 ( 3222) covalent geometry : bond 0.00311 (24961) covalent geometry : angle 0.58274 (33805) *********************** 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 268 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 3.448 Fit side-chains revert: symmetry clash REVERT: A 614 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: A 655 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8089 (mpt) REVERT: B 482 ARG cc_start: 0.7871 (tmt170) cc_final: 0.7539 (tmt170) REVERT: C 477 ASN cc_start: 0.8271 (p0) cc_final: 0.7730 (p0) REVERT: D 477 ASN cc_start: 0.8408 (p0) cc_final: 0.7997 (p0) REVERT: D 756 MET cc_start: 0.8873 (ttm) cc_final: 0.8374 (ttm) REVERT: E 579 LYS cc_start: 0.8317 (pttt) cc_final: 0.7977 (ptmt) REVERT: F 462 LEU cc_start: 0.8252 (mm) cc_final: 0.7931 (mm) REVERT: F 595 ILE cc_start: 0.7928 (tp) cc_final: 0.7656 (pp) REVERT: F 608 LEU cc_start: 0.7105 (mt) cc_final: 0.6781 (mt) REVERT: F 618 ASN cc_start: 0.7877 (t0) cc_final: 0.7634 (m-40) REVERT: F 630 LEU cc_start: 0.8551 (mt) cc_final: 0.8300 (mp) outliers start: 47 outliers final: 12 residues processed: 248 average time/residue: 2.1089 time to fit residues: 602.8407 Evaluate side-chains 215 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 3.875 ------------------------------------------------------------------------------- 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 685 ASP Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 569 MET 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 641 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 465 LEU 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 248 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 307 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 26 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: D 711 ASN ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 827 GLN E 934 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098465 restraints weight = 33504.375| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.88 r_work: 0.3061 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2115 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= 0.151 Angle : 0.593 8.738 33805 Z= 0.291 Chirality : 0.042 0.177 3893 Planarity : 0.005 0.054 4320 Dihedral : 6.483 124.625 3449 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 11.71 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3091 helix: 1.43 (0.14), residues: 1384 sheet: 0.46 (0.26), residues: 384 loop : -0.31 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 464 HIS 0.003 0.001 HIS A 839 PHE 0.045 0.002 PHE A 455 TYR 0.015 0.001 TYR B 939 ARG 0.007 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1113) hydrogen bonds : angle 4.82953 ( 3222) covalent geometry : bond 0.00363 (24961) covalent geometry : angle 0.59258 (33805) *********************** 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 257 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 2.658 Fit side-chains REVERT: A 419 GLU cc_start: 0.7526 (pm20) cc_final: 0.7322 (pm20) REVERT: A 559 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7364 (mtpm) REVERT: A 614 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: A 655 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8076 (mpt) REVERT: A 937 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: B 422 ARG cc_start: 0.8726 (mmt-90) cc_final: 0.8382 (tpp-160) REVERT: B 482 ARG cc_start: 0.7871 (tmt170) cc_final: 0.7443 (tmt170) REVERT: C 482 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7699 (tmt170) REVERT: C 833 ASP cc_start: 0.7450 (t0) cc_final: 0.7177 (t0) REVERT: D 477 ASN cc_start: 0.8617 (p0) cc_final: 0.8314 (p0) REVERT: D 756 MET cc_start: 0.8804 (ttm) cc_final: 0.8335 (ttm) REVERT: E 579 LYS cc_start: 0.8271 (pttt) cc_final: 0.7911 (ptmt) REVERT: E 783 SER cc_start: 0.8944 (p) cc_final: 0.8629 (t) REVERT: F 435 MET cc_start: 0.7748 (mmm) cc_final: 0.7340 (mmt) REVERT: F 462 LEU cc_start: 0.8156 (mm) cc_final: 0.7846 (mm) REVERT: F 595 ILE cc_start: 0.7923 (tp) cc_final: 0.7616 (pp) REVERT: F 608 LEU cc_start: 0.6939 (mt) cc_final: 0.6612 (mt) REVERT: F 618 ASN cc_start: 0.7961 (t0) cc_final: 0.7679 (m-40) REVERT: F 630 LEU cc_start: 0.8459 (mt) cc_final: 0.8193 (mp) outliers start: 43 outliers final: 13 residues processed: 242 average time/residue: 1.6084 time to fit residues: 445.8672 Evaluate side-chains 212 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 681 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 482 ARG Chi-restraints excluded: chain C residue 569 MET 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 608 LEU Chi-restraints excluded: chain E residue 886 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 155 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 HIS B 827 GLN 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 = 0.3722 r_free = 0.3722 target = 0.135521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103954 restraints weight = 32970.716| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.75 r_work: 0.3155 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24961 Z= 0.174 Angle : 0.606 9.082 33805 Z= 0.298 Chirality : 0.043 0.198 3893 Planarity : 0.005 0.060 4320 Dihedral : 6.562 124.089 3449 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 12.