Starting phenix.real_space_refine on Mon Dec 30 01:11:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eih_28156/12_2024/8eih_28156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eih_28156/12_2024/8eih_28156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eih_28156/12_2024/8eih_28156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eih_28156/12_2024/8eih_28156.map" model { file = "/net/cci-nas-00/data/ceres_data/8eih_28156/12_2024/8eih_28156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eih_28156/12_2024/8eih_28156.cif" } resolution = 3.04 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 96 5.16 5 C 7437 2.51 5 N 2050 2.21 5 O 2079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11674 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3299 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3337 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2447 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 309} Chain breaks: 4 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1714 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 243} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 224 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 813 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 151 SG CYS A 435 82.339 69.538 117.544 1.00126.66 S ATOM 171 SG CYS A 438 81.281 73.151 117.466 1.00137.29 S ATOM 294 SG CYS A 455 79.289 70.608 119.511 1.00127.10 S ATOM 316 SG CYS A 458 79.063 70.486 115.782 1.00133.66 S ATOM 495 SG CYS A 478 82.756 68.639 105.514 1.00130.80 S ATOM 515 SG CYS A 481 81.670 70.990 108.262 1.00128.12 S ATOM 639 SG CYS A 500 82.879 72.468 104.918 1.00142.38 S ATOM 661 SG CYS A 503 85.252 70.755 107.426 1.00142.63 S ATOM 567 SG CYS A 490 87.160 59.995 96.197 1.00133.23 S ATOM 600 SG CYS A 495 85.877 57.393 98.769 1.00138.50 S ATOM 811 SG CYS A 524 88.313 60.156 99.814 1.00149.11 S ATOM 837 SG CYS A 527 89.406 57.214 97.792 1.00153.35 S ATOM 3458 SG CYS B 435 26.482 34.984 43.928 1.00107.06 S ATOM 3478 SG CYS B 438 25.642 38.354 42.529 1.00105.38 S ATOM 3608 SG CYS B 455 28.783 36.531 41.264 1.00 89.91 S ATOM 3630 SG CYS B 458 28.748 37.867 44.764 1.00 82.47 S ATOM 3806 SG CYS B 478 24.908 38.963 55.421 1.00103.60 S ATOM 3826 SG CYS B 481 25.343 40.377 51.937 1.00 99.08 S ATOM 3962 SG CYS B 500 23.000 42.234 54.368 1.00119.13 S ATOM 3984 SG CYS B 503 22.182 38.800 52.801 1.00114.49 S ATOM 3889 SG CYS B 490 24.814 34.219 67.626 1.00114.77 S ATOM 3922 SG CYS B 495 27.722 32.185 65.949 1.00117.36 S ATOM 4126 SG CYS B 524 24.328 32.272 64.366 1.00115.56 S ATOM 4152 SG CYS B 527 25.004 30.342 67.524 1.00118.61 S ATOM 6757 SG CYS C 435 69.941 73.987 51.066 1.00137.66 S ATOM 6892 SG CYS C 455 69.420 71.287 52.692 1.00120.67 S ATOM 6914 SG CYS C 458 67.087 72.382 51.309 1.00118.17 S ATOM 7093 SG CYS C 478 63.180 78.816 42.041 1.00120.84 S ATOM 7113 SG CYS C 481 63.031 77.580 45.608 1.00122.77 S ATOM 7251 SG CYS C 500 60.681 80.337 44.593 1.00131.73 S ATOM 7273 SG CYS C 503 64.397 81.021 44.984 1.00134.42 S ATOM 7178 SG CYS C 490 64.153 82.721 29.454 1.00131.14 S ATOM 7211 SG CYS C 495 66.343 79.492 29.223 1.00138.37 S ATOM 7405 SG CYS C 524 67.100 82.180 31.639 1.00146.42 S ATOM 7428 SG CYS C 527 67.794 82.641 27.924 1.00141.68 S Time building chain proxies: 8.36, per 1000 atoms: 0.72 Number of scatterers: 11674 At special positions: 0 Unit cell: (110, 111.1, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 96 16.00 O 2079 8.00 N 2050 7.00 C 7437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 455 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 435 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 438 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 458 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 481 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 503 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 478 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 500 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 527 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 495 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 490 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 458 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 435 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 438 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 503 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 481 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 500 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 524 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 455 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 435 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 458 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 481 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 503 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 500 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 478 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 524 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 495 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 527 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 490 " Number of angles added : 48 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2890 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 14 sheets defined 38.