Starting phenix.real_space_refine on Fri Mar 15 12:59:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eih_28156/03_2024/8eih_28156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eih_28156/03_2024/8eih_28156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eih_28156/03_2024/8eih_28156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eih_28156/03_2024/8eih_28156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eih_28156/03_2024/8eih_28156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eih_28156/03_2024/8eih_28156_updated.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 96 5.16 5 C 7437 2.51 5 N 2050 2.21 5 O 2079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "D GLU 715": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11674 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3299 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3337 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2447 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 309} Chain breaks: 4 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1714 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 243} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 224 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 813 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 151 SG CYS A 435 82.339 69.538 117.544 1.00126.66 S ATOM 171 SG CYS A 438 81.281 73.151 117.466 1.00137.29 S ATOM 294 SG CYS A 455 79.289 70.608 119.511 1.00127.10 S ATOM 316 SG CYS A 458 79.063 70.486 115.782 1.00133.66 S ATOM 495 SG CYS A 478 82.756 68.639 105.514 1.00130.80 S ATOM 515 SG CYS A 481 81.670 70.990 108.262 1.00128.12 S ATOM 639 SG CYS A 500 82.879 72.468 104.918 1.00142.38 S ATOM 661 SG CYS A 503 85.252 70.755 107.426 1.00142.63 S ATOM 567 SG CYS A 490 87.160 59.995 96.197 1.00133.23 S ATOM 600 SG CYS A 495 85.877 57.393 98.769 1.00138.50 S ATOM 811 SG CYS A 524 88.313 60.156 99.814 1.00149.11 S ATOM 837 SG CYS A 527 89.406 57.214 97.792 1.00153.35 S ATOM 3458 SG CYS B 435 26.482 34.984 43.928 1.00107.06 S ATOM 3478 SG CYS B 438 25.642 38.354 42.529 1.00105.38 S ATOM 3608 SG CYS B 455 28.783 36.531 41.264 1.00 89.91 S ATOM 3630 SG CYS B 458 28.748 37.867 44.764 1.00 82.47 S ATOM 3806 SG CYS B 478 24.908 38.963 55.421 1.00103.60 S ATOM 3826 SG CYS B 481 25.343 40.377 51.937 1.00 99.08 S ATOM 3962 SG CYS B 500 23.000 42.234 54.368 1.00119.13 S ATOM 3984 SG CYS B 503 22.182 38.800 52.801 1.00114.49 S ATOM 3889 SG CYS B 490 24.814 34.219 67.626 1.00114.77 S ATOM 3922 SG CYS B 495 27.722 32.185 65.949 1.00117.36 S ATOM 4126 SG CYS B 524 24.328 32.272 64.366 1.00115.56 S ATOM 4152 SG CYS B 527 25.004 30.342 67.524 1.00118.61 S ATOM 6757 SG CYS C 435 69.941 73.987 51.066 1.00137.66 S ATOM 6892 SG CYS C 455 69.420 71.287 52.692 1.00120.67 S ATOM 6914 SG CYS C 458 67.087 72.382 51.309 1.00118.17 S ATOM 7093 SG CYS C 478 63.180 78.816 42.041 1.00120.84 S ATOM 7113 SG CYS C 481 63.031 77.580 45.608 1.00122.77 S ATOM 7251 SG CYS C 500 60.681 80.337 44.593 1.00131.73 S ATOM 7273 SG CYS C 503 64.397 81.021 44.984 1.00134.42 S ATOM 7178 SG CYS C 490 64.153 82.721 29.454 1.00131.14 S ATOM 7211 SG CYS C 495 66.343 79.492 29.223 1.00138.37 S ATOM 7405 SG CYS C 524 67.100 82.180 31.639 1.00146.42 S ATOM 7428 SG CYS C 527 67.794 82.641 27.924 1.00141.68 S Time building chain proxies: 6.45, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 4.10 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 455 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 435 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 438 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 458 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 481 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 503 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 478 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 500 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 527 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 495 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 490 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 458 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 435 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 438 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 503 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 481 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 500 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 524 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 455 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 435 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 458 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 481 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 503 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 500 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 478 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 524 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 495 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 527 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 490 " Number of angles added : 48 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 10 sheets defined 31.