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3091 helix: 1.40 (0.14), residues: 1384 sheet: 0.43 (0.26), residues: 384 loop : -0.42 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 464 HIS 0.003 0.001 HIS A 839 PHE 0.027 0.002 PHE E 547 TYR 0.017 0.002 TYR B 939 ARG 0.009 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 1113) hydrogen bonds : angle 4.83595 ( 3222) covalent geometry : bond 0.00425 (24961) covalent geometry : angle 0.60622 (33805) *********************** 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 261 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 3.367 Fit side-chains revert: symmetry clash REVERT: A 559 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7648 (mtpm) REVERT: A 614 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: A 655 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.7969 (mpt) REVERT: A 937 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8204 (mm-30) REVERT: B 423 GLU cc_start: 0.8592 (tp30) cc_final: 0.8327 (tp30) REVERT: B 482 ARG cc_start: 0.7935 (tmt170) cc_final: 0.7699 (tmt170) REVERT: C 833 ASP cc_start: 0.7516 (t0) cc_final: 0.7267 (t0) REVERT: D 477 ASN cc_start: 0.8586 (p0) cc_final: 0.8345 (p0) REVERT: D 756 MET cc_start: 0.8923 (ttm) cc_final: 0.8476 (ttm) REVERT: E 579 LYS cc_start: 0.8298 (pttt) cc_final: 0.7927 (ptmt) REVERT: E 632 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8158 (mttm) REVERT: E 783 SER cc_start: 0.8889 (p) cc_final: 0.8661 (t) REVERT: F 435 MET cc_start: 0.7441 (mmm) cc_final: 0.6951 (mmt) REVERT: F 462 LEU cc_start: 0.8215 (mm) cc_final: 0.7889 (mm) REVERT: F 595 ILE cc_start: 0.7965 (tp) cc_final: 0.7663 (pp) REVERT: F 608 LEU cc_start: 0.7099 (mt) cc_final: 0.6726 (mt) REVERT: F 618 ASN cc_start: 0.8032 (t0) cc_final: 0.7762 (m-40) REVERT: F 630 LEU cc_start: 0.8561 (mt) cc_final: 0.8319 (mp) REVERT: F 922 ASP cc_start: 0.8308 (t0) cc_final: 0.8070 (t0) outliers start: 53 outliers final: 20 residues processed: 242 average time/residue: 2.0260 time to fit residues: 560.5804 Evaluate side-chains 220 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 SER 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 576 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 569 MET 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 656 ILE Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 777 THR 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 D residue 771 THR Chi-restraints excluded: chain E residue 632 LYS Chi-restraints excluded: chain E residue 808 GLU Chi-restraints excluded: chain E residue 886 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 160 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 301 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 304 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN E 575 GLN E 827 GLN F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105915 restraints weight = 32833.683| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.66 r_work: 0.3193 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24961 Z= 0.139 Angle : 0.588 9.620 33805 Z= 0.287 Chirality : 0.042 0.173 3893 Planarity : 0.004 0.057 4320 Dihedral : 6.465 123.995 3449 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.00 % Allowed : 13.18 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3091 helix: 1.53 (0.14), residues: 1383 sheet: 0.47 (0.26), residues: 384 loop : -0.38 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 464 HIS 0.003 0.001 HIS B 433 PHE 0.038 0.002 PHE A 455 TYR 0.015 0.001 TYR C 939 ARG 0.009 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1113) hydrogen bonds : angle 4.74058 ( 3222) covalent geometry : bond 0.00335 (24961) covalent geometry : angle 0.58778 (33805) *********************** 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 254 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 2.794 Fit side-chains revert: symmetry clash REVERT: A 559 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7737 (mtpm) REVERT: A 614 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: A 937 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: B 482 ARG cc_start: 0.7902 (tmt170) cc_final: 0.7685 (tmt170) REVERT: D 477 ASN cc_start: 0.8601 (p0) cc_final: 0.8345 (p0) REVERT: D 756 MET cc_start: 0.8898 (ttm) cc_final: 0.8468 (ttm) REVERT: E 488 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: E 579 LYS cc_start: 0.8309 (pttt) cc_final: 0.7940 (ptmt) REVERT: E 632 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8215 (mttm) REVERT: E 907 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8252 (t) REVERT: F 435 MET cc_start: 0.7387 (mmm) cc_final: 0.6852 (mmt) REVERT: F 462 LEU cc_start: 0.8207 (mm) cc_final: 0.7900 (mm) REVERT: F 575 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: F 578 LYS cc_start: 0.8736 (mtpm) cc_final: 0.8272 (mtpt) REVERT: F 