Starting phenix.real_space_refine on Wed Mar 4 07:26:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eih_28156/03_2026/8eih_28156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eih_28156/03_2026/8eih_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eih_28156/03_2026/8eih_28156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eih_28156/03_2026/8eih_28156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eih_28156/03_2026/8eih_28156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eih_28156/03_2026/8eih_28156.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 6, 'ARG: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: {'ASP:plan': 3, 'ARG:plan': 3, 'GLU:plan': 7, 'ASN:plan1': 1, 'GLN:plan1': 1} 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: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1} 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: {'ASP:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 5, 'PHE:plan': 7, 'HIS:plan': 2, 'GLU:plan': 13, 'GLN:plan1': 2, 'TYR:plan': 5, 'TRP:plan': 1} 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, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2, 'HIS:plan': 1} 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: 2.85, per 1000 atoms: 0.24 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: 0.90 Conformation dependent library (CDL) restraints added in 556.9 milliseconds 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: 0.46 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: 1.74 Time building geometry restraints manager: 1.26 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 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 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (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 ARG 0.005 0.000 ARG D 683 TYR 0.010 0.001 TYR D 734 PHE 0.015 0.001 PHE B 789 TRP 0.011 0.001 TRP B 736 HIS 0.007 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00351 (11935) covalent geometry : angle 0.62263 (16219) hydrogen bonds : bond 0.24837 ( 330) hydrogen bonds : angle 7.45342 ( 894) metal coordination : bond 0.00485 ( 35) metal coordination : angle 3.07869 ( 48) *********************** 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 : 0.458 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: 0.7583 (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: 0.1160 time to fit residues: 25.2607 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 : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 GLN C 656 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 = 0.4421 r_free = 0.4421 target = 0.205177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153739 restraints weight = 13224.173| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.25 r_work: 0.3407 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11970 Z= 0.131 Angle : 0.573 9.250 16267 Z= 0.282 Chirality : 0.040 0.138 1785 Planarity : 0.004 0.046 2107 Dihedral : 4.221 25.269 1693 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.18 % Allowed : 14.13 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1526 helix: -0.06 (0.26), residues: 460 sheet: -0.56 (0.39), residues: 177 loop : -0.88 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 537 TYR 0.011 0.001 TYR D 734 PHE 0.015 0.001 PHE B 789 TRP 0.014 0.001 TRP B 736 HIS 0.006 0.001 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00315 (11935) covalent geometry : angle 0.54993 (16219) hydrogen bonds : bond 0.04207 ( 330) hydrogen bonds : angle 5.59900 ( 894) metal coordination : bond 0.00438 ( 35) metal coordination : angle 3.00752 ( 48) *********************** 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 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.451 Fit side-chains REVERT: A 419 GLN cc_start: 0.7564 (mp10) cc_final: 0.7220 (mp10) REVERT: A 653 ASP cc_start: 0.7891 (t0) cc_final: 0.7366 (t0) REVERT: B 633 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8508 (tttt) REVERT: B 798 ASP cc_start: 0.8444 (t0) cc_final: 0.8191 (t0) REVERT: D 635 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8233 (t0) REVERT: D 697 GLU cc_start: 0.7456 (tp30) cc_final: 0.7001 (tp30) REVERT: D 720 MET cc_start: 0.6627 (mtp) cc_final: 0.4672 (tpt) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.1121 