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 456 through 465 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 505 removed outlier: 3.938A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 505' Processing helix chain 'A' and resid 513 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 542 through 551 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 586 through 594 Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.555A pdb=" N ALA A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.587A pdb=" N GLU A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.579A pdb=" N ARG A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 671 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 672 " --> pdb=" O GLY A 669 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 679 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 681 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 3.564A pdb=" N ASP A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 756 through 759 Processing helix chain 'A' and resid 802 through 809 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 823 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 836 through 848 Proline residue: A 845 - end of helix removed outlier: 5.477A pdb=" N ASP A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 456 through 465 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 505 removed outlier: 4.180A pdb=" N GLU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 505' Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 542 through 551 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 586 through 593 Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.676A pdb=" N ALA B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.852A pdb=" N GLU B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 removed outlier: 3.633A pdb=" N ARG B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 671 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 672 " --> pdb=" O GLY B 669 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 679 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 681 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 714 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 756 through 759 Processing helix chain 'B' and resid 802 through 809 removed outlier: 3.525A pdb=" N ARG B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 831 Processing helix chain 'B' and resid 836 through 848 removed outlier: 3.509A pdb=" N HIS B 841 " --> pdb=" O PRO B 837 " (cutoff:3.500A) Proline residue: B 845 - end of helix removed outlier: 5.507A pdb=" N ASP B 848 " --> pdb=" O ALA B 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 426 removed outlier: 3.515A pdb=" N ALA C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 456 through 467 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) removed outlier: 6.184A pdb=" N TYR C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 506 No H-bonds generated for 'chain 'C' and resid 503 through 506' Processing helix chain 'C' and resid 512 through 517 Processing helix chain 'C' and resid 545 through 550 removed outlier: 3.557A pdb=" N PHE C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 586 through 593 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 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 669 through 682 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 704 through 714 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 848 Proline residue: C 845 - end of helix removed outlier: 5.768A pdb=" N ASP C 848 " --> pdb=" O ALA C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 removed outlier: 3.759A pdb=" N ASP D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 549 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 586 through 594 removed outlier: 3.713A pdb=" N VAL D 590 " --> pdb=" O THR D 586 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 594 " --> pdb=" O VAL D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 630 No H-bonds generated for 'chain 'D' and resid 628 through 630' Processing helix chain 'D' and resid 633 through 639 Processing helix chain 'D' and resid 669 through 682 removed outlier: 4.184A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 714 Processing helix chain 'D' and resid 723 through 725 No H-bonds generated for 'chain 'D' and resid 723 through 725' Processing helix