595 ILE cc_start: 0.7973 (tp) cc_final: 0.7689 (pp) REVERT: F 608 LEU cc_start: 0.7119 (mt) cc_final: 0.6748 (mt) REVERT: F 618 ASN cc_start: 0.8008 (t0) cc_final: 0.7747 (m-40) REVERT: F 630 LEU cc_start: 0.8589 (mt) cc_final: 0.8388 (mp) REVERT: F 922 ASP cc_start: 0.8340 (t0) cc_final: 0.8104 (t0) outliers start: 53 outliers final: 24 residues processed: 242 average time/residue: 1.4372 time to fit residues: 398.7944 Evaluate side-chains 225 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 SER 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 681 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 569 MET 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 656 ILE Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 LYS 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 488 GLU Chi-restraints excluded: chain E residue 608 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 907 VAL Chi-restraints excluded: chain F residue 465 LEU 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 264 optimal weight: 0.0000 chunk 66 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 123 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 228 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 827 GLN F 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107326 restraints weight = 32791.604| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.67 r_work: 0.3224 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24961 Z= 0.104 Angle : 0.574 10.595 33805 Z= 0.277 Chirality : 0.041 0.146 3893 Planarity : 0.004 0.055 4320 Dihedral : 6.267 123.674 3449 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 13.86 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3091 helix: 1.72 (0.14), residues: 1385 sheet: 0.47 (0.26), residues: 394 loop : -0.25 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 464 HIS 0.003 0.001 HIS D 491 PHE 0.027 0.001 PHE E 547 TYR 0.010 0.001 TYR B 939 ARG 0.009 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 1113) hydrogen bonds : angle 4.62067 ( 3222) covalent geometry : bond 0.00236 (24961) covalent geometry : angle 0.57367 (33805) *********************** 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 253 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 3.058 Fit side-chains revert: symmetry clash REVERT: A 614 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: A 937 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: B 482 ARG cc_start: 0.7853 (tmt170) cc_final: 0.7631 (tmt170) REVERT: B 796 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7269 (pptt) REVERT: B 918 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7766 (mmmm) REVERT: D 756 MET cc_start: 0.8823 (ttm) cc_final: 0.8409 (ttm) REVERT: E 445 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7181 (tp) REVERT: E 488 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: E 579 LYS cc_start: 0.8301 (pttt) cc_final: 0.7916 (ptmt) REVERT: E 632 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8148 (mttm) REVERT: E 907 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8203 (t) REVERT: F 435 MET cc_start: 0.7388 (mmm) cc_final: 0.6874 (mmt) REVERT: F 575 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: F 578 LYS cc_start: 0.8664 (mtpm) cc_final: 0.8298 (mtpt) REVERT: F 595 ILE cc_start: 0.7961 (tp) cc_final: 0.7646 (pp) REVERT: F 608 LEU cc_start: 0.7070 (mt) cc_final: 0.6699 (mt) REVERT: F 618 ASN cc_start: 0.7994 (t0) cc_final: 0.7708 (m-40) REVERT: F 922 ASP cc_start: 0.8336 (t0) cc_final: 0.8106 (t0) outliers start: 48 outliers final: 21 residues processed: 239 average time/residue: 1.5210 time to fit residues: 416.9567 Evaluate side-chains 216 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU 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 752 THR Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 569 MET 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 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 553 THR 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 445 LEU Chi-restraints excluded: chain E residue 488 GLU 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 907 VAL Chi-restraints excluded: chain F residue 575 GLN 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 102 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 chunk 145 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.138383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108448 restraints weight = 32684.465| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.65 r_work: 0.3234 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24961 Z= 0.115 Angle : 0.586 11.071 33805 Z= 0.282 Chirality : 0.041 0.153 3893 Planarity : 0.004 0.057 4320 Dihedral : 6.230 123.100 3449 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.89 % Allowed : 14.36 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3091 helix: 1.76 (0.14), residues: 1385 sheet: 0.56 (0.26), residues: 388 loop : -0.25 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 464 HIS 0.003 0.001 HIS B 433 PHE 0.039 0.001 PHE A 455 TYR 0.012 0.001 TYR B 939 ARG 0.009 