Starting phenix.real_space_refine on Mon Aug 10 08:03:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e00_47344/08_2026/9e00_47344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e00_47344/08_2026/9e00_47344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e00_47344/08_2026/9e00_47344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e00_47344/08_2026/9e00_47344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e00_47344/08_2026/9e00_47344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e00_47344/08_2026/9e00_47344.map" } resolution = 3.75 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= 0.003 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 642 5.49 5 S 165 5.16 5 C 25740 2.51 5 N 8024 2.21 5 O 9293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43873 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 785 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "O" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "Q" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 752 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 6614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 6614 Classifications: {'DNA': 321} Link IDs: {'rna3p': 320} Chain: "J" Number of atoms: 6547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 6547 Classifications: {'DNA': 321} Link IDs: {'rna3p': 320} Chain: "V" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2793 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 3 Chain: "Z" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1478 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 4 Chain: "U" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2346 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 18, 'TRANS': 271} Chain breaks: 1 Chain: "Y" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "L" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2777 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 2 Chain: "X" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain breaks: 4 Chain: "W" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2346 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 18, 'TRANS': 271} Chain breaks: 1 Chain: "K" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2321 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 18, 'TRANS': 268} Chain breaks: 1 Chain: "V" 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: "U" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "Y" 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: "L" 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: "W" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24963 SG CYS V 415 79.144 132.016 125.686 1.00227.46 S ATOM 24983 SG CYS V 418 77.677 133.529 122.408 1.00237.74 S ATOM 25113 SG CYS V 435 77.876 135.942 125.078 1.00231.32 S ATOM 25135 SG CYS V 438 75.367 133.438 125.253 1.00234.01 S ATOM 25317 SG CYS V 458 68.819 124.744 130.860 1.00248.56 S ATOM 25337 SG CYS V 461 70.563 125.542 127.052 1.00250.83 S ATOM 25479 SG CYS V 480 68.754 122.621 127.630 1.00233.96 S ATOM 25501 SG CYS V 483 72.074 123.084 128.724 1.00225.82 S ATOM 25406 SG CYS V 470 63.874 119.948 142.033 1.00218.85 S ATOM 25439 SG CYS V 475 65.490 123.986 142.487 1.00226.43 S ATOM 25654 SG CYS V 504 67.445 121.352 141.371 1.00214.14 S ATOM 25680 SG CYS V 507 66.750 121.348 144.703 1.00206.83 S ATOM 31584 SG CYS Y 494 114.654 156.027 71.942 1.00429.70 S ATOM 31604 SG CYS Y 497 113.402 151.968 71.002 1.00420.66 S ATOM 31726 SG CYS Y 514 112.208 155.008 69.150 1.00377.94 S ATOM 31749 SG CYS Y 517 111.032 153.859 71.948 1.00344.66 S ATOM 31917 SG CYS Y 537 110.392 153.999 83.199 1.00374.92 S ATOM 31938 SG CYS Y 540 110.713 151.508 80.054 1.00385.86 S ATOM 32075 SG CYS Y 559 111.809 150.500 83.525 1.00406.39 S ATOM 32097 SG CYS Y 562 113.831 152.537 81.353 1.00433.99 S ATOM 32001 SG CYS Y 549 107.912 160.686 93.881 1.00357.08 S ATOM 32035 SG CYS Y 554 105.970 162.714 91.734 1.00317.13 S ATOM 32248 SG CYS Y 583 110.051 162.339 91.417 1.00399.39 S ATOM 32274 SG CYS Y 586 109.035 164.893 93.301 1.00398.86 S ATOM 34984 SG CYS L 415 76.644 75.638 100.922 1.00261.93 S ATOM 35004 SG CYS L 418 76.146 74.216 104.464 1.00262.72 S ATOM 35134 SG CYS L 435 75.717 72.042 101.908 1.00256.21 S ATOM 35156 SG CYS L 438 73.089 73.931 101.911 1.00254.52 S ATOM 35338 SG CYS L 458 67.225 82.056 97.060 1.00245.74 S ATOM 35358 SG CYS L 461 68.395 80.649 100.387 1.00254.15 S ATOM 35500 SG CYS L 480 67.529 84.296 100.028 1.00233.15 S ATOM 35522 SG CYS L 483 70.579 83.707 99.204 1.00230.37 S ATOM 35427 SG CYS L 470 61.784 87.351 86.689 1.00217.61 S ATOM 35460 SG CYS L 475 62.944 83.426 85.407 1.00211.12 S ATOM 35675 SG CYS L 504 65.054 85.847 86.892 1.00197.47 S ATOM 35701 SG CYS L 507 64.412 86.209 83.300 1.00186.65 S Time building chain proxies: 8.73, per 1000 atoms: 0.20 Number of scatterers: 43873 At special positions: 0 Unit cell: (141.588, 207, 227.