chain 'D' and resid 836 through 848 Proline residue: D 845 - end of helix removed outlier: 5.831A pdb=" N ASP D 848 " --> pdb=" O ALA D 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 296 through 312 Processing helix chain 'E' and resid 330 through 337 Processing helix chain 'E' and resid 346 through 348 No H-bonds generated for 'chain 'E' and resid 346 through 348' Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.559A pdb=" N GLU A 697 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 648 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 577 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR A 601 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 579 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 603 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS A 623 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 791 through 793 removed outlier: 3.641A pdb=" N VAL A 791 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 487 through 489 Processing sheet with id= E, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.553A pdb=" N GLU B 697 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 648 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL B 577 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR B 601 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER B 579 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 603 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 623 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 791 through 793 removed outlier: 3.849A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 577 through 580 removed outlier: 6.086A pdb=" N LEU C 644 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU C 580 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE C 646 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE C 693 " --> pdb=" O VAL C 645 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY C 647 " --> pdb=" O PHE C 693 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET C 695 " --> pdb=" O GLY C 647 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.727A pdb=" N ALA C 603 " --> pdb=" O LYS C 623 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 719 through 722 removed outlier: 3.670A pdb=" N ASN D 698 " --> pdb=" O TYR D 734 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP D 736 " --> pdb=" O PHE D 696 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 644 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL D 577 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR D 601 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N SER D 579 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA D 603 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 241 through 243 249 hydrogen bonds defined for protein. 678 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: 2.78 Time building geometry restraints manager: 4.52 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: 91.50 - 100.01: 4 100.01 - 108.52: 591 108.52 - 117.03: 7570 117.03 - 125.54: 7833 125.54 - 134.04: 221 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: 2174 2.77 - 3.30: 10192 3.30 - 3.83: 17401 3.83 - 4.37: 20322 4.37 - 4.90: 36187 Nonbonded interactions: 86276 Sorted by model distance: nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR A 632 " pdb=" OD1 ASN A 635 " model vdw 2.241 2.440 nonbonded pdb=" O PHE C 450 " pdb=" NH2 ARG C 539 " model vdw 2.268 2.520 nonbonded pdb=" O SER B 819 " pdb=" OG SER B 819 " model vdw 2.295 2.440 nonbonded pdb=" O GLY D 453 " pdb="ZN ZN D 901 " model vdw 2.296 2.230 ... (remaining 86271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 414 through 427 or (resid 428 and (name N or name CA or na \ me C or name O or name CB )) or resid 429 through 470 or (resid 471 through 472 \ and (name N or name CA or name C or name O or name CB )) or resid 473 through 51 \ 4 or (resid 515 through 516 and (name N or name CA or name C or name O or name C \ B )) or resid 517 through 519 or (resid 520 and (name N or name CA or name C or \ name O or name CB )) or resid 521 through 555 or (resid 556 through 557 and (nam \ e N or name CA or name C or name O or name CB )) or resid 558 through 561 or (re \ sid 562 and (name N or name CA or name C or name O or name CB or name CG )) or r \ esid 563 through 607 or (resid 608 and (name N or name CA or name C or name O or \ name CB )) or resid 609 through 633 or (resid 634 and (name N or name CA or nam \ e C or name O or name CB )) or resid 635 through 707 or (resid 708 and (name N o \ r name CA or name C or name O or name CB )) or resid 709 through 724 or (resid 7 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 726 through \ 773 or (resid 774 and (name N or name CA or name C or name O or name CB )) or r \ esid 788 through 