Starting phenix.real_space_refine on Wed Jul 30 00:54:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eih_28156/07_2025/8eih_28156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eih_28156/07_2025/8eih_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_28156/07_2025/8eih_28156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eih_28156/07_2025/8eih_28156.map" model { file = "/net/cci-nas-00/data/ceres_data/8eih_28156/07_2025/8eih_28156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eih_28156/07_2025/8eih_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11674 Number of models: 1 Model: "" Number of chains: 9 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} 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: 8.63, per 1000 atoms: 0.74 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: 2.91 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 38.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 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: 3.23 Time building geometry restraints manager: 3.46 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 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 through 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.690 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- 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 11970 Z= 0.161 Angle : 0.644 10.268 16267 Z= 0.314 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 Details of bonding type rmsd hydrogen bonds : bond 0.24837 ( 330) hydrogen bonds : angle 7.45342 ( 894) metal coordination : bond 0.00485 ( 35) metal coordination : angle 3.07869 ( 48) covalent geometry : bond 0.00351 (11935) covalent geometry : angle 0.62263 (16219) *********************** 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 : 1.402 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: 0.2485 time to fit residues: 53.7430 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 : 1.244 ------------------------------------------------------------------------------- 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: 0.7980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.205969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153491 restraints weight = 13139.446| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.22 r_work: 0.3422 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11970 Z= 0.109 Angle : 0.550 9.280 16267 Z= 0.271 Chirality : 0.039 0.132 1785 Planarity : 0.004 0.046 2107 Dihedral : 4.100 26.506 1693 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.00 % Allowed : 13.95 % Favored : 85.05 % 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: -0.83 (0.22), residues: 1526 helix: 0.03 (0.26), residues: 454 sheet: -0.52 (0.39), residues: 177 loop : -0.84 (0.21), residues: 895 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 0.005 0.000 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 330) hydrogen bonds : angle 5.56722 ( 894) metal coordination : bond 0.00405 ( 35) metal coordination : angle 2.85718 ( 48) covalent geometry : bond 0.00249 (11935) covalent geometry : angle 0.52817 (16219) *********************** 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: 11 poor density : 150 time to evaluate : 1.386 Fit side-chains REVERT: A 419 GLN cc_start: 0.7565 (mp10) cc_final: 0.7223 (mp10) REVERT: A 653 ASP cc_start: 0.7864 (t0) cc_final: 0.7383 (t0) REVERT: B 633 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8489 (tttt) REVERT: B 798 ASP cc_start: 0.8381 (t0) cc_final: 0.8148 (t0) REVERT: D 635 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8208 (t0) REVERT: D 697 GLU cc_start: 0.7364 (tp30) cc_final: 0.7076 (tp30) REVERT: D 720 MET cc_start: 0.6659 (mtp) cc_final: 0.4684 (tpt) outliers start: 11 outliers final: 5 residues processed: 156 average time/residue: 0.2614 time to fit residues: 57.6862 Evaluate side-chains 155 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 MET 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 635 ASN 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 129 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.0470 chunk 2 optimal weight: 30.0000 overall best weight: 0.5084 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.206958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154731 restraints weight = 13331.853| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.26 r_work: 0.3434 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11970 Z= 0.091 Angle : 0.507 7.778 16267 Z= 0.249 Chirality : 0.039 0.130 1785 Planarity : 0.004 0.038 2107 Dihedral : 3.844 19.040 1693 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.17 % Allowed : 13.95 % Favored : 83.88 % 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: -0.71 (0.22), residues: 1526 helix: 0.23 (0.26), residues: 466 sheet: -0.36 (0.39), residues: 173 loop : -0.86 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 736 HIS 0.004 0.001 HIS B 677 PHE 0.033 0.001 PHE D 581 TYR 0.008 0.001 TYR B 734 ARG 0.003 0.000 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 330) hydrogen bonds : angle 5.05398 ( 894) metal coordination : bond 0.00365 ( 35) metal coordination : angle 2.52330 ( 48) covalent geometry : bond 0.00208 (11935) covalent geometry : angle 0.48919 (16219) *********************** 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 183 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.252 Fit side-chains REVERT: A 419 GLN cc_start: 0.7592 (mp10) cc_final: 0.7252 (mp10) REVERT: A 498 CYS cc_start: 0.6255 (p) cc_final: 0.5672 (t) REVERT: A 653 ASP cc_start: 0.7754 (t0) cc_final: 0.7333 (t0) REVERT: B 470 ASP cc_start: 0.7946 (m-30) cc_final: 0.7697 (m-30) REVERT: B 633 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7916 (tttt) REVERT: C 456 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7980 (tm-30) REVERT: D 639 TRP cc_start: 0.7670 (m-10) cc_final: 0.7376 (m-10) REVERT: D 697 GLU cc_start: 0.7466 (tp30) cc_final: 0.7261 (tp30) REVERT: D 720 MET cc_start: 0.6499 (mtp) cc_final: 0.4609 (tpt) outliers start: 24 outliers final: 10 residues processed: 173 average time/residue: 0.2476 time to fit residues: 61.2064 Evaluate side-chains 156 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 625 VAL Chi-restraints excluded: chain D residue 699 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 GLN D 698 ASN D 841 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.203780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153322 restraints weight = 13166.927| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.24 r_work: 0.3377 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11970 Z= 0.171 Angle : 0.591 7.386 16267 Z= 0.291 Chirality : 0.042 0.184 1785 Planarity : 0.004 0.039 2107 Dihedral : 4.171 22.411 1693 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.81 % Allowed : 14.58 % Favored : 82.61 % 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: 0.25 (0.26), residues: 464 sheet: -0.48 (0.37), residues: 189 loop : -0.89 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 736 HIS 0.009 0.002 HIS B 677 PHE 0.013 0.002 PHE B 673 TYR 0.012 0.001 TYR B 815 ARG 0.003 0.000 ARG A 708 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 330) hydrogen bonds : angle 5.16379 ( 894) metal coordination : bond 0.00468 ( 35) metal coordination : angle 2.93345 ( 48) covalent geometry : bond 0.00432 (11935) covalent geometry : angle 0.57007 (16219) *********************** 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 183 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.230 Fit side-chains REVERT: A 419 GLN cc_start: 0.7637 (mp10) cc_final: 0.7269 (mp10) REVERT: A 498 CYS cc_start: 0.6190 (p) cc_final: 0.5679 (t) REVERT: A 653 ASP cc_start: 0.7860 (t0) cc_final: 0.7355 (t0) REVERT: B 456 GLN cc_start: 0.8229 (tp40) cc_final: 0.7917 (tp-100) REVERT: B 470 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: B 633 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8384 (tttt) REVERT: C 607 CYS cc_start: 0.8281 (t) cc_final: 0.7341 (m) REVERT: D 639 TRP cc_start: 0.7667 (m-10) cc_final: 0.7351 (m-10) REVERT: D 707 LYS cc_start: 0.7478 (ttpp) cc_final: 0.7111 (ttpp) REVERT: D 720 MET cc_start: 0.6651 (mtp) cc_final: 0.4611 (tpt) REVERT: D 743 ASN cc_start: 0.5444 (m110) cc_final: 0.5125 (t0) REVERT: E 247 LYS cc_start: 0.5211 (mttp) cc_final: 0.4998 (mttm) outliers start: 31 outliers final: 23 residues processed: 173 average time/residue: 0.2365 time to fit residues: 58.7876 Evaluate side-chains 171 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.203656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150679 restraints weight = 13053.920| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.18 r_work: 0.3374 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11970 Z= 0.166 Angle : 0.586 7.345 16267 Z= 0.288 Chirality : 0.042 0.204 1785 Planarity : 0.004 0.034 2107 Dihedral : 4.221 21.086 1693 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.08 % Allowed : 15.13 % 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: -0.74 (0.22), residues: 1526 helix: 0.28 (0.26), residues: 462 sheet: -0.48 (0.37), residues: 188 loop : -0.90 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 335 HIS 0.007 0.001 HIS B 677 PHE 0.038 0.002 PHE D 581 TYR 0.011 0.001 TYR B 815 ARG 0.003 0.000 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 330) hydrogen bonds : angle 5.10575 ( 894) metal coordination : bond 0.00475 ( 35) metal coordination : angle 3.03580 ( 48) covalent geometry : bond 0.00418 (11935) covalent geometry : angle 0.56323 (16219) *********************** 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 