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 165 16.00 P 642 15.00 O 9293 8.00 N 8024 7.00 C 25740 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: 4.06 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 438 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 435 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 418 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 415 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 461 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 480 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 483 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 458 " pdb=" ZN L1003 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 504 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 470 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 475 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 507 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 418 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 435 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 415 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 438 " pdb=" ZN V1002 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 480 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 458 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 483 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 461 " pdb=" ZN V1003 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 504 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 507 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 470 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 475 " pdb=" ZN Y1001 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 497 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 514 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 517 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 494 " pdb=" ZN Y1002 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 537 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 562 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 540 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 559 " pdb=" ZN Y1003 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 583 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 549 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 554 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 586 " Number of angles added : 54 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7114 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 37 sheets defined 52.2% alpha, 7.4% beta 317 base pairs and 535 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.560A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.686A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.847A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.510A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.590A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.401A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.599A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.930A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.972A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.692A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.831A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.519A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.575A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.201A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.289A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 55 removed outlier: 3.678A pdb=" N GLN M 55 " --> pdb=" O ILE M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.665A pdb=" N PHE M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 50 through 74 removed outlier: 4.210A pdb=" N ARG N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 26 through 36 Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.442A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 89 Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'P' and resid 34 through 46 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.667A pdb=" N LYS P 113 " --> pdb=" O SER P 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 76 removed outlier: 3.511A pdb=" N PHE Q 67 " --> pdb=" O ARG Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.695A pdb=" N ARG Q 131 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 27 removed outlier: 4.294A pdb=" N ILE R 26 " --> pdb=" O ARG R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 42 Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.069A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR R 71 " --> pdb=" O ARG R 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA R 76 " --> pdb=" O TYR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 removed