796 or (resid 797 and (name N or name CA or name C or name O or \ name CB )) or resid 798 through 853 or resid 901 or resid 902 through 904)) selection = (chain 'B' and ((resid 414 and (name N or name CA or name C or name O or name CB \ )) or resid 415 through 422 or (resid 423 and (name N or name CA or name C or n \ ame O or name CB )) or resid 424 through 426 or (resid 427 through 428 and (name \ N or name CA or name C or name O or name CB )) or resid 429 through 432 or (res \ id 433 and (name N or name CA or name C or name O or name CB )) or resid 434 thr \ ough 440 or (resid 441 through 442 and (name N or name CA or name C or name O or \ name CB )) or resid 443 through 482 or (resid 483 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 484 through 487 and (name N or name CA or \ name C or name O or name CB )) or resid 488 through 495 or (resid 496 and (name \ N or name CA or name C or name O or name CB )) or resid 497 through 530 or (resi \ d 531 and (name N or name CA or name C or name O or name CB )) or resid 532 thro \ ugh 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) o \ r resid 538 through 539 or (resid 540 and (name N or name CA or name C or name O \ or name CB )) or resid 541 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 572 or (resid 573 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE )) \ or resid 574 through 702 or (resid 703 and (name N or name CA or name C or name \ O or name CB )) or resid 704 through 766 or (resid 767 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or resid 768 through 774 o \ r resid 788 through 795 or (resid 796 through 797 and (name N or name CA or name \ C or name O or name CB )) or resid 798 through 853 or resid 901 or resid 902 th \ rough 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.820 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.450 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 11935 Z= 0.241 Angle : 0.623 10.268 16219 Z= 0.313 Chirality : 0.041 0.187 1785 Planarity : 0.004 0.083 2107 Dihedral : 14.895 90.178 4092 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.27 % Allowed : 13.41 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1526 helix: -0.40 (0.26), residues: 441 sheet: -1.17 (0.39), residues: 189 loop : -0.89 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 736 HIS 0.007 0.001 HIS A 618 PHE 0.015 0.001 PHE B 789 TYR 0.010 0.001 TYR D 734 ARG 0.005 0.000 ARG D 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 1.411 Fit side-chains REVERT: A 419 GLN cc_start: 0.7478 (mp10) cc_final: 0.7257 (mp10) REVERT: D 639 TRP cc_start: 0.7793 (m-10) cc_final: 0.7569 (m-10) REVERT: D 720 MET cc_start: 0.7335 (mtp) cc_final: 0.5308 (tpt) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.2449 time to fit residues: 53.1626 Evaluate side-chains 150 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.0000 chunk 139 optimal weight: 3.9990 overall best weight: 0.5484 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11935 Z= 0.149 Angle : 0.498 9.375 16219 Z= 0.251 Chirality : 0.039 0.129 1785 Planarity : 0.004 0.045 2107 Dihedral : 3.978 25.034 1693 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.00 % Allowed : 14.49 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1526 helix: -0.24 (0.26), residues: 454 sheet: -0.49 (0.40), residues: 173 loop : -0.86 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 736 HIS 0.006 0.001 HIS D 841 PHE 0.013 0.001 PHE B 789 TYR 0.009 0.001 TYR D 734 ARG 0.005 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.278 Fit side-chains REVERT: A 419 GLN cc_start: 0.7490 (mp10) cc_final: 0.7218 (mp10) REVERT: B 633 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (tttt) REVERT: D 707 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7483 (ttpp) REVERT: D 720 MET cc_start: 0.7108 (mtp) cc_final: 0.5398 (tpt) outliers start: 11 outliers final: 6 residues processed: 161 average time/residue: 0.2535 time to fit residues: 57.0448 Evaluate side-chains 158 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 695 MET Chi-restraints excluded: chain D residue 699 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 38 optimal weight: 0.0980 chunk 140 optimal weight: 0.0970 chunk 151 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 GLN D 635 ASN D 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11935 Z= 0.141 Angle : 0.480 7.679 16219 Z= 0.240 Chirality : 0.039 0.129 1785 Planarity : 0.004 0.040 2107 Dihedral : 3.768 18.544 1693 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.08 % Allowed : 14.04 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1526 helix: -0.00 (0.26), residues: 451 sheet: -0.35 (0.40), residues: 173 loop : -0.84 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 736 HIS 0.005 0.001 HIS B 677 