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.324 Fit side-chains REVERT: A 419 GLN cc_start: 0.7598 (mp10) cc_final: 0.7220 (mp10) REVERT: A 498 CYS cc_start: 0.5937 (p) cc_final: 0.5712 (t) REVERT: A 653 ASP cc_start: 0.7872 (t0) cc_final: 0.7379 (t0) REVERT: A 720 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8254 (ttp) REVERT: A 769 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7979 (ptpp) REVERT: B 633 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8265 (tttt) REVERT: C 456 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 607 CYS cc_start: 0.8496 (t) cc_final: 0.7572 (m) REVERT: C 733 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6856 (mtt90) REVERT: D 639 TRP cc_start: 0.7709 (m-10) cc_final: 0.7472 (m-10) REVERT: D 674 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7971 (mm-30) REVERT: D 697 GLU cc_start: 0.7241 (tp30) cc_final: 0.6912 (tp30) REVERT: D 720 MET cc_start: 0.6578 (mtp) cc_final: 0.4523 (tpt) REVERT: D 735 PHE cc_start: 0.7229 (m-80) cc_final: 0.6948 (m-80) REVERT: D 743 ASN cc_start: 0.5420 (m110) cc_final: 0.5146 (t0) outliers start: 34 outliers final: 23 residues processed: 180 average time/residue: 0.2435 time to fit residues: 62.6795 Evaluate side-chains 176 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 702 MET 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 793 MET 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 C residue 733 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 123 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.204729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150500 restraints weight = 13334.487| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.16 r_work: 0.3433 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11970 Z= 0.087 Angle : 0.499 7.249 16267 Z= 0.246 Chirality : 0.039 0.194 1785 Planarity : 0.003 0.030 2107 Dihedral : 3.824 19.796 1693 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.08 % Allowed : 16.85 % 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: -0.53 (0.22), residues: 1526 helix: 0.49 (0.26), residues: 467 sheet: -0.31 (0.37), residues: 188 loop : -0.80 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 335 HIS 0.003 0.001 HIS B 677 PHE 0.039 0.001 PHE D 581 TYR 0.009 0.001 TYR B 734 ARG 0.003 0.000 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 330) hydrogen bonds : angle 4.75745 ( 894) metal coordination : bond 0.00354 ( 35) metal coordination : angle 2.41941 ( 48) covalent geometry : bond 0.00196 (11935) covalent geometry : angle 0.48255 (16219) *********************** 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 172 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 4.628 Fit side-chains REVERT: A 419 GLN cc_start: 0.7602 (mp10) cc_final: 0.7222 (mp10) REVERT: A 498 CYS cc_start: 0.6187 (p) cc_final: 0.5680 (t) REVERT: A 653 ASP cc_start: 0.7714 (t0) cc_final: 0.7323 (t70) REVERT: B 470 ASP cc_start: 0.7768 (m-30) cc_final: 0.7516 (m-30) REVERT: C 456 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 607 CYS cc_start: 0.8408 (t) cc_final: 0.7409 (m) REVERT: D 635 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8064 (t0) REVERT: D 639 TRP cc_start: 0.7709 (m-10) cc_final: 0.7505 (m-10) REVERT: D 707 LYS cc_start: 0.7334 (ttpp) cc_final: 0.6949 (ttpp) REVERT: D 720 MET cc_start: 0.6510 (mtp) cc_final: 0.4543 (tpt) REVERT: D 743 ASN cc_start: 0.5354 (m110) cc_final: 0.5091 (t0) outliers start: 23 outliers final: 15 residues processed: 165 average time/residue: 0.3957 time to fit residues: 94.6459 Evaluate side-chains 160 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU 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 653 ASP 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 635 ASN Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 126 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.204413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154258 restraints weight = 13411.299| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.34 r_work: 0.3408 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11970 Z= 0.095 Angle : 0.514 7.395 16267 Z= 0.252 Chirality : 0.040 0.231 1785 Planarity : 0.004 0.039 2107 Dihedral : 3.780 19.179 1693 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.08 % Allowed : 16.39 % Favored : 81.52 % 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: -0.44 (0.22), residues: 1526 helix: 0.57 (0.26), residues: 467 sheet: -0.26 (0.37), residues: 188 loop : -0.75 (0.22), residues: 871 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 0.042 0.001 PHE D 581 TYR 0.010 0.001 TYR D 734 ARG 0.002 0.000 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 330) hydrogen bonds : angle 4.73779 ( 894) metal coordination : bond 0.00348 ( 35) metal coordination : angle 2.44034 ( 