outlier: 3.594A pdb=" N VAL R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.672A pdb=" N VAL S 30 " --> pdb=" O PRO S 26 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG S 35 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.390A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 89 removed outlier: 3.629A pdb=" N LEU S 83 " --> pdb=" O ILE S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'T' and resid 34 through 46 Processing helix chain 'T' and resid 52 through 81 removed outlier: 3.630A pdb=" N ASN T 81 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 99 Processing helix chain 'T' and resid 101 through 120 removed outlier: 3.869A pdb=" N SER T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 396 through 407 removed outlier: 3.828A pdb=" N ALA V 405 " --> pdb=" O ALA V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 445 Processing helix chain 'V' and resid 481 through 487 Processing helix chain 'V' and resid 491 through 499 removed outlier: 4.003A pdb=" N LEU V 498 " --> pdb=" O ALA V 494 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 532 removed outlier: 3.522A pdb=" N SER V 532 " --> pdb=" O ALA V 528 " (cutoff:3.500A) Processing helix chain 'V' and resid 565 through 575 Processing helix chain 'V' and resid 589 through 598 removed outlier: 3.805A pdb=" N VAL V 593 " --> pdb=" O GLU V 589 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL V 596 " --> pdb=" O ALA V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 613 through 620 removed outlier: 3.766A pdb=" N GLU V 617 " --> pdb=" O LYS V 613 " (cutoff:3.500A) Processing helix chain 'V' and resid 650 through 663 removed outlier: 3.500A pdb=" N GLU V 654 " --> pdb=" O ARG V 650 " (cutoff:3.500A) Processing helix chain 'V' and resid 683 through 695 Processing helix chain 'V' and resid 751 through 760 removed outlier: 4.425A pdb=" N VAL V 755 " --> pdb=" O TRP V 751 " (cutoff:3.500A) Processing helix chain 'V' and resid 760 through 766 removed outlier: 3.781A pdb=" N LYS V 764 " --> pdb=" O PHE V 760 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP V 765 " --> pdb=" O ALA V 761 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR V 766 " --> pdb=" O PRO V 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 760 through 766' Processing helix chain 'Z' and resid 565 through 574 Processing helix chain 'Z' and resid 587 through 598 removed outlier: 3.664A pdb=" N ILE Z 591 " --> pdb=" O CYS Z 587 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS Z 598 " --> pdb=" O GLY Z 594 " (cutoff:3.500A) Processing helix chain 'Z' and resid 612 through 620 Processing helix chain 'Z' and resid 645 through 663 Processing helix chain 'Z' and resid 683 through 695 Processing helix chain 'Z' and resid 753 through 760 Processing helix chain 'Z' and resid 760 through 767 Processing helix chain 'U' and resid 627 through 631 removed outlier: 3.565A pdb=" N ARG U 631 " --> pdb=" O ALA U 628 " (cutoff:3.500A) Processing helix chain 'U' and resid 644 through 654 Processing helix chain 'U' and resid 666 through 677 Processing helix chain 'U' and resid 691 through 698 Processing helix chain 'U' and resid 725 through 728 Processing helix chain 'U' and resid 729 through 742 Processing helix chain 'U' and resid 762 through 774 Processing helix chain 'U' and resid 814 through 819 removed outlier: 3.648A pdb=" N CYS U 818 " --> pdb=" O GLU U 814 " (cutoff:3.500A) Processing helix chain 'U' and resid 860 through 868 Processing helix chain 'U' and resid 881 through 892 Processing helix chain 'U' and resid 894 through 903 Processing helix chain 'U' and resid 904 through 908 Processing helix chain 'Y' and resid 477 through 484 Processing helix chain 'Y' and resid 489 through 493 removed outlier: 3.651A pdb=" N ILE Y 493 " --> pdb=" O ILE Y 490 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 525 Processing helix chain 'Y' and resid 560 through 566 Processing helix chain 'Y' and resid 571 through 578 Processing helix chain 'Y' and resid 600 through 611 removed outlier: 3.734A pdb=" N GLN Y 606 " --> pdb=" O PRO Y 602 " (cutoff:3.500A) Processing helix chain 'Y' and resid 644 through 654 removed outlier: 3.655A pdb=" N LEU Y 648 " --> pdb=" O ALA Y 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 666 through 677 Processing helix chain 'Y' and resid 686 through 690 Processing helix chain 'Y' and resid 691 through 698 Processing helix chain 'Y' and resid 725 through 728 removed outlier: 3.686A pdb=" N GLY Y 728 " --> pdb=" O GLU Y 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 725 through 728' Processing helix chain 'Y' and resid 729 through 742 removed outlier: 3.830A pdb=" N GLU Y 733 " --> pdb=" O ARG Y 729 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Y' and resid 814 through 819 removed outlier: 3.738A pdb=" N CYS Y 818 " --> pdb=" O GLU Y 814 " (cutoff:3.500A) Processing helix chain 'Y' and resid 860 through 869 Processing helix chain 'Y' and resid 881 through 892 Processing helix chain 'Y' and resid 894 through 903 Processing helix chain 'Y' and resid 904 through 908 removed outlier: 3.747A pdb=" N GLU Y 907 " --> pdb=" O PRO Y 904 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 407 removed outlier: 4.243A pdb=" N ALA L 405 " --> pdb=" O ALA L 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN L 406 " --> pdb=" O SER L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 445 removed outlier: 3.558A pdb=" N GLU L 444 " --> pdb=" O ASP L 440 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU L 445 " --> pdb=" O ARG L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 488 removed outlier: 3.569A pdb=" N VAL L 488 " --> pdb=" O LEU L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 499 removed outlier: 3.877A pdb=" N LEU L 498 " --> pdb=" O ALA L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 532 removed outlier: 3.668A pdb=" N PHE L 530 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 575 Processing helix chain 'L' and resid 588 through 599 removed outlier: 3.785A pdb=" N ALA L 592 " --> pdb=" O GLU L 588 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL L 596 " --> pdb=" O ALA L 592 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS L 597 " --> pdb=" O VAL L 593 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS L 598 " --> pdb=" O GLY L 594 " (cutoff:3.500A) Processing helix chain 'L' and resid 607 through 611 removed outlier: 3.629A pdb=" N ILE L 611 " --> pdb=" O VAL L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 613 through 619 removed outlier: 4.376A pdb=" N GLU L 617 " --> pdb=" O LYS L 613 " (cutoff:3.500A) Processing helix chain 'L' and resid 643 through 663 Processing helix chain 'L' and resid 683 through 695 Processing helix chain 'L' and resid 741 through 748 Processing helix chain 'L' and resid 751 through 761 removed outlier: 3.806A pdb=" N VAL L 755 " --> pdb=" O TRP L 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 762 through 764 No H-bonds generated for 'chain 'L' and resid 762 through 764' Processing helix chain 'X' and resid 565 through 575 removed outlier: 3.560A pdb=" N LEU X 569 " --> pdb=" O ALA X 565 " (cutoff:3.500A) Processing helix chain 'X' and resid 587 through 598 removed outlier: 3.719A pdb=" N ILE X 591 " --> pdb=" O CYS X 587 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA X 592 " --> pdb=" O GLU X 588 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS X 597 " --> pdb=" O VAL X 593 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS X 598 " --> pdb=" O GLY X 594 " (cutoff:3.500A) Processing helix chain 'X' and resid 607 through 611 removed outlier: 3.583A pdb=" N ASN X 610 " --> pdb=" O ASP X 607 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE X 611 " --> pdb=" O VAL X 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 607 through 611' Processing helix chain 'X' and resid 612 through 620 removed outlier: 3.679A pdb=" N TRP X 619 " --> pdb=" O ASN X 615 " (cutoff:3.500A) Processing helix chain 'X' and resid 641 through 662 removed outlier: 3.779A pdb=" N PHE X 652 " --> pdb=" O THR X 648 " (cutoff:3.500A) Processing helix chain 'X' and resid 683 through 694 Processing helix chain 'X' and resid 752 through 760 removed outlier: 3.601A pdb=" N ILE X 756 " --> pdb=" O SER X 752 " (cutoff:3.500A) Processing helix chain 'X' and resid 760 through 767 Processing helix chain 'W' and resid 627 through 631 removed outlier: 3.683A pdb=" N ARG W 631 " --> pdb=" O ALA W 628 " (cutoff:3.500A) Processing helix chain 'W' and resid 644 through 654 Processing helix chain 'W' and resid 666 through 677 Processing helix chain 'W' and resid 691 through 698 Processing helix chain 'W' and resid 725 through 728 Processing helix chain 'W' and resid 729 through 742 Processing helix chain 'W' and resid 762 through 774 Processing helix chain 'W' and resid 814 through 819 removed outlier: 3.773A pdb=" N CYS W 818 " --> pdb=" O GLU W 814 " (cutoff:3.500A) Processing helix chain 'W' and resid 860 through 868 Processing helix chain 'W' and resid 881 through 892 Processing helix chain 'W' and resid 894 through 903 Processing helix chain 'W' and resid 904 through 908 Processing helix chain 'K' and resid 627 through 631 Processing helix chain 'K' and resid 644 through 654 removed outlier: 3.618A pdb=" N LEU K 648 " --> pdb=" O ALA K 644 " (cutoff:3.500A) Processing helix chain 'K' and resid 666 through 677 Processing helix chain 'K' and resid 686 through 690 Processing helix chain 'K' and resid 691 through 698 Processing helix chain 'K' and resid 725 through 728 Processing helix chain 'K' and resid 729 through 742 removed outlier: 3.540A pdb=" N GLU K 733 " --> pdb=" O