PHE 0.032 0.001 PHE D 581 TYR 0.008 0.001 TYR C 525 ARG 0.003 0.000 ARG D 683 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.408 Fit side-chains REVERT: A 419 GLN cc_start: 0.7510 (mp10) cc_final: 0.7204 (mp10) REVERT: A 498 CYS cc_start: 0.5814 (p) cc_final: 0.5229 (t) REVERT: A 653 ASP cc_start: 0.7737 (t0) cc_final: 0.7032 (t0) REVERT: B 633 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8334 (tttt) REVERT: D 635 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8105 (t0) REVERT: D 639 TRP cc_start: 0.7794 (m-10) cc_final: 0.7405 (m-10) REVERT: D 707 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7592 (ttpp) REVERT: D 720 MET cc_start: 0.6966 (mtp) cc_final: 0.5357 (tpt) outliers start: 23 outliers final: 11 residues processed: 168 average time/residue: 0.2475 time to fit residues: 58.8797 Evaluate side-chains 161 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 30.0000 chunk 105 optimal weight: 0.2980 chunk 72 optimal weight: 0.2980 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 0.0170 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS B 419 GLN D 698 ASN D 841 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11935 Z= 0.126 Angle : 0.468 7.298 16219 Z= 0.236 Chirality : 0.038 0.138 1785 Planarity : 0.004 0.038 2107 Dihedral : 3.663 17.971 1693 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.17 % Allowed : 14.49 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1526 helix: 0.07 (0.26), residues: 459 sheet: -0.30 (0.39), residues: 173 loop : -0.81 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 736 HIS 0.007 0.001 HIS D 841 PHE 0.011 0.001 PHE B 789 TYR 0.007 0.001 TYR B 734 ARG 0.004 0.000 ARG B 537 *********************** 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 177 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.342 Fit side-chains REVERT: A 419 GLN cc_start: 0.7512 (mp10) cc_final: 0.7185 (mp10) REVERT: A 498 CYS cc_start: 0.5856 (p) cc_final: 0.5320 (t) REVERT: A 653 ASP cc_start: 0.7793 (t0) cc_final: 0.7090 (t0) REVERT: B 633 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8337 (tttt) REVERT: D 674 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7461 (mm-30) REVERT: D 707 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7618 (ttpp) REVERT: D 720 MET cc_start: 0.6951 (mtp) cc_final: 0.5286 (tpt) outliers start: 24 outliers final: 13 residues processed: 168 average time/residue: 0.2588 time to fit residues: 60.7664 Evaluate side-chains 162 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 682 SER Chi-restraints excluded: chain D residue 699 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 30.0000 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN D 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11935 Z= 0.289 Angle : 0.571 8.085 16219 Z= 0.288 Chirality : 0.042 0.153 1785 Planarity : 0.004 0.037 2107 Dihedral : 4.154 23.489 1693 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.99 % Allowed : 14.40 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1526 helix: -0.11 (0.26), residues: 457 sheet: -0.46 (0.37), residues: 188 loop : -0.84 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 335 HIS 0.011 0.002 HIS B 677 PHE 0.036 0.002 PHE D 581 TYR 0.013 0.001 TYR B 815 ARG 0.006 0.000 ARG D 683 *********************** 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 187 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.336 Fit side-chains REVERT: A 419 GLN cc_start: 0.7541 (mp10) cc_final: 0.7179 (mp10) REVERT: A 653 ASP cc_start: 0.7829 (t0) cc_final: 0.7078 (t0) REVERT: B 633 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8484 (tttt) REVERT: C 847 LYS cc_start: 0.9046 (mmtp) cc_final: 0.8831 (mttm) REVERT: D 674 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7499 (mm-30) REVERT: D 707 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7701 (ttpp) REVERT: D 720 MET cc_start: 0.7073 (mtp) cc_final: 0.5380 (tpt) outliers start: 33 outliers final: 25 residues processed: 173 average time/residue: 0.2427 time to fit residues: 60.4373 Evaluate side-chains 174 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 682 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.0010 chunk 78 optimal weight: 0.0870 overall best weight: 0.6966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN D 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11935 Z= 0.159 Angle : 0.491 7.294 16219 Z= 0.248 Chirality : 0.039 0.134 1785 Planarity : 0.004 0.036 2107 Dihedral : 3.879 19.165 1693 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.99 % Allowed : 15.31 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1526 helix: -0.05 (0.26), residues: 458 sheet: -0.28 (0.38), residues: 183 loop : -0.83 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 736 