time to fit residues: 25.1437 Evaluate side-chains 159 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 818 VAL 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 Chi-restraints excluded: chain D residue 717 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.207030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154732 restraints weight = 13340.233| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.19 r_work: 0.3449 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1053 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= 0.089 Angle : 0.506 7.814 16267 Z= 0.248 Chirality : 0.039 0.129 1785 Planarity : 0.004 0.037 2107 Dihedral : 3.869 19.248 1693 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.99 % Allowed : 14.31 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1526 helix: 0.28 (0.26), residues: 462 sheet: -0.38 (0.39), residues: 173 loop : -0.86 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 683 TYR 0.008 0.001 TYR B 734 PHE 0.033 0.001 PHE D 581 TRP 0.013 0.001 TRP B 736 HIS 0.003 0.001 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00199 (11935) covalent geometry : angle 0.48774 (16219) hydrogen bonds : bond 0.03137 ( 330) hydrogen bonds : angle 5.06508 ( 894) metal coordination : bond 0.00349 ( 35) metal coordination : angle 2.50219 ( 48) *********************** 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 178 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.419 Fit side-chains REVERT: A 419 GLN cc_start: 0.7589 (mp10) cc_final: 0.7249 (mp10) REVERT: A 498 CYS cc_start: 0.6222 (p) cc_final: 0.5646 (t) REVERT: A 653 ASP cc_start: 0.7718 (t0) cc_final: 0.7278 (t0) REVERT: B 470 ASP cc_start: 0.7946 (m-30) cc_final: 0.7689 (m-30) REVERT: B 633 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.7883 (tttt) REVERT: C 456 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 477 TYR cc_start: 0.8241 (m-80) cc_final: 0.8008 (m-80) REVERT: D 639 TRP cc_start: 0.7624 (m-10) cc_final: 0.7270 (m-10) REVERT: D 697 GLU cc_start: 0.7510 (tp30) cc_final: 0.7301 (tp30) REVERT: D 720 MET cc_start: 0.6549 (mtp) cc_final: 0.4609 (tpt) REVERT: D 735 PHE cc_start: 0.7355 (m-80) cc_final: 0.6994 (m-80) REVERT: E 242 MET cc_start: 0.6568 (tpp) cc_final: 0.6366 (tpt) outliers start: 22 outliers final: 9 residues processed: 169 average time/residue: 0.1053 time to fit residues: 25.4986 Evaluate side-chains 152 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 110 optimal weight: 0.0000 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 135 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 GLN B 456 GLN D 698 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 = 0.4439 r_free = 0.4439 target = 0.206825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154473 restraints weight = 13333.465| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.09 r_work: 0.3403 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1203 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= 0.095 Angle : 0.509 7.281 16267 Z= 0.251 Chirality : 0.039 0.175 1785 Planarity : 0.004 0.039 2107 Dihedral : 3.792 18.586 1693 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.45 % Allowed : 14.31 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1526 helix: 0.41 (0.26), residues: 465 sheet: -0.39 (0.37), residues: 189 loop : -0.80 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 708 TYR 0.007 0.001 TYR C 525 PHE 0.010 0.001 PHE B 673 TRP 0.013 0.001 TRP B 736 HIS 0.007 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00222 (11935) covalent geometry : angle 0.49194 (16219) hydrogen bonds : bond 0.03018 ( 330) hydrogen bonds : angle 4.88634 ( 894) metal coordination : bond 0.00356 ( 35) metal coordination : angle 2.44626 ( 48) *********************** 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: 27 poor density : 156 time to evaluate : 0.409 Fit side-chains REVERT: A 419 GLN cc_start: 0.7578 (mp10) cc_final: 0.7209 (mp10) REVERT: A 498 CYS cc_start: 0.6186 (p) cc_final: 0.5640 (t) REVERT: A 653 ASP cc_start: 0.7700 (t0) cc_final: 0.7269 (t0) REVERT: A 702 MET cc_start: 0.8363 (ptt) cc_final: 0.8035 (ptt) REVERT: B 470 ASP cc_start: 0.7882 (m-30) cc_final: 0.7635 (m-30) REVERT: B 633 