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.586A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.532A pdb=" N GLY A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.568A pdb=" N ARG A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.938A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 506' Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.864A pdb=" N LEU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.336A pdb=" N GLN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.628A pdb=" N LEU A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.555A pdb=" N ALA A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.747A pdb=" N ILE A 631 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.536A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 removed outlier: 3.579A pdb=" N ARG A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 682 removed outlier: 3.774A pdb=" N PHE A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 715 removed outlier: 3.564A pdb=" N ASP A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 755 through 760 removed outlier: 3.849A pdb=" N LEU A 760 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 810 removed outlier: 3.612A pdb=" N GLU A 806 " --> pdb=" O CYS A 802 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.778A pdb=" N LYS A 828 " --> pdb=" O GLY A 824 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 844 Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.977A pdb=" N ASP A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 849 " --> pdb=" O LEU A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 845 through 849' Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.600A pdb=" N ASP B 433 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 434' Processing helix chain 'B' and resid 455 through 466 removed outlier: 3.674A pdb=" N ARG B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.180A pdb=" N GLU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 506' Processing helix chain 'B' and resid 511 through 519 removed outlier: 4.022A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 removed outlier: 3.690A pdb=" N GLN B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 594 removed outlier: 3.616A pdb=" N LEU B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 618 removed outlier: 3.628A pdb=" N ILE B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.624A pdb=" N ILE B 631 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 640 removed outlier: 3.771A pdb=" N ILE B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 670 removed outlier: 3.633A pdb=" N ARG B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 683 removed outlier: 3.593A pdb=" N PHE B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 680 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 715 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 801 through 810 removed outlier: 3.525A pdb=" N ARG B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 832 removed outlier: 3.696A pdb=" N ARG B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 844 removed outlier: 3.509A pdb=" N HIS B 841 " --> pdb=" O PRO B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 removed outlier: 4.033A pdb=" N ASP B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.810A pdb=" N MET C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.706A pdb=" N ASP C 433 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY C 434 " --> pdb=" O LEU C 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 434' Processing helix chain 'C' and resid 455 through 466 removed outlier: 3.642A pdb=" N ASP C 460 " --> pdb=" O GLN C 456 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG C 461 " --> pdb=" O THR C 457 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE C 462 " --> pdb=" O CYS C 458 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.005A pdb=" N LEU C 518 " --> pdb=" O ALA C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.557A pdb=" N PHE C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 551 " --> pdb=" O GLN C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.784A pdb=" N ARG C 572 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 594 removed outlier: 3.769A pdb=" N VAL C 590 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 591 " --> pdb=" O GLY C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 632 through 640 Processing helix chain 'C' and resid 661 through 667 removed outlier: 4.343A pdb=" N TYR C 665 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 683 removed