48) covalent geometry : bond 0.00221 (11935) covalent geometry : angle 0.49700 (16219) *********************** 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 170 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.344 Fit side-chains REVERT: A 419 GLN cc_start: 0.7709 (mp10) cc_final: 0.7377 (mp10) REVERT: A 498 CYS cc_start: 0.6074 (p) cc_final: 0.5661 (t) REVERT: A 653 ASP cc_start: 0.7609 (t0) cc_final: 0.7242 (t70) REVERT: B 456 GLN cc_start: 0.8111 (tp40) cc_final: 0.7793 (tp-100) REVERT: B 470 ASP cc_start: 0.7644 (m-30) cc_final: 0.7408 (m-30) REVERT: C 607 CYS cc_start: 0.8186 (t) cc_final: 0.7340 (m) REVERT: D 697 GLU cc_start: 0.6996 (tp30) cc_final: 0.6744 (tp30) REVERT: D 707 LYS cc_start: 0.7338 (ttpp) cc_final: 0.6918 (ttpp) REVERT: D 720 MET cc_start: 0.6631 (mtp) cc_final: 0.4566 (tpt) REVERT: D 743 ASN cc_start: 0.5269 (m110) cc_final: 0.5016 (t0) outliers start: 23 outliers final: 16 residues processed: 163 average time/residue: 0.2767 time to fit residues: 65.7967 Evaluate side-chains 157 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU 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 755 GLU 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 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 0.0060 chunk 86 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 88 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.2552 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.207760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155226 restraints weight = 13275.666| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.18 r_work: 0.3460 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11970 Z= 0.082 Angle : 0.496 7.255 16267 Z= 0.245 Chirality : 0.039 0.214 1785 Planarity : 0.003 0.038 2107 Dihedral : 3.581 17.960 1693 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.26 % Allowed : 16.39 % Favored : 81.34 % 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: -0.30 (0.22), residues: 1526 helix: 0.77 (0.26), residues: 463 sheet: -0.15 (0.37), residues: 183 loop : -0.72 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 335 HIS 0.002 0.000 HIS B 677 PHE 0.043 0.001 PHE D 581 TYR 0.008 0.001 TYR B 734 ARG 0.007 0.000 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.02472 ( 330) hydrogen bonds : angle 4.54940 ( 894) metal coordination : bond 0.00312 ( 35) metal coordination : angle 2.13982 ( 48) covalent geometry : bond 0.00180 (11935) covalent geometry : angle 0.48283 (16219) *********************** 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 : 1.518 Fit side-chains REVERT: A 419 GLN cc_start: 0.7738 (mp10) cc_final: 0.7364 (mp10) REVERT: A 498 CYS cc_start: 0.6198 (p) cc_final: 0.5770 (t) REVERT: A 653 ASP cc_start: 0.7646 (t0) cc_final: 0.7356 (t70) REVERT: B 456 GLN cc_start: 0.8157 (tp40) cc_final: 0.7834 (tp-100) REVERT: B 533 HIS cc_start: 0.8077 (m90) cc_final: 0.7327 (m90) REVERT: B 798 ASP cc_start: 0.7733 (t0) cc_final: 0.7528 (t0) REVERT: C 607 CYS cc_start: 0.8270 (t) cc_final: 0.7303 (m) REVERT: D 639 TRP cc_start: 0.7692 (m-10) cc_final: 0.7371 (m-10) REVERT: D 695 MET cc_start: 0.8405 (ttp) cc_final: 0.7902 (tmm) REVERT: D 720 MET cc_start: 0.6495 (mtp) cc_final: 0.4462 (tpt) REVERT: D 743 ASN cc_start: 0.5288 (m110) cc_final: 0.5068 (t0) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 0.2347 time to fit residues: 57.7707 Evaluate side-chains 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 657 VAL 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 653 ASP Chi-restraints excluded: chain B residue 755 GLU 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 699 VAL Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 0.0020 chunk 116 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.206416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.156574 restraints weight = 13350.676| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.31 r_work: 0.3366 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11970 Z= 0.102 Angle : 0.525 7.559 16267 Z= 0.258 Chirality : 0.040 0.251 1785 Planarity : 0.004 0.037 2107 Dihedral : 3.658 18.447 1693 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.54 % Allowed : 17.57 % Favored : 80.89 % 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: -0.27 (0.22), residues: 1526 helix: 0.79 (0.26), residues: 465 sheet: -0.12 (0.37), residues: 183 loop : -0.70 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 736 HIS 0.004 0.001 HIS B 677 PHE 0.044 0.001 PHE D 581 TYR 0.010 0.001 TYR D 734 ARG 0.006 0.000 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 330) hydrogen bonds : angle 4.63187 ( 894) metal coordination : bond 0.00340 ( 35) metal coordination : angle 2.28209 ( 48) covalent geometry : bond 0.00244 (11935) covalent geometry : angle 0.51112 (16219) *********************** 