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (tttt) REVERT: C 477 TYR cc_start: 0.8283 (m-80) cc_final: 0.8054 (m-80) REVERT: C 607 CYS cc_start: 0.8340 (t) cc_final: 0.7342 (m) REVERT: D 639 TRP cc_start: 0.7636 (m-10) cc_final: 0.7326 (m-10) REVERT: D 697 GLU cc_start: 0.7570 (tp30) cc_final: 0.7326 (tp30) REVERT: D 707 LYS cc_start: 0.7363 (ttpp) cc_final: 0.7070 (ttpp) REVERT: D 720 MET cc_start: 0.6438 (mtp) cc_final: 0.4556 (tpt) REVERT: D 735 PHE cc_start: 0.7292 (m-80) cc_final: 0.6948 (m-80) REVERT: D 743 ASN cc_start: 0.5371 (m110) cc_final: 0.5094 (t0) REVERT: D 852 CYS cc_start: 0.2120 (OUTLIER) cc_final: 0.1904 (m) outliers start: 27 outliers final: 17 residues processed: 177 average time/residue: 0.1086 time to fit residues: 27.4983 Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 852 CYS 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 37 optimal weight: 0.8980 chunk 122 optimal weight: 50.0000 chunk 65 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.0470 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.207226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154997 restraints weight = 13312.730| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.12 r_work: 0.3457 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1341 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= 0.089 Angle : 0.496 7.278 16267 Z= 0.245 Chirality : 0.039 0.198 1785 Planarity : 0.004 0.031 2107 Dihedral : 3.679 18.082 1693 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.36 % Allowed : 14.86 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1526 helix: 0.55 (0.26), residues: 464 sheet: -0.24 (0.38), residues: 184 loop : -0.77 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.007 0.001 TYR A 665 PHE 0.039 0.001 PHE D 581 TRP 0.029 0.001 TRP E 335 HIS 0.004 0.001 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00205 (11935) covalent geometry : angle 0.48055 (16219) hydrogen bonds : bond 0.02823 ( 330) hydrogen bonds : angle 4.73548 ( 894) metal coordination : bond 0.00325 ( 35) metal coordination : angle 2.30661 ( 48) *********************** 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 184 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.455 Fit side-chains REVERT: A 419 GLN cc_start: 0.7525 (mp10) cc_final: 0.7152 (mp10) REVERT: A 498 CYS cc_start: 0.6207 (p) cc_final: 0.5712 (t) REVERT: A 653 ASP cc_start: 0.7613 (t0) cc_final: 0.7251 (t70) REVERT: B 633 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8198 (tttt) REVERT: C 477 TYR cc_start: 0.8277 (m-80) cc_final: 0.8057 (m-80) REVERT: C 607 CYS cc_start: 0.8377 (t) cc_final: 0.7413 (m) REVERT: D 639 TRP cc_start: 0.7712 (m-10) cc_final: 0.7457 (m-10) REVERT: D 707 LYS cc_start: 0.7435 (ttpp) cc_final: 0.7067 (ttpp) REVERT: D 714 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6628 (mm) REVERT: D 715 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6644 (mm-30) REVERT: D 720 MET cc_start: 0.6436 (mtp) cc_final: 0.4511 (tpt) REVERT: D 734 TYR cc_start: 0.7277 (m-80) cc_final: 0.7065 (m-80) REVERT: E 247 LYS cc_start: 0.5614 (mttm) cc_final: 0.5243 (mttp) outliers start: 26 outliers final: 19 residues processed: 177 average time/residue: 0.1006 time to fit residues: 25.8675 Evaluate side-chains 168 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 479 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU 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 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 100 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.0170 chunk 121 optimal weight: 40.0000 chunk 150 optimal weight: 6.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS B 456 GLN D 635 ASN ** D 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 841 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.202980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149615 restraints weight = 13187.196| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.03 r_work: 0.3379 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11970 Z= 0.212 Angle : 0.628 7.813 16267 Z= 0.310 Chirality : 0.043 0.215 1785 Planarity : 0.005 0.038 2107 Dihedral : 4.298 23.415 1693 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1526 helix: 0.35 (0.26), residues: 464 sheet: -0.41 (0.37), residues: 189 loop : -0.86 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 683 TYR 0.013 0.002 TYR B 815 PHE 0.037 0.002 PHE D 581 TRP 0.016 0.002 TRP B 736 HIS 0.009 0.002 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00534 (11935) covalent geometry : angle 0.60622 (16219) hydrogen bonds : bond 0.04787 ( 330) hydrogen bonds : angle 5.10662 ( 894) metal coordination : bond 0.00526 ( 35) metal coordination : angle 3.08861 ( 48) *********************** 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 192 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.373 Fit side-chains REVERT: A 419 GLN cc_start: 0.7610 (mp10) cc_final: 0.7228 (mp10) REVERT: A 498 CYS cc_start: 0.5826 (p) cc_final: 0.5594 (t) REVERT: A 653 ASP cc_start: 0.7902 (t0) cc_final: 0.7407 (t0) REVERT: B 456 GLN cc_start: 0.8178 (tp40) cc_final: 0.7824 (tp-100) REVERT: B 470 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: B 633 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8391 (tttt) REVERT: C 607 CYS cc_start: 0.8392 (t) cc_final: 0.7408 (m) REVERT: D 635 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8151 (t0) REVERT: D 707 LYS cc_start: 0.7404 (ttpp) cc_final: 0.6931 (ttpp) REVERT: D 720 MET cc_start: 0.6563 (mtp) cc_final: 0.4534 (tpt) outliers start: 34 outliers final: 26 residues processed: 182 average time/residue: 0.1038 time to fit residues: 27.4191 Evaluate side-chains 185 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 747 ILE 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 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 755 GLU 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 D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 841 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 0.0070 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.205486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152869 restraints weight = 13168.347| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.21 r_work: 0.3413 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11970 Z= 0.102 Angle : 0.533 7.577 16267 Z= 0.261 Chirality : 0.040 0.218 1785 Planarity : 0.004 0.038 2107 Dihedral : 4.005 19.791 1693 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.72 % Allowed : 16.12 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1526 helix: 0.43 (0.26), residues: 467 sheet: -0.34 (0.37), residues: 188 loop : -0.78 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 683 TYR 0.016 0.001 TYR C 477 PHE 0.042 0.001 PHE D 581 TRP 0.016 0.001 TRP E 335 HIS 0.018 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00240 (11935) covalent geometry : angle 0.51455 (16219) hydrogen bonds : bond 0.03208 ( 330) hydrogen bonds : angle 4.82916 ( 894) metal coordination : bond 0.00381 ( 35) metal coordination : angle 2.63855 ( 48) *********************** 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 185 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.436 Fit side-chains REVERT: A 419 GLN cc_start: 0.7706 (mp10) cc_final: 0.7353 (mp10) REVERT: A 498 CYS cc_start: 0.5761 (p) cc_final: 0.5538 (t) REVERT: A 653 ASP cc_start: 0.7705 (t0) cc_final: 0.7258 (t0) REVERT: A 720 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8266 (ttp) REVERT: B 456 GLN cc_start: 0.8157 (tp40) cc_final: 0.7779 (tp-100) REVERT: B 633 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8246 (tttt) REVERT: C 607 CYS cc_start: 0.8448 (t) cc_final: 0.7406 (m) REVERT: D 639 TRP cc_start: 0.7604 (m-10) cc_final: 0.7256 (m-10) REVERT: D 697 GLU cc_start: 0.7047 (tp30) cc_final: 0.6796 (tp30) REVERT: D 702 MET cc_start: 0.6555 (ttm) cc_final: 0.5826 (mtm) REVERT: D 707 LYS cc_start: 0.7215 (ttpp) cc_final: 0.6888 (ttpp) REVERT: D 720 MET cc_start: 0.6516 (mtp) cc_final: 0.4543 (tpt) REVERT: D 734 TYR cc_start: 0.7425 (m-80) cc_final: 0.7065 (m-80) REVERT: E 247 LYS cc_start: 0.5800 (mttp) cc_final: 0.5587 (mttm) outliers start: 30 outliers final: 21 residues processed: 177 average time/residue: 0.1073 time to fit residues: 27.2931 Evaluate side-chains 173 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 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 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 755 GLU 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 