outlier: 3.688A pdb=" N PHE C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 673 " --> pdb=" O GLY C 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 674 " --> pdb=" O ARG C 670 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 675 " --> pdb=" O LEU C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 715 removed outlier: 3.781A pdb=" N LYS C 707 " --> pdb=" O LYS C 703 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 708 " --> pdb=" O VAL C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 844 Processing helix chain 'C' and resid 845 through 849 removed outlier: 4.296A pdb=" N ASP C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.759A pdb=" N ASP D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 550 removed outlier: 3.743A pdb=" N LEU D 546 " --> pdb=" O TRP D 542 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 548 " --> pdb=" O VAL D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 593 removed outlier: 4.020A pdb=" N LEU D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 590 " --> pdb=" O THR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 631 removed outlier: 3.529A pdb=" N ILE D 631 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 640 Processing helix chain 'D' and resid 668 through 683 removed outlier: 3.611A pdb=" N PHE D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 715 Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 836 through 844 Processing helix chain 'D' and resid 845 through 849 removed outlier: 3.640A pdb=" N TYR D 849 " --> pdb=" O LEU D 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 3.915A pdb=" N PHE E 287 " --> pdb=" O SER E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 295 through 313 removed outlier: 3.660A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 338 Processing helix chain 'E' and resid 345 through 349 removed outlier: 3.658A pdb=" N LYS E 349 " --> pdb=" O GLU E 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.772A pdb=" N LEU A 488 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 625 removed outlier: 9.114A pdb=" N LYS A 623 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR A 601 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 625 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA A 603 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 575 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR A 601 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 577 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA A 603 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER A 579 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 648 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 697 " --> pdb=" O GLY A 647 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 766 removed outlier: 3.509A pdb=" N ILE A 765 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 791 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AA7, first strand: chain 'B' and resid 623 through 625 removed outlier: 8.908A pdb=" N LYS B 623 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR B 601 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL B 625 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 603 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 575 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR B 601 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 577 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA B 603 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER B 579 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 648 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 697 " --> pdb=" O GLY B 647 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.849A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB1, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AB2, first strand: chain 'C' and resid 622 through 624 removed outlier: 7.670A pdb=" N TYR C 601 " --> pdb=" O LYS C 623 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB4, first strand: chain 'D' and resid 622 through 624 removed outlier: 8.869A pdb=" N LYS D 623 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR D 601 " --> pdb=" O LYS D 623 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE D 575 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR D 601 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL D 577 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA D 603 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 579 " --> pdb=" O ALA D 603 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 644 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP D 736 " --> pdb=" O PHE D 696 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 698 " --> pdb=" O TYR D 734 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 228 through 229 removed outlier: 4.068A pdb=" N VAL E 229 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 241 " --> pdb=" O VAL E 229 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2431 