ARG K 729 " (cutoff:3.500A) Processing helix chain 'K' and resid 762 through 774 Processing helix chain 'K' and resid 814 through 819 removed outlier: 3.715A pdb=" N CYS K 818 " --> pdb=" O GLU K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 860 through 868 Processing helix chain 'K' and resid 881 through 892 removed outlier: 3.513A pdb=" N SER K 892 " --> pdb=" O LEU K 888 " (cutoff:3.500A) Processing helix chain 'K' and resid 894 through 903 Processing helix chain 'K' and resid 904 through 906 No H-bonds generated for 'chain 'K' and resid 904 through 906' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.245A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.221A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.321A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.662A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.351A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'M' and resid 83 through 84 removed outlier: 7.113A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'N' and resid 96 through 97 removed outlier: 6.535A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.511A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.974A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.454A pdb=" N ARG S 42 " --> pdb=" O ILE T 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'V' and resid 467 through 469 removed outlier: 3.762A pdb=" N PHE V 479 " --> pdb=" O LEU V 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 512 through 513 Processing sheet with id=AB9, first strand: chain 'V' and resid 578 through 584 removed outlier: 5.577A pdb=" N ILE V 555 " --> pdb=" O VAL V 578 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS V 580 " --> pdb=" O ILE V 555 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER V 584 " --> pdb=" O SER V 559 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL V 625 " --> pdb=" O MET V 675 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU V 677 " --> pdb=" O VAL V 625 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY V 627 " --> pdb=" O GLU V 677 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL V 679 " --> pdb=" O GLY V 627 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG V 713 " --> pdb=" O ILE V 701 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE V 701 " --> pdb=" O ARG V 713 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 603 through 605 removed outlier: 8.929A pdb=" N LYS Z 603 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR Z 581 " --> pdb=" O LYS Z 603 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL Z 605 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 605 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE Z 555 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR Z 581 " --> pdb=" O ILE Z 555 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL Z 557 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 557 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N SER Z 559 " --> pdb=" O ALA Z 583 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL Z 625 " --> pdb=" O MET Z 675 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLU Z 677 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY Z 627 " --> pdb=" O GLU Z 677 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 682 through 684 removed outlier: 8.931A pdb=" N MET U 682 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR U 660 " --> pdb=" O MET U 682 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL U 684 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA U 662 " --> pdb=" O VAL U 684 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE U 634 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR U 660 " --> pdb=" O ILE U 634 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL U 636 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA U 662 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER U 638 " --> pdb=" O ALA U 662 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY U 707 " --> pdb=" O LEU U 639 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL U 704 " --> pdb=" O LEU U 754 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLU U 756 " --> pdb=" O VAL U 704 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY U 706 " --> pdb=" O GLU U 756 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N VAL U 758 " --> pdb=" O GLY U 706 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 788 through 789 Processing sheet with id=AC4, first strand: chain 'U' and resid 823 through 825 removed outlier: 4.293A pdb=" N VAL U 850 " --> pdb=" O ASP U 857 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 504 through 505 Processing sheet with id=AC6, first strand: chain 'Y' and resid 546 through 548 Processing sheet with id=AC7, first strand: chain 'Y' and resid 591 through 592 Processing