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 1113) hydrogen bonds : angle 4.57874 ( 3222) covalent geometry : bond 0.00274 (24961) covalent geometry : angle 0.58638 (33805) *********************** 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 244 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 3.019 Fit side-chains revert: symmetry clash REVERT: A 614 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: B 482 ARG cc_start: 0.7847 (tmt170) cc_final: 0.7631 (tmt170) REVERT: B 796 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7082 (pptt) REVERT: B 918 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7809 (mmmm) REVERT: D 756 MET cc_start: 0.8802 (ttm) cc_final: 0.8343 (ttm) REVERT: E 488 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: E 579 LYS cc_start: 0.8250 (pttt) cc_final: 0.7884 (ptmt) REVERT: E 614 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: E 632 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8172 (mttm) REVERT: E 907 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8185 (t) REVERT: F 435 MET cc_start: 0.7410 (mmm) cc_final: 0.6885 (mmt) REVERT: F 462 LEU cc_start: 0.8102 (mm) cc_final: 0.7787 (mm) REVERT: F 569 MET cc_start: 0.6961 (mmm) cc_final: 0.6279 (mmt) REVERT: F 575 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: F 578 LYS cc_start: 0.8755 (mtpm) cc_final: 0.8391 (mtpt) REVERT: F 595 ILE cc_start: 0.7938 (tp) cc_final: 0.7650 (pp) REVERT: F 608 LEU cc_start: 0.7138 (mt) cc_final: 0.6762 (mt) REVERT: F 618 ASN cc_start: 0.7944 (t0) cc_final: 0.7704 (m-40) outliers start: 50 outliers final: 27 residues processed: 234 average time/residue: 1.4810 time to fit residues: 397.4420 Evaluate side-chains 221 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 576 CYS 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 569 MET Chi-restraints excluded: chain C residue 590 ASP 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 656 ILE Chi-restraints excluded: chain C residue 752 THR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 LYS 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 488 GLU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 614 GLU 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 517 LYS Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 658 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 129 optimal weight: 0.0870 chunk 173 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 290 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** E 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107815 restraints weight = 32934.888| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.70 r_work: 0.3217 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24961 Z= 0.120 Angle : 0.589 12.185 33805 Z= 0.285 Chirality : 0.041 0.153 3893 Planarity : 0.004 0.058 4320 Dihedral : 6.218 122.709 3449 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.47 % Allowed : 15.07 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3091 helix: 1.79 (0.14), residues: 1378 sheet: 0.54 (0.25), residues: 398 loop : -0.26 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 464 HIS 0.002 0.001 HIS B 433 PHE 0.028 0.001 PHE E 547 TYR 0.013 0.001 TYR B 939 ARG 0.010 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 1113) hydrogen bonds : angle 4.57170 ( 3222) covalent geometry : bond 0.00289 (24961) covalent geometry : angle 0.58933 (33805) *********************** 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 238 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 2.897 Fit side-chains REVERT: A 423 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8149 (mt-10) REVERT: A 614 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: B 423 GLU cc_start: 0.8542 (tp30) cc_final: 0.8205 (tp30) REVERT: B 482 ARG cc_start: 0.7856 (tmt170) cc_final: 0.7492 (tmt170) REVERT: B 796 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7053 (pptt) REVERT: B 918 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7796 (mmmm) REVERT: D 552 MET cc_start: 0.6834 (tpt) cc_final: 0.6623 (tpt) REVERT: D 756 MET cc_start: 0.8785 (ttm) cc_final: 0.8485 (ttm) REVERT: E 579 LYS cc_start: 0.8269 (pttt) cc_final: 0.7892 (ptmt) REVERT: E 614 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: E 632 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8148 (mttm) REVERT: E 907 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8184 (t) REVERT: F 435 MET cc_start: 0.7424 (mmm) cc_final: 0.6884 (mmt) REVERT: F 462 LEU cc_start: 0.8069 (mm) cc_final: 0.7796 (mm) REVERT: F 569 MET cc_start: 0.6951 (mmm) cc_final: 0.6422 (mmt) REVERT: F 595 ILE cc_start: 0.7924 (tp) cc_final: 0.7629 (pp) REVERT: F 608 LEU cc_start: 0.7097 (mt) cc_final: 0.6717 (mt) REVERT: F 618 ASN cc_start: 0.7965 (t0) cc_final: 0.7701 (m-40) REVERT: F 929 GLU cc_start: 0.6880 (pm20) cc_final: 0.6608 (pm20) outliers start: 39 outliers final: 27 residues processed: 227 average time/residue: 1.4528 time to fit residues: 378.2137 Evaluate side-chains 221 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 576 CYS 