HIS 0.005 0.001 HIS B 677 PHE 0.040 0.001 PHE D 581 TYR 0.008 0.001 TYR B 734 ARG 0.005 0.000 ARG D 683 *********************** 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 186 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.469 Fit side-chains REVERT: A 419 GLN cc_start: 0.7550 (mp10) cc_final: 0.7210 (mp10) REVERT: A 653 ASP cc_start: 0.7834 (t0) cc_final: 0.7112 (t0) REVERT: A 769 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7687 (ptpp) REVERT: B 633 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8463 (tttt) REVERT: D 635 ASN cc_start: 0.8688 (t0) cc_final: 0.8148 (t0) REVERT: D 639 TRP cc_start: 0.7734 (m-10) cc_final: 0.7294 (m-10) REVERT: D 674 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7495 (mm-30) REVERT: D 707 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7669 (ttpp) REVERT: D 720 MET cc_start: 0.7027 (mtp) cc_final: 0.5318 (tpt) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.2494 time to fit residues: 61.6478 Evaluate side-chains 172 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU 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 682 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11935 Z= 0.201 Angle : 0.521 7.880 16219 Z= 0.261 Chirality : 0.040 0.137 1785 Planarity : 0.004 0.035 2107 Dihedral : 3.930 19.345 1693 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.99 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1526 helix: -0.04 (0.26), residues: 459 sheet: -0.34 (0.37), residues: 188 loop : -0.79 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 736 HIS 0.007 0.001 HIS B 677 PHE 0.048 0.001 PHE D 581 TYR 0.013 0.001 TYR C 474 ARG 0.006 0.000 ARG D 683 *********************** 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 184 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.043 Fit side-chains REVERT: A 419 GLN cc_start: 0.7560 (mp10) cc_final: 0.7208 (mp10) REVERT: A 653 ASP cc_start: 0.7830 (t0) cc_final: 0.7120 (t0) REVERT: A 720 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: A 769 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7778 (ptpp) REVERT: B 633 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8382 (tttt) REVERT: C 847 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8825 (mttm) REVERT: D 635 ASN cc_start: 0.8707 (t0) cc_final: 0.8270 (t0) REVERT: D 639 TRP cc_start: 0.7765 (m-10) cc_final: 0.7450 (m-10) REVERT: D 707 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7628 (ttpp) REVERT: D 720 MET cc_start: 0.7047 (mtp) cc_final: 0.5324 (tpt) REVERT: D 743 ASN cc_start: 0.5508 (m110) cc_final: 0.4449 (p0) outliers start: 33 outliers final: 24 residues processed: 173 average time/residue: 0.2388 time to fit residues: 58.6331 Evaluate side-chains 175 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 682 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11935 Z= 0.173 Angle : 0.503 7.501 16219 Z= 0.252 Chirality : 0.039 0.133 1785 Planarity : 0.004 0.035 2107 Dihedral : 3.856 19.341 1693 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.17 % Allowed : 16.30 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1526 helix: 0.00 (0.26), residues: 460 sheet: -0.30 (0.37), residues: 188 loop : -0.76 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 736 HIS 0.005 0.001 HIS B 677 PHE 0.046 0.001 PHE D 581 TYR 0.008 0.001 TYR B 734 ARG 0.006 0.000 ARG D 683 *********************** 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 183 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.482 Fit side-chains REVERT: A 419 GLN cc_start: 0.7595 (mp10) cc_final: 0.7232 (mp10) REVERT: A 653 ASP cc_start: 0.7821 (t0) cc_final: 0.7128 (t0) REVERT: A 720 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8332 (ttp) REVERT: A 769 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7680 (ptpp) REVERT: B 633 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8357 (tttt) REVERT: C 847 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8821 (mttm) REVERT: D 635 ASN cc_start: 0.8684 (t0) cc_final: 0.8313 (t0) REVERT: D 707 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7623 (ttpp) REVERT: D 720 MET cc_start: 0.7065 (mtp) cc_final: 0.5336 (tpt) REVERT: D 743 ASN cc_start: 0.5290 (m110) cc_final: 0.5084 (t0) outliers start: 35 outliers final: 29 residues processed: 171 average time/residue: 0.2369 time to fit residues: 57.8786 Evaluate side-chains 179 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 457 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 755 GLU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 821 MET Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 682 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 20.0000 chunk 129 optimal weight: 0.0370 chunk 138 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN D 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11935 Z= 0.380 Angle : 0.625 8.203 16219 Z= 0.314 Chirality : 0.044 0.154 1785 Planarity : 0.005 0.034 2107 Dihedral : 4.490 29.720 1693 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.26 % Allowed : 16.30 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1526 helix: -0.26 (0.25), residues: 458 sheet: -0.44 (0.37), residues: 187 loop : -0.89 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 736 HIS 0.011 0.002 HIS B 677 PHE 0.049 0.002 PHE D 581 TYR 0.014 0.002 TYR B 815 ARG 0.006 0.000 ARG D 683 *********************** 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 189 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.407 Fit side-chains REVERT: A 419 GLN cc_start: 0.7609 (mp10) cc_final: 0.7233 (mp10) REVERT: A 592 LYS cc_start: 0.8522 (mmtt) cc_final: 0.7899 (mmmt) REVERT: A 720 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: A 769 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7979 (ptpp) REVERT: B 633 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8472 (tttt) REVERT: C 847 LYS cc_start: 0.9065 (mmtp) cc_final: 0.8830 (mttp) REVERT: D 707 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7627 (ttpp) REVERT: D 720 MET cc_start: 0.7147 (mtp) cc_final: 0.5352 (tpt) REVERT: D 743 ASN cc_start: 0.5510 (m110) cc_final: 0.5243 (t0) outliers start: 36 outliers final: 31 residues processed: 176 average time/residue: 0.2318 time to fit residues: 58.7347 Evaluate side-chains 186 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 821 MET Chi-restraints excluded: chain B residue 457 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 653 ASP 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 B residue 821 MET Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 682 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 153 optimal weight: 0.0470 chunk 141 optimal weight: 0.6980 chunk 122 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN D 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11935 Z= 0.155 Angle : 0.506 8.231 16219 Z= 0.255 Chirality : 0.039 0.129 1785 Planarity : 0.004 0.035 2107 Dihedral : 4.010 21.446 1693 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.90 % Allowed : 17.21 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1526 helix: -0.07 (0.26), residues: 458 sheet: -0.35 (0.37), residues: 188 loop : -0.77 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 736 HIS 0.004 0.001 HIS B 677 PHE 0.051 0.001 PHE D 581 TYR 0.009 0.001 TYR B 734 ARG 0.005 0.000 ARG D 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.267 Fit side-chains REVERT: A 419 GLN cc_start: 0.7592 (mp10) cc_final: 0.7227 (mp10) REVERT: A 653 ASP cc_start: 0.7699 (t0) cc_final: 0.6996 (t0) REVERT: A 720 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.8270 (ttp) REVERT: A 769 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7735 (ptpp) REVERT: B 633 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7540 (tttt) REVERT: C 847 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8837 (mttp) REVERT: D 707 LYS cc_start: 0.7852 (ttpp) cc_final: 0.7576 (ttpp) REVERT: D 720 MET cc_start: 0.7110 (mtp) cc_final: 0.5346 (tpt) outliers start: 32 outliers final: 26 residues processed: 178 average time/residue: 0.2466 time to fit residues: 62.4157 Evaluate side-chains 183 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 457 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 755 GLU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 674 GLU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 682 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 122 optimal weight: 40.0000 chunk 51 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 0.0060 chunk 22 optimal weight: 0.0170 chunk 107 optimal weight: 4.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 ASN D 698 ASN D 841 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.205068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150705 restraints weight = 13260.967| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.26 r_work: 0.3452 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11935 Z= 0.123 Angle : 0.490 8.137 16219 Z= 0.246 Chirality : 0.039 0.133 1785 Planarity : 0.004 0.034 2107 Dihedral : 3.662 19.212 1693 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.26 % Allowed : 17.30 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1526 helix: 0.04 (0.26), residues: 462 sheet: -0.22 (0.38), residues: 183 loop : -0.71 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 639 HIS 0.008 0.001 HIS D 841 PHE 0.049 0.001 PHE D 581 TYR 0.010 0.001 TYR D 676 ARG 0.006 0.000 ARG D 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.48 seconds wall clock time: 51 minutes 45.66 seconds (3105.66 seconds total)