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 714 LEU 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 2 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 0.0970 chunk 5 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 841 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.206143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.153823 restraints weight = 13272.612| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.21 r_work: 0.3444 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1534 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= 0.096 Angle : 0.520 7.538 16267 Z= 0.256 Chirality : 0.039 0.228 1785 Planarity : 0.004 0.036 2107 Dihedral : 3.824 19.368 1693 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.36 % Allowed : 16.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1526 helix: 0.61 (0.27), residues: 465 sheet: -0.32 (0.37), residues: 189 loop : -0.71 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 683 TYR 0.012 0.001 TYR C 477 PHE 0.043 0.001 PHE D 581 TRP 0.015 0.001 TRP E 335 HIS 0.007 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00222 (11935) covalent geometry : angle 0.50341 (16219) hydrogen bonds : bond 0.02944 ( 330) hydrogen bonds : angle 4.68201 ( 894) metal coordination : bond 0.00354 ( 35) metal coordination : angle 2.44203 ( 48) *********************** 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 174 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.439 Fit side-chains REVERT: A 419 GLN cc_start: 0.7731 (mp10) cc_final: 0.7361 (mp10) REVERT: A 498 CYS cc_start: 0.6245 (p) cc_final: 0.5816 (t) REVERT: A 653 ASP cc_start: 0.7731 (t0) cc_final: 0.7337 (t70) REVERT: B 798 ASP cc_start: 0.7851 (t0) cc_final: 0.7615 (t0) REVERT: C 607 CYS cc_start: 0.8243 (t) cc_final: 0.7306 (m) REVERT: D 639 TRP cc_start: 0.7616 (m-10) cc_final: 0.7272 (m-10) REVERT: D 695 MET cc_start: 0.8454 (ttp) cc_final: 0.7954 (tmm) REVERT: D 707 LYS cc_start: 0.7267 (ttpp) cc_final: 0.7061 (ttpp) REVERT: D 720 MET cc_start: 0.6518 (mtp) cc_final: 0.4555 (tpt) REVERT: D 734 TYR cc_start: 0.7420 (m-80) cc_final: 0.7194 (m-80) outliers start: 26 outliers final: 22 residues processed: 169 average time/residue: 0.1087 time to fit residues: 26.3274 Evaluate side-chains 161 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 841 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 83 optimal weight: 0.0370 chunk 41 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 GLN D 841 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.206734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.153393 restraints weight = 13088.342| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.10 r_work: 0.3407 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1609 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= 0.090 Angle : 0.516 7.330 16267 Z= 0.253 Chirality : 0.039 0.238 1785 Planarity : 0.004 0.037 2107 Dihedral : 3.734 18.919 1693 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.36 % Allowed : 16.85 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1526 helix: 0.71 (0.26), residues: 465 sheet: -0.29 (0.37), residues: 189 loop : -0.68 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 683 TYR 0.012 0.001 TYR C 477 PHE 0.046 0.001 PHE D 581 TRP 0.014 0.001 TRP E 335 HIS 0.016 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00204 (11935) covalent geometry : angle 0.50106 (16219) hydrogen bonds : bond 0.02737 ( 330) hydrogen bonds : angle 4.61178 ( 894) metal coordination : bond 0.00335 ( 35) metal coordination : angle 2.33274 ( 48) *********************** 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 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.392 Fit side-chains REVERT: A 419 GLN cc_start: 0.7730 (mp10) cc_final: 0.7347 (mp10) REVERT: A 498 CYS cc_start: 0.6270 (p) cc_final: 0.5810 (t) REVERT: A 653 ASP cc_start: 0.7697 (t0) cc_final: 0.7383 (t70) REVERT: A 720 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8254 (ttp) REVERT: C 607 CYS cc_start: 0.8268 (t) cc_final: 0.7341 (m) REVERT: D 639 TRP cc_start: 0.7654 (m-10) cc_final: 0.7330 (m-10) REVERT: D 695 MET cc_start: 0.8481 (ttp) cc_final: 0.7978 (tmm) REVERT: D 720 MET cc_start: 0.6456 (mtp) cc_final: 0.4521 (tpt) REVERT: D 