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 569 MET 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 764 VAL Chi-restraints excluded: chain C residue 777 THR 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 777 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 614 GLU 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 907 VAL Chi-restraints excluded: chain F residue 517 LYS 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 36 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 158 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 HIS E 477 ASN E 827 GLN F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.145131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113190 restraints weight = 32174.962| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.84 r_work: 0.3356 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24961 Z= 0.114 Angle : 0.597 13.255 33805 Z= 0.288 Chirality : 0.041 0.151 3893 Planarity : 0.004 0.057 4320 Dihedral : 6.169 122.139 3449 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.47 % Allowed : 15.30 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3091 helix: 1.84 (0.14), residues: 1377 sheet: 0.59 (0.25), residues: 399 loop : -0.26 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 464 HIS 0.002 0.001 HIS B 433 PHE 0.032 0.001 PHE A 455 TYR 0.012 0.001 TYR F 461 ARG 0.011 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 1113) hydrogen bonds : angle 4.54893 ( 3222) covalent geometry : bond 0.00272 (24961) covalent geometry : angle 0.59715 (33805) ********************** 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 231 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 2.684 Fit side-chains revert: symmetry clash REVERT: A 423 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8161 (mt-10) REVERT: A 482 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.7130 (ttt-90) REVERT: A 614 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: B 482 ARG cc_start: 0.7912 (tmt170) cc_final: 0.7563 (tmt170) REVERT: B 796 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6977 (pptt) REVERT: B 918 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7846 (mmmm) REVERT: D 756 MET cc_start: 0.8803 (ttm) cc_final: 0.8534 (ttm) REVERT: E 488 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: E 579 LYS cc_start: 0.8286 (pttt) cc_final: 0.7913 (ptmt) REVERT: E 614 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: E 632 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8159 (mttm) REVERT: E 647 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7865 (tm-30) REVERT: E 907 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8165 (t) REVERT: F 435 MET cc_start: 0.7360 (mmm) cc_final: 0.6820 (mmt) REVERT: F 462 LEU cc_start: 0.8042 (mm) cc_final: 0.7732 (mm) REVERT: F 517 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7038 (tttt) REVERT: F 575 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: F 595 ILE cc_start: 0.7963 (tp) cc_final: 0.7697 (pp) REVERT: F 608 LEU cc_start: 0.7102 (mt) cc_final: 0.6725 (mt) REVERT: F 618 ASN cc_start: 0.7957 (t0) cc_final: 0.7701 (m-40) REVERT: F 929 GLU cc_start: 0.6890 (pm20) cc_final: 0.6621 (pm20) outliers start: 39 outliers final: 26 residues processed: 221 average time/residue: 1.4529 time to fit residues: 368.6779 Evaluate side-chains 224 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 576 CYS 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 569 MET 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 764 VAL Chi-restraints excluded: chain C residue 777 THR 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 777 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 614 GLU 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 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 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 292 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 214 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 146 optimal weight: 0.0470 chunk 173 optimal weight: 2.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113151 restraints weight = 31806.249| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.61 r_work: 0.3370 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 24961 Z= 0.183 Angle : 0.757 59.172 33805 Z= 0.415 Chirality : 0.042 0.298 3893 Planarity : 0.005 0.153 4320 Dihedral : 6.174 122.089 3449 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.44 % Allowed : 15.49 % Favored : 83.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3091 helix: 1.82 (0.14), residues: 1378 sheet: 0.59 (0.25), residues: 399 loop : -0.26 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 464 HIS 0.002 0.001 HIS C 433 PHE 0.027 0.001 PHE E 547 TYR 0.013 0.001 TYR C 939 ARG 0.008 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 1113) hydrogen bonds : angle 4.54803 ( 3222) covalent geometry : bond 0.00400 (24961) covalent geometry : angle 0.75671 (33805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17835.42 seconds wall clock time: 314 minutes 13.19 seconds (18853.19 seconds total)