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 164 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.259 Fit side-chains REVERT: A 419 GLN cc_start: 0.7749 (mp10) cc_final: 0.7378 (mp10) REVERT: A 498 CYS cc_start: 0.6058 (p) cc_final: 0.5618 (t) REVERT: A 653 ASP cc_start: 0.7570 (t0) cc_final: 0.7279 (t70) REVERT: B 456 GLN cc_start: 0.8146 (tp40) cc_final: 0.7832 (tp-100) REVERT: C 504 LEU cc_start: 0.7592 (mt) cc_final: 0.7302 (mt) REVERT: C 607 CYS cc_start: 0.8270 (t) cc_final: 0.7369 (m) REVERT: D 639 TRP cc_start: 0.7605 (m-10) cc_final: 0.7253 (m-10) REVERT: D 695 MET cc_start: 0.8343 (ttp) cc_final: 0.7802 (tmm) REVERT: D 720 MET cc_start: 0.6574 (mtp) cc_final: 0.4472 (tpt) REVERT: D 743 ASN cc_start: 0.5322 (m110) cc_final: 0.5103 (t0) outliers start: 17 outliers final: 17 residues processed: 158 average time/residue: 0.2471 time to fit residues: 56.1176 Evaluate side-chains 157 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 818 VAL 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 755 GLU 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 699 VAL Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 141 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 142 optimal weight: 20.0000 chunk 113 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.206943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155573 restraints weight = 13224.125| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.21 r_work: 0.3433 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11970 Z= 0.091 Angle : 0.513 8.032 16267 Z= 0.252 Chirality : 0.039 0.236 1785 Planarity : 0.004 0.037 2107 Dihedral : 3.581 18.407 1693 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.45 % Allowed : 17.84 % Favored : 80.71 % 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: -0.23 (0.22), residues: 1526 helix: 0.81 (0.26), residues: 467 sheet: -0.09 (0.37), residues: 183 loop : -0.67 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 335 HIS 0.003 0.001 HIS B 677 PHE 0.045 0.001 PHE D 581 TYR 0.007 0.001 TYR B 734 ARG 0.007 0.000 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 330) hydrogen bonds : angle 4.57845 ( 894) metal coordination : bond 0.00323 ( 35) metal coordination : angle 2.16293 ( 48) covalent geometry : bond 0.00211 (11935) covalent geometry : angle 0.49988 (16219) ********************** 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 157 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 2.204 Fit side-chains REVERT: A 419 GLN cc_start: 0.7736 (mp10) cc_final: 0.7356 (mp10) REVERT: A 498 CYS cc_start: 0.6211 (p) cc_final: 0.5808 (t) REVERT: A 653 ASP cc_start: 0.7637 (t0) cc_final: 0.7353 (t70) REVERT: B 456 GLN cc_start: 0.8192 (tp40) cc_final: 0.7875 (tp-100) REVERT: B 798 ASP cc_start: 0.7821 (t0) cc_final: 0.7517 (t0) REVERT: C 607 CYS cc_start: 0.8280 (t) cc_final: 0.7344 (m) REVERT: D 639 TRP cc_start: 0.7675 (m-10) cc_final: 0.7269 (m-10) REVERT: D 695 MET cc_start: 0.8373 (ttp) cc_final: 0.7898 (tmm) REVERT: D 707 LYS cc_start: 0.7355 (ttpp) cc_final: 0.7144 (ttpp) REVERT: D 720 MET cc_start: 0.6563 (mtp) cc_final: 0.4462 (tpt) REVERT: D 743 ASN cc_start: 0.5288 (m110) cc_final: 0.4415 (p0) outliers start: 16 outliers final: 16 residues processed: 153 average time/residue: 0.3545 time to fit residues: 77.4914 Evaluate side-chains 157 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 657 VAL 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 755 GLU 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 699 VAL Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 127 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.206473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.154405 restraints weight = 13152.983| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.05 r_work: 0.3446 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11970 Z= 0.098 Angle : 0.524 8.024 16267 Z= 0.258 Chirality : 0.040 0.255 1785 Planarity : 0.004 0.037 2107 Dihedral : 3.605 18.542 1693 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.81 % Allowed : 17.48 % Favored : 80.71 % 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: -0.21 (0.22), residues: 1526 helix: 0.83 (0.26), residues: 467 sheet: -0.10 (0.38), residues: 183 loop : -0.66 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 736 HIS 0.004 0.001 HIS B 677 PHE 0.045 0.001 PHE D 581 TYR 0.010 0.001 TYR D 734 ARG 0.006 0.000 ARG D 683 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 330) hydrogen bonds : angle 4.59224 ( 894) metal coordination : bond 0.00327 ( 35) metal coordination : angle 2.21165 ( 48) covalent geometry : bond 0.00231 (11935) covalent geometry : angle 0.51064 (16219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8405.23 seconds wall clock time: 147 minutes 24.48 seconds (8844.48 seconds total)