1.33 - 1.45: 2891 1.45 - 1.57: 6483 1.57 - 1.70: 1 1.70 - 1.82: 129 Bond restraints: 11935 Sorted by residual: bond pdb=" CA ALA C 660 " pdb=" C ALA C 660 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.40e-02 5.10e+03 8.52e+00 bond pdb=" C2 SAH A 901 " pdb=" N3 SAH A 901 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C2 SAH B 901 " pdb=" N3 SAH B 901 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" C8 SAH B 901 " pdb=" N7 SAH B 901 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" C8 SAH A 901 " pdb=" N7 SAH A 901 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.75e+00 ... (remaining 11930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15994 2.05 - 4.11: 170 4.11 - 6.16: 37 6.16 - 8.21: 10 8.21 - 10.27: 8 Bond angle restraints: 16219 Sorted by residual: angle pdb=" CA PRO B 443 " pdb=" N PRO B 443 " pdb=" CD PRO B 443 " ideal model delta sigma weight residual 112.00 104.96 7.04 1.40e+00 5.10e-01 2.53e+01 angle pdb=" C ALA C 660 " pdb=" N ARG C 661 " pdb=" CA ARG C 661 " ideal model delta sigma weight residual 121.92 114.83 7.09 1.73e+00 3.34e-01 1.68e+01 angle pdb=" N VAL C 508 " pdb=" CA VAL C 508 " pdb=" C VAL C 508 " ideal model delta sigma weight residual 112.96 109.28 3.68 1.00e+00 1.00e+00 1.35e+01 angle pdb=" CG SAH B 901 " pdb=" SD SAH B 901 " pdb=" C5' SAH B 901 " ideal model delta sigma weight residual 101.77 91.50 10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CG SAH A 901 " pdb=" SD SAH A 901 " pdb=" C5' SAH A 901 " ideal model delta sigma weight residual 101.77 91.87 9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 16214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 6246 18.04 - 36.07: 578 36.07 - 54.11: 138 54.11 - 72.14: 13 72.14 - 90.18: 7 Dihedral angle restraints: 6982 sinusoidal: 2493 harmonic: 4489 Sorted by residual: dihedral pdb=" CA PHE A 789 " pdb=" C PHE A 789 " pdb=" N PRO A 790 " pdb=" CA PRO A 790 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU C 488 " pdb=" C LEU C 488 " pdb=" N LEU C 489 " pdb=" CA LEU C 489 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PHE A 581 " pdb=" C PHE A 581 " pdb=" N ASP A 582 " pdb=" CA ASP A 582 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 6979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1204 0.037 - 0.075: 463 0.075 - 0.112: 95 0.112 - 0.150: 22 0.150 - 0.187: 1 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA ALA C 660 " pdb=" N ALA C 660 " pdb=" C ALA C 660 " pdb=" CB ALA C 660 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PRO A 790 " pdb=" N PRO A 790 " pdb=" C PRO A 790 " pdb=" CB PRO A 790 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE B 567 " pdb=" N ILE B 567 " pdb=" C ILE B 567 " pdb=" CB ILE B 567 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1782 not shown) Planarity restraints: 2107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 442 " 0.058 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 443 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 658 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO C 659 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 659 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 659 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 640 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 641 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 641 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 641 " -0.019 5.00e-02 4.00e+02 ... (remaining 2104 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2169 2.77 - 3.30: 10124 3.30 - 3.83: 17334 3.83 - 4.37: 20171 4.37 - 4.90: 36154 Nonbonded interactions: 85952 Sorted by model distance: nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 632 " pdb=" OD1 ASN A 635 " model vdw 2.241 3.040 nonbonded pdb=" O PHE C 450 " pdb=" NH2 ARG C 539 " model vdw 2.268 3.120 nonbonded pdb=" O SER B 819 " pdb=" OG SER B 819 " model vdw 2.295 3.040 nonbonded pdb=" O GLY D 453 " pdb="ZN ZN D 901 " model vdw 2.296 2.230 ... (remaining 85947 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 414 through 427 or (resid 428 and (name N or name CA or na \ me C or name O or name CB )) or resid 429 through 470 or (resid 471 through 472 \ and (name N or name CA or name C or name O or name CB )) or resid 473 through 51 \ 4 or (resid 515 through 516 and (name N or name CA or name C or name O or name C \ B )) or resid 517 through 519 or (resid 520 and (name N or name CA or name C or \ name O or name CB )) or resid 521 through 555 or (resid 556 through 557 and (nam \ e N or name CA or name C or name O or name CB )) or resid 558 through 561 or (re \ sid 562 and (name N or name CA or name C or name O or name CB or name CG )) or r \ esid 563 through 607 or (resid 608 and (name N or name CA or name C or name O or \ name CB )) or resid 609 through 633 or (resid 634 and (name N or name CA or nam \ e C or name O or name CB )) or resid 635 through 707 or (resid 708 and (name N o \ r name CA or name C or name O or name CB )) or resid 709 through 724 or (resid 7 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 726 through \ 773 or (resid 774 and (name N or name CA or name C or name O or name CB )) or r \ esid 788 through 796 or (resid 797 and (name N or name CA or name C or name O or \ name CB )) or resid 798 through 853 or resid 901 or resid 902 through 904)) selection = (chain 'B' and ((resid 414 and (name N or name CA or name C or name O or name CB \ )) or resid 415 through 422 or (resid 423 and (name N or name CA or name C or n \ ame O or name CB )) or resid 424 through 426 or (resid 427 through 428 and (name \ N or name CA or name C or name O or name CB )) or resid 429 through 432 or (res \ id 433 and (name N or name CA or name C or name O or name CB )) or resid 434 thr \ ough 440 or (resid 441 through 442 and (name N or name CA or name C or name O or \ name CB )) or resid 443 through 482 or (resid 483 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 484 through 487 and (name N or name CA or \ name C or name O or name CB )) or resid 488 through 495 or (resid 496 and (name \ N or name CA or name C or name O or name CB )) or resid 497 through 530 or (resi \ d 531 and (name N or name CA or name C or name O or name CB )) or resid 532 thro \ ugh 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) o \ r resid 538 through 539 or (resid 540 and (name N or name CA or name C or name O \ or name CB )) or resid 541 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 572 or (resid 573 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE )) \ or resid 574 through 702 or (resid 703 and (name N or name CA or name C or name \ O or name CB )) or resid 704 through 766 or (resid 767 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or resid 768 through 774 o \ r resid 788 through 795 or (resid 796 through 797 and (name N or name CA or name \ C or name O or name CB )) or resid 798 through 853 or resid 901 or resid 902 th \ rough 904)) } 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.730 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 11935 Z= 0.239 Angle : 0.623 10.268 16219 Z= 0.313 Chirality : 0.041 0.187 1785 Planarity : 0.004 0.083 2107 Dihedral : 14.895 90.178 4092 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.27 % Allowed : 13.41 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1526 helix: -0.40 (0.26), residues: 441 sheet: -1.17 (0.39), residues: 189 loop : -0.89 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 736 HIS 0.007 0.001 HIS A 618 PHE 0.015 0.001 PHE B 789 TYR 0.010 0.001 TYR D 734 ARG 0.005 0.000 ARG D 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 1.371 Fit side-chains REVERT: A 419 GLN cc_start: 0.7478 (mp10) cc_final: 0.7257 (mp10) REVERT: D 639 TRP cc_start: 0.7793 (m-10) cc_final: 0.7569 (m-10) REVERT: D 720 MET cc_start: 0.7335 (mtp) cc_final: 0.5308 (tpt) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.2678 time to fit residues: 57.8321 Evaluate side-chains 150 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0980 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 30.0000 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS B 419 GLN C 656 ASN D 841 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11935 Z= 0.163 Angle : 0.523 9.399 16219 Z= 0.266 Chirality : 0.039 0.131 1785 Planarity : 0.004 0.046 2107 Dihedral : 4.092 26.440 1693 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.91 % Allowed : 13.95 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.84 (0.22), residues: 1526 helix: 0.03 (0.26), residues: 454 sheet: -0.56 (0.39), residues: 178 loop : -0.83 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 736 HIS 0.006 0.001 HIS D 841 PHE 0.014 0.001 PHE B 789 TYR 0.010 0.001 TYR D 734 ARG 0.004 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.204 Fit side-chains REVERT: A 419 GLN cc_start: 0.7521 (mp10) cc_final: 0.7215 (mp10) REVERT: A 653 ASP cc_start: 0.7665 (t0) cc_final: 0.7069 (t0) REVERT: B 470 ASP cc_start: 0.7809 (m-30) cc_final: 0.7511 (m-30) REVERT: B 633 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8431 (tttt) REVERT: B 798 ASP cc_start: 0.8409 (t0) cc_final: 0.8183 (t0) REVERT: C 847 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8852 (mttm) REVERT: D 720 MET cc_start: 0.7049 (mtp) cc_final: 0.5401 (tpt) outliers start: 10 outliers final: 4 residues processed: 156 average time/residue: 0.2634 time to fit residues: 57.7886 Evaluate side-chains 155 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 695 MET Chi-restraints excluded: chain D residue 699 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 GLN D 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11935 Z= 0.186 Angle : 0.518 7.737 16219 Z= 0.262 Chirality : 0.040 0.136 1785 Planarity : 0.004 0.038 2107 Dihedral : 4.018 21.177 1693 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.36 % Allowed : 