734 TYR cc_start: 0.7432 (m-80) cc_final: 0.7078 (m-80) REVERT: E 247 LYS cc_start: 0.6313 (mttm) cc_final: 0.6107 (mttp) outliers start: 26 outliers final: 24 residues processed: 159 average time/residue: 0.1011 time to fit residues: 23.3827 Evaluate side-chains 162 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 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 755 GLU 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 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 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 841 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 97 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 841 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.205653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155285 restraints weight = 13295.720| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.34 r_work: 0.3357 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11970 Z= 0.120 Angle : 0.543 7.657 16267 Z= 0.266 Chirality : 0.040 0.252 1785 Planarity : 0.004 0.036 2107 Dihedral : 3.803 19.103 1693 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.36 % Allowed : 17.03 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1526 helix: 0.67 (0.26), residues: 465 sheet: -0.29 (0.37), residues: 189 loop : -0.70 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 683 TYR 0.012 0.001 TYR C 477 PHE 0.047 0.001 PHE D 581 TRP 0.014 0.001 TRP B 736 HIS 0.019 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00292 (11935) covalent geometry : angle 0.52725 (16219) hydrogen bonds : bond 0.03264 ( 330) hydrogen bonds : angle 4.69029 ( 894) metal coordination : bond 0.00372 ( 35) metal coordination : angle 2.46972 ( 48) ********************** 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 165 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.456 Fit side-chains REVERT: A 419 GLN cc_start: 0.7747 (mp10) cc_final: 0.7374 (mp10) REVERT: A 498 CYS cc_start: 0.5998 (p) cc_final: 0.5604 (t) REVERT: A 653 ASP cc_start: 0.7621 (t0) cc_final: 0.7284 (t70) REVERT: A 720 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8201 (ttp) REVERT: B 798 ASP cc_start: 0.7654 (t0) cc_final: 0.7427 (t0) REVERT: C 592 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7242 (mmmm) REVERT: C 607 CYS cc_start: 0.8227 (t) cc_final: 0.7331 (m) REVERT: D 639 TRP cc_start: 0.7602 (m-10) cc_final: 0.7302 (m-10) REVERT: D 695 MET cc_start: 0.8421 (ttp) cc_final: 0.7859 (tmm) REVERT: D 720 MET cc_start: 0.6528 (mtp) cc_final: 0.4555 (tpt) REVERT: D 734 TYR cc_start: 0.7417 (m-80) cc_final: 0.7121 (m-80) REVERT: E 247 LYS cc_start: 0.6274 (mttm) cc_final: 0.6049 (mttp) outliers start: 26 outliers final: 24 residues processed: 159 average time/residue: 0.1041 time to fit residues: 23.9792 Evaluate side-chains 163 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 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 755 GLU Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 841 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 92 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 115 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 GLN D 841 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.205918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152499 restraints weight = 13286.079| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11970 Z= 0.109 Angle : 0.537 7.832 16267 Z= 0.263 Chirality : 0.040 0.244 1785 Planarity : 0.004 0.036 2107 Dihedral : 3.801 18.970 1693 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.36 % Allowed : 17.21 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1526 helix: 0.70 (0.26), residues: 465 sheet: -0.25 (0.37), residues: 188 loop : -0.70 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 683 TYR 0.012 0.001 TYR C 477 PHE 0.047 0.001 PHE D 581 TRP 0.014 0.001 TRP B 736 HIS 0.016 0.001 HIS D 841 Details of bonding type rmsd covalent geometry : bond 0.00264 (11935) covalent geometry : angle 0.52094 (16219) hydrogen bonds : bond 0.03135 ( 330) hydrogen bonds : angle 4.67587 ( 894) metal coordination : bond 0.00361 ( 35) metal coordination : angle 2.43944 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.59 seconds wall clock time: 66 minutes 31.84 seconds (3991.84 seconds total)