14.13 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.75 (0.22), residues: 1526 helix: 0.21 (0.26), residues: 462 sheet: -0.44 (0.38), residues: 183 loop : -0.87 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 736 HIS 0.006 0.001 HIS B 677 PHE 0.033 0.001 PHE D 581 TYR 0.008 0.001 TYR B 815 ARG 0.003 0.000 ARG D 683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.335 Fit side-chains REVERT: A 419 GLN cc_start: 0.7522 (mp10) cc_final: 0.7225 (mp10) REVERT: A 498 CYS cc_start: 0.5828 (p) cc_final: 0.5255 (t) REVERT: A 653 ASP cc_start: 0.7613 (t0) cc_final: 0.7022 (t0) REVERT: B 456 GLN cc_start: 0.8216 (tp40) cc_final: 0.7982 (tp-100) REVERT: B 470 ASP cc_start: 0.7687 (m-30) cc_final: 0.7411 (m-30) REVERT: B 633 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7669 (tttt) REVERT: C 456 GLN cc_start: 0.8230 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 847 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8831 (mttp) REVERT: D 639 TRP cc_start: 0.7719 (m-10) cc_final: 0.7492 (m-10) REVERT: D 720 MET cc_start: 0.7050 (mtp) cc_final: 0.5412 (tpt) REVERT: E 247 LYS cc_start: 0.4738 (mttp) cc_final: 0.4494 (mttm) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 0.2599 time to fit residues: 63.3555 Evaluate side-chains 162 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain D residue 852 CYS Chi-restraints excluded: chain E residue 258 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 0.0270 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 chunk 94 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN D 698 ASN D 841 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11935 Z= 0.296 Angle : 0.582 7.353 16219 Z= 0.296 Chirality : 0.042 0.177 1785 Planarity : 0.004 0.033 2107 Dihedral : 4.273 21.153 1693 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.81 % Allowed : 15.22 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.80 (0.22), residues: 1526 helix: 0.23 (0.26), residues: 462 sheet: -0.49 (0.37), residues: 188 loop : -0.93 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 736 HIS 0.009 0.002 HIS B 677 PHE 0.013 0.002 PHE B 789 TYR 0.015 0.001 TYR C 477 ARG 0.003 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.279 Fit side-chains REVERT: A 419 GLN cc_start: 0.7490 (mp10) cc_final: 0.7172 (mp10) REVERT: A 498 CYS cc_start: 0.5813 (p) cc_final: 0.5297 (t) REVERT: A 653 ASP cc_start: 0.7644 (t0) cc_final: 0.6972 (t0) REVERT: A 702 MET cc_start: 0.8300 (ptt) cc_final: 0.7845 (ptt) REVERT: B 633 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8349 (tttt) REVERT: C 607 CYS cc_start: 0.8299 (t) cc_final: 0.7431 (m) REVERT: C 847 LYS cc_start: 0.9060 (mmtp) cc_final: 0.8760 (mttp) REVERT: D 635 ASN cc_start: 0.8694 (t0) cc_final: 0.8192 (t0) REVERT: D 639 TRP cc_start: 0.7786 (m-10) cc_final: 0.7560 (m-10) REVERT: D 707 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7784 (ttpp) REVERT: D 720 MET cc_start: 0.7115 (mtp) cc_final: 0.5393 (tpt) REVERT: D 743 ASN cc_start: 0.5432 (m110) cc_final: 0.5144 (t0) outliers start: 31 outliers final: 23 residues processed: 178 average time/residue: 0.2561 time to fit residues: 64.9492 Evaluate side-chains 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain D residue 852 CYS Chi-restraints excluded: chain E residue 258 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 0.0030 chunk 110 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11935 Z= 0.135 Angle : 0.490 7.238 16219 Z= 0.249 Chirality : 0.039 0.196 1785 Planarity : 0.004 0.030 2107 Dihedral : 3.858 19.685 1693 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.45 % Allowed : 15.76 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1526 helix: 0.42 (0.26), residues: 464 sheet: -0.40 (0.36), residues: 188 loop : -0.85 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 335 HIS 0.003 0.001 HIS B 677 PHE 0.039 0.001 PHE D 581 TYR 0.010 0.001 TYR C 477 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.523 Fit side-chains REVERT: A 419 GLN cc_start: 0.7441 (mp10) cc_final: 0.7122 (mp10) REVERT: A 498 CYS cc_start: 0.5830 (p) cc_final: 0.5344 (t) REVERT: A 653 ASP cc_start: 0.7543 (t0) cc_final: 0.7043 (t0) REVERT: A 769 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7710 (ptpp) REVERT: B 470 ASP cc_start: 0.7577 (m-30) cc_final: 0.7310 (m-30) REVERT: B 633 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8294 (tttt) REVERT: C 456 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 607 CYS cc_start: 0.8195 (t) cc_final: 0.7290 (m) REVERT: C 847 LYS cc_start: 0.9072 (mmtp) cc_final: 0.8842 (mttm) REVERT: D 635 ASN cc_start: 0.8674 (t0) cc_final: 0.8195 (t0) REVERT: D 706 ASP cc_start: 0.8037 (m-30) cc_final: 0.7784 (m-30) REVERT: D 707 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7853 (ttpp) REVERT: D 720 MET cc_start: 0.7062 (mtp) cc_final: 0.5358 (tpt) REVERT: D 743 ASN cc_start: 0.5338 (m110) cc_final: 0.5130 (t0) outliers start: 27 outliers final: 16 residues processed: 173 average time/residue: 0.2583 time to fit residues: 63.7312 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN ** D 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11935 Z= 0.379 Angle : 0.621 7.377 16219 Z= 0.315 Chirality : 0.044 0.213 1785 Planarity : 0.005 0.033 2107 Dihedral : 4.396 25.229 1693 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.17 % Allowed : 15.76 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.80 (0.22), residues: 1526 helix: 0.26 (0.26), residues: 464 sheet: -0.51 (0.37), residues: 189 loop : -0.95 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 736 HIS 0.010 0.002 HIS B 677 PHE 0.037 0.002 PHE D 581 TYR 0.014 0.002 TYR B 815 ARG 0.005 0.001 ARG A 764 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.232 Fit side-chains REVERT: A 419 GLN cc_start: 0.7559 (mp10) cc_final: 0.7219 (mp10) REVERT: A 653 ASP cc_start: 0.7723 (t0) cc_final: 0.7051 (t0) REVERT: A 720 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8369 (ttp) REVERT: A 769 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7948 (ptpp) REVERT: B 633 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8363 (tttt) REVERT: C 504 LEU cc_start: 0.7623 (mt) cc_final: 0.7419 (mt) REVERT: C 607 CYS cc_start: 0.8459 (t) cc_final: 0.7553 (m) REVERT: C 847 LYS cc_start: 0.9059 (mmtp) cc_final: 0.8815 (mttm) REVERT: D 639 TRP cc_start: 0.7728 (m-10) cc_final: 0.7381 (m-10) REVERT: D 707 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7881 (ttpp) REVERT: D 720 MET cc_start: 0.7062 (mtp) cc_final: 0.5306 (tpt) REVERT: D 743 ASN cc_start: 0.5488 (m110) cc_final: 0.5217 (t0) REVERT: E 247 LYS cc_start: 0.4431 (mttp) cc_final: 0.4067 (mttm) outliers start: 35 outliers final: 25 residues processed: 178 average time/residue: 0.2496 time to fit residues: 63.5541 Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 717 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11935 Z= 0.156 Angle : 0.511 7.639 16219 Z= 0.258 Chirality : 0.040 0.211 1785 Planarity : 0.004 0.031 2107 Dihedral : 4.016 20.537 1693 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.26 % Allowed : 17.30 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.56 (0.22), residues: 1526 helix: 0.46 (0.26), residues: 464 sheet: -0.36 (0.37), residues: 188 loop : -0.81 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 335 HIS 0.004 0.001 HIS B 677 PHE 0.041 0.001 PHE D 581 TYR 0.010 0.001 TYR B 734 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.347 Fit side-chains REVERT: A 419 GLN cc_start: 0.7577 (mp10) cc_final: 0.7220 (mp10) REVERT: A 653 ASP cc_start: 0.7547 (t0) cc_final: 0.7016 (t0) REVERT: A 720 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8289 (ttp) REVERT: A 769 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7712 (ptpp) REVERT: B 470 ASP cc_start: 0.7626 (m-30) cc_final: 0.7345 (m-30) REVERT: B 633 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8341 (tttt) REVERT: B 798 ASP cc_start: 0.7881 (t0) cc_final: 0.7677 (t0) REVERT: C 456 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7991 (tm-30) REVERT: C 607 CYS cc_start: 0.8189 (t) cc_final: 0.7231 (m) REVERT: C 847 LYS cc_start: 0.9070 (mttp) cc_final: 0.8823 (mttm) REVERT: D 639 TRP cc_start: 0.7801 (m-10) cc_final: 0.7561 (m-10) REVERT: D 706 ASP cc_start: 0.8060 (m-30) cc_final: 0.7764 (m-30) REVERT: D 707 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7718 (ttpp) REVERT: D 720 MET cc_start: 0.7011 (mtp) cc_final: 0.5255 (tpt) REVERT: E 247 LYS cc_start: 0.4299 (mttp) cc_final: 0.3979 (mttm) outliers start: 25 outliers final: 19 residues processed: 170 average time/residue: 0.2407 time to fit residues: 58.6704 Evaluate side-chains 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11935 Z= 0.180 Angle : 0.524 7.596 16219 Z= 0.265 Chirality : 0.040 0.238 1785 Planarity : 0.004 0.031 2107 Dihedral : 3.967 20.033 1693 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.26 % Allowed : 17.21 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.51 (0.22), residues: 1526 helix: 0.52 (0.26), residues: 467 sheet: -0.32 (0.37), residues: 188 loop : -0.80 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 736 HIS 0.005 0.001 HIS B 677 PHE 0.044 0.001 PHE D 581 TYR 0.009 0.001 TYR B 734 ARG 0.002 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.294 Fit side-chains REVERT: A 419 GLN cc_start: 0.7660 (mp10) cc_final: 0.7341 (mp10) REVERT: A 653 ASP cc_start: 0.7603 (t0) cc_final: 0.7143 (t70) REVERT: A 720 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8362 (ttp) REVERT: A 769 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7689 (ptpp) REVERT: B 470 ASP cc_start: 0.7595 (m-30) cc_final: 0.7320 (m-30) REVERT: B 633 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8221 (tttt) REVERT: C 456 GLN cc_start: 0.8247 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 607 CYS cc_start: 0.8162 (t) cc_final: 0.7198 (m) REVERT: C 847 LYS cc_start: 0.9075 (mttp) cc_final: 0.8832 (mttm) REVERT: D 639 TRP cc_start: 0.7795 (m-10) cc_final: 0.7572 (m-10) REVERT: D 707 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7686 (ttpp) REVERT: D 720 MET cc_start: 0.7072 (mtp) cc_final: 0.5350 (tpt) REVERT: E 247 LYS cc_start: 0.4647 (mttp) cc_final: 0.4367 (mttm) outliers start: 25 outliers final: 21 residues processed: 171 average time/residue: 0.2598 time to fit residues: 63.3126 Evaluate side-chains 166 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 40.0000 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11935 Z= 0.220 Angle : 0.550 8.157 16219 Z= 0.277 Chirality : 0.041 0.235 1785 Planarity : 0.004 0.042 2107 Dihedral : 4.069 20.203 1693 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.63 % Allowed : 17.21 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.50 (0.22), residues: 1526 helix: 0.55 (0.26), residues: 463 sheet: -0.34 (0.37), residues: 188 loop : -0.80 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 736 HIS 0.006 0.001 HIS B 677 PHE 0.044 0.001 PHE D 581 TYR 0.009 0.001 TYR B 815 ARG 0.003 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.342 Fit side-chains REVERT: A 419 GLN cc_start: 0.7666 (mp10) cc_final: 0.7342 (mp10) REVERT: A 653 ASP cc_start: 0.7591 (t70) cc_final: 0.7111 (t70) REVERT: A 720 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8340 (ttp) REVERT: A 769 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7763 (ptpp) REVERT: B 470 ASP cc_start: 0.7619 (m-30) cc_final: 0.7328 (m-30) REVERT: B 633 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8385 (ttmt) REVERT: C 456 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 607 CYS cc_start: 0.8126 (t) cc_final: 0.7138 (m) REVERT: C 847 LYS cc_start: 0.9076 (mttp) cc_final: 0.8833 (mttm) REVERT: D 707 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7678 (ttpp) REVERT: D 720 MET cc_start: 0.7101 (mtp) cc_final: 0.5355 (tpt) REVERT: E 247 LYS cc_start: 0.4657 (mttp) cc_final: 0.4391 (mttm) outliers start: 29 outliers final: 24 residues processed: 168 average time/residue: 0.2602 time to fit residues: 61.6030 Evaluate side-chains 167 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 122 optimal weight: 30.0000 chunk 12 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11935 Z= 0.163 Angle : 0.528 8.275 16219 Z= 0.266 Chirality : 0.040 0.251 1785 Planarity : 0.004 0.043 2107 Dihedral : 3.907 19.678 1693 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.36 % Allowed : 17.57 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.47 (0.22), residues: 1526 helix: 0.55 (0.26), residues: 469 sheet: -0.30 (0.37), residues: 188 loop : -0.76 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 736 HIS 0.004 0.001 HIS B 677 PHE 0.046 0.001 PHE D 581 TYR 0.010 0.001 TYR D 734 ARG 0.007 0.000 ARG D 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.326 Fit side-chains REVERT: A 419 GLN cc_start: 0.7662 (mp10) cc_final: 0.7341 (mp10) REVERT: A 653 ASP cc_start: 0.7574 (t70) cc_final: 0.7120 (t70) REVERT: A 720 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8341 (ttp) REVERT: A 769 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7648 (ptpp) REVERT: B 470 ASP cc_start: 0.7545 (m-30) cc_final: 0.7282 (m-30) REVERT: B 633 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8224 (tttt) REVERT: C 456 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7998 (tm-30) REVERT: C 607 CYS cc_start: 0.8139 (t) cc_final: 0.7194 (m) REVERT: C 847 LYS cc_start: 0.9064 (mttp) cc_final: 0.8819 (mttm) REVERT: D 707 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7705 (ttpp) REVERT: D 720 MET cc_start: 0.7088 (mtp) cc_final: 0.5359 (tpt) REVERT: E 247 LYS cc_start: 0.4562 (mttp) cc_final: 0.4298 (mttm) outliers start: 26 outliers final: 23 residues processed: 164 average time/residue: 0.2329 time to fit residues: 55.8168 Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 122 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.205706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153830 restraints weight = 13186.579| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.23 r_work: 0.3506 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11935 Z= 0.169 Angle : 0.529 8.136 16219 Z= 0.266 Chirality : 0.040 0.240 1785 Planarity : 0.004 0.041 2107 Dihedral : 3.865 19.231 1693 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.45 % Allowed : 17.75 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % 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: -0.41 (0.22), residues: 1526 helix: 0.61 (0.26), residues: 469 sheet: -0.30 (0.37), residues: 188 loop : -0.73 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 639 HIS 0.004 0.001 HIS B 677 PHE 0.046 0.001 PHE D 581 TYR 0.011 0.001 TYR D 734 ARG 0.007 0.000 ARG D 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.62 seconds wall clock time: 47 minutes 28.32 seconds (2848.32 seconds total)