sheet with id=AC8, first strand: chain 'Y' and resid 681 through 684 removed outlier: 7.682A pdb=" N ILE Y 634 " --> pdb=" O ASP Y 658 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR Y 660 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL Y 636 " --> pdb=" O TYR Y 660 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA Y 662 " --> pdb=" O VAL Y 636 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER Y 638 " --> pdb=" O ALA Y 662 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL Y 704 " --> pdb=" O LEU Y 754 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLU Y 756 " --> pdb=" O VAL Y 704 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 824 through 825 removed outlier: 3.911A pdb=" N VAL Y 850 " --> pdb=" O ASP Y 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 467 through 469 Processing sheet with id=AD2, first strand: chain 'L' and resid 512 through 513 removed outlier: 3.555A pdb=" N LEU L 516 " --> pdb=" O HIS L 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 604 through 605 removed outlier: 7.648A pdb=" N ALA L 583 " --> pdb=" O VAL L 605 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL L 582 " --> pdb=" O VAL L 557 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER L 559 " --> pdb=" O VAL L 582 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER L 584 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL L 625 " --> pdb=" O MET L 675 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 678 through 679 Processing sheet with id=AD5, first strand: chain 'X' and resid 578 through 584 removed outlier: 7.224A pdb=" N ILE X 555 " --> pdb=" O GLY X 579 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR X 581 " --> pdb=" O ILE X 555 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL X 557 " --> pdb=" O TYR X 581 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA X 583 " --> pdb=" O VAL X 557 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER X 559 " --> pdb=" O ALA X 583 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG X 556 " --> pdb=" O LEU X 624 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE X 626 " --> pdb=" O ARG X 556 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU X 558 " --> pdb=" O ILE X 626 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU X 677 " --> pdb=" O GLY X 627 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 682 through 684 removed outlier: 8.953A pdb=" N MET W 682 " --> pdb=" O ASP W 658 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR W 660 " --> pdb=" O MET W 682 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL W 684 " --> pdb=" O TYR W 660 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA W 662 " --> pdb=" O VAL W 684 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE W 634 " --> pdb=" O ASP W 658 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR W 660 " --> pdb=" O ILE W 634 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL W 636 " --> pdb=" O TYR W 660 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA W 662 " --> pdb=" O VAL W 636 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER W 638 " --> pdb=" O ALA W 662 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL W 704 " --> pdb=" O LEU W 754 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLU W 756 " --> pdb=" O VAL W 704 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY W 706 " --> pdb=" O GLU W 756 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N VAL W 758 " --> pdb=" O GLY W 706 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 788 through 789 Processing sheet with id=AD8, first strand: chain 'W' and resid 823 through 825 removed outlier: 4.351A pdb=" N VAL W 850 " --> pdb=" O ASP W 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 682 through 684 removed outlier: 7.387A pdb=" N ILE K 634 " --> pdb=" O ASP K 658 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR K 660 " --> pdb=" O ILE K 634 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL K 636 " --> pdb=" O TYR K 660 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA K 662 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER K 638 " --> pdb=" O ALA K 662 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG K 635 " --> pdb=" O LEU K 703 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE K 705 " --> pdb=" O ARG K 635 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU K 637 " --> pdb=" O ILE K 705 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLY K 707 " --> pdb=" O LEU K 637 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU K 639 " --> pdb=" O GLY K 707 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL K 704 " --> pdb=" O LEU K 754 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLU K 756 " --> pdb=" O VAL K 704 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY K 706 " --> pdb=" O GLU K 756 " (cutoff:3.500A) removed outlier: 9.825A pdb=" N VAL K 758 " --> pdb=" O GLY K 706 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 823 through 825 removed outlier: 4.344A pdb=" N VAL K 850 " --> pdb=" O ASP K 857 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 3999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 818 hydrogen bonds 1632 hydrogen bond angles 0 basepair planarities 317 basepair parallelities 535 stacking parallelities Total time for adding SS restraints: 11.85 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10117 1.34 - 1.46: 12268 1.46 - 1.58: 22186 1.58 - 1.70: 1282 1.70 - 1.82: 245 Bond restraints: 46098 Sorted by residual: bond pdb=" C LYS U 829 " pdb=" N VAL U 830 " ideal model delta sigma weight residual 1.329 1.216 0.113 1.32e-02 5.74e+03 7.27e+01 bond pdb=" N ILE X 564 " pdb=" CA ILE X 564 " ideal model delta sigma weight residual 1.460 1.497 -0.036 8.60e-03 1.35e+04 1.80e+01 bond pdb=" N VAL K 665 " pdb=" CA VAL K 665 " ideal model delta sigma weight residual 1.456 1.492 -0.035 9.50e-03 1.11e+04 1.37e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.35e+01 bond pdb=" N ASN L 422 " pdb=" CA ASN L 422 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.10e-03 1.21e+04 1.31e+01 ... (remaining 46093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 48689 1.47 - 2.93: 14478 2.93 - 4.40: 1822 4.40 - 5.86: 37 5.86 - 7.33: 8 Bond angle restraints: 65034 Sorted by residual: angle pdb=" C SER V 752 " pdb=" N VAL V 753 " pdb=" CA VAL V 753 " ideal model delta sigma weight residual 120.33 125.59 -5.26 8.00e-01 1.56e+00 4.32e+01 angle pdb=" O5' DA I 10 " pdb=" C5' DA I 10 " pdb=" C4' DA I 10 " ideal model delta sigma weight residual 109.40 113.47 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" O4' DA I 130 " pdb=" C4' DA I 130 " pdb=" C3' DA I 130 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" O4' DA I 285 " pdb=" C4' DA I 285 " pdb=" C3' DA I 285 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.96 108.76 4.20 1.00e+00 1.00e+00 1.77e+01 ... (remaining 65029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 22919 35.06 - 70.13: 2914 70.13 - 105.19: 47 105.19 - 140.25: 1 140.25 - 175.32: 4 Dihedral angle restraints: 25885 sinusoidal: 14846 harmonic: 11039 Sorted by residual: dihedral pdb=" CA GLU V 500 " pdb=" C GLU V 500 " pdb=" N PRO V 501 " pdb=" CA PRO V 501 " ideal model delta harmonic sigma weight residual 0.00 -22.71 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN V 422 " pdb=" C ASN V 422 " pdb=" N PRO V 423 " pdb=" CA PRO V 423 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C4' DG I 3 " pdb=" C3' DG I 3 " pdb=" O3' DG I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual -140.00 35.32 -175.32 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 25882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5256 0.075 - 0.151: 1794 0.151 - 0.226: 121 0.226 - 0.301: 1 0.301 - 0.377: 4 Chirality restraints: 7176 Sorted by residual: chirality pdb=" C3' DC I 290 " pdb=" C4' DC I 290 " pdb=" O3' DC I 290 " pdb=" C2' DC I 290 " both_signs ideal model delta sigma weight residual False -2.73 -2.35 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C3' DG I 316 " pdb=" C4' DG I 316 " pdb=" O3' DG I 316 " pdb=" C2' DG I 316 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C3' DG I 3 " pdb=" C4' DG I 3 " pdb=" O3' DG I 3 " pdb=" C2' DG I 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 7173 not shown) Planarity restraints: 6080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS U 829 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C LYS U 829 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS U 829 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL U 830 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 130 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C ILE A 130 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 130 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG A 131 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 252 " -0.025 2.00e-02 2.50e+03 1.29e-02 4.19e+00 pdb=" N1 DT I 252 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DT I 252 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT I 252 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 252 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 252 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 252 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DT I 252 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 252 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 252 " 0.002 2.00e-02 2.50e+03 ... (remaining 6077 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3659 2.75 - 3.29: 39074 3.29 - 3.83: 75503 3.83 - 4.36: 95630 4.36 - 4.90: 137748 Nonbonded interactions: 351614 Sorted by model distance: nonbonded pdb=" O PHE L 430 " pdb=" NE ARG L 519 " model vdw 2.219 3.120 nonbonded pdb=" OD1 ASP Y 641 " pdb=" N ALA Y 644 " model vdw 2.257 3.120 nonbonded pdb=" OH TYR P 37 " pdb=" OP1 DG J 132 " model vdw 2.267 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.278 3.040 nonbonded pdb=" O CYS L 415 " pdb=" CA GLY L 419 " model vdw 2.287 3.440 ... (remaining 351609 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 40 through 134) selection = (chain 'E' and resid 40 through 134) selection = (chain 'M' and resid 40 through 134) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' selection = chain 'N' selection = (chain 'R' and resid 24 through 101) } ncs_group { reference = (chain 'C' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = (chain 'G' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = (chain 'O' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = chain 'S' } ncs_group { reference = (chain 'D' and resid 31 through 121) selection = (chain 'H' and resid 31 through 121) selection = chain 'P' selection = (chain 'T' and resid 31 through 121) } ncs_group { reference = chain 'K' selection = (chain 'U' and (resid 610 through 829 or resid 846 through 1001)) selection = (chain 'W' and (resid 610 through 829 or resid 846 through 1001)) } ncs_group { reference = (chain 'L' and (resid 394 through 633 or resid 647 through 718 or resid 739 thro \ ugh 741 or resid 749 through 1003)) selection = (chain 'V' and (resid 394 through 718 or resid 721 or resid 724 or resid 727 or \ resid 743 or resid 750 through 766 or resid 1001 through 1003)) } ncs_group { reference = (chain 'X' and (resid 541 through 629 or resid 644 through 719 or resid 740 thro \ ugh 750 or resid 753 through 767)) selection = (chain 'Z' and (resid 541 through 629 or resid 644 through 700 or resid 713 thro \ ugh 719 or resid 740 through 767)) } 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=0.71 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.550 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: 0.040 Extract box with map and model: 0.900 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 48.780 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.010 0.162 46134 Z= 0.760 Angle : 1.327 24.911 65088 Z= 0.978 Chirality : 0.067 0.377 7176 Planarity : 0.003 0.031 6080 Dihedral : 22.084 175.318 18771 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -2.32 (0.11), residues: 3738 helix: -1.24 (0.10), residues: 1815 sheet: -0.90 (0.29), residues: 241 loop : -1.89 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 598 TYR 0.023 0.002 TYR N 51 PHE 0.027 0.002 PHE X 652 TRP 0.014 0.002 TRP Y 795 HIS 0.008 0.002 HIS Z 657 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.76 (46098) covalent geometry : angle 1.26586 / 0.98 (65034) hydrogen bonds : bond 0.14951 / 10.40 ( 2188) hydrogen bonds : angle 5.99766 / 4.38 ( 5631) metal coordination : bond 0.05289 / 3.48 ( 36) metal coordination : angle 13.93449 / 9.27 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 984 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.8233 (mt) cc_final: 0.7672 (mt) REVERT: B 74 GLU cc_start: 0.6814 (pt0) cc_final: 0.6488 (pt0) REVERT: D 39 TYR cc_start: 0.7507 (t80) cc_final: 0.7016 (t80) REVERT: D 68 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6694 (tm-30) REVERT: D 113 LYS cc_start: 0.7716 (tttt) cc_final: 0.7306 (tptt) REVERT: D 117 LYS cc_start: 0.8308 (tptm) cc_final: 0.7872 (tptt) REVERT: E 57 SER cc_start: 0.8243 (p) cc_final: 0.7794 (p) REVERT: E 59 GLU cc_start: 0.7311 (pm20) cc_final: 0.6932 (pm20) REVERT: F 63 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7039 (mt-10) REVERT: F 91 LYS cc_start: 0.8265 (tttt) cc_final: 0.8049 (tttm) REVERT: G 36 LYS cc_start: 0.7894 (tttt) cc_final: 0.7516 (tttt) REVERT: G 50 TYR cc_start: 0.8450 (t80) cc_final: 0.8099 (t80) REVERT: H 87 THR cc_start: 0.8629 (p) cc_final: 0.8414 (p) REVERT: M 56 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8052 (tttt) REVERT: N 30 THR cc_start: 0.8261 (p) cc_final: 0.7896 (t) REVERT: N 31 LYS cc_start: 0.8791 (tttt) cc_final: 0.8403 (tttp) REVERT: N 59 LYS cc_start: 0.8603 (tttm) cc_final: 0.8095 (ttpt) REVERT: N 79 LYS cc_start: 0.8588 (mttt) cc_final: 0.8260 (mttp) REVERT: N 82 THR cc_start: 0.9016 (p) cc_final: 0.8728 (p) REVERT: N 91 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8187 (tttt) REVERT: O 15 LYS cc_start: 0.6998 (tppt) cc_final: 0.6675 (ttmt) REVERT: P 65 ASP cc_start: 0.7969 (t0) cc_final: 0.7722 (t0) REVERT: P 68 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7253 (tm-30) REVERT: P 73 GLU cc_start: 0.7764 (tp30) cc_final: 0.7417 (tp30) REVERT: P 85 THR cc_start: 0.8374 (m) cc_final: 0.8097 (p) REVERT: P 117 LYS cc_start: 0.8426 (tttt) cc_final: 0.7932 (tttm) REVERT: Q 50 GLU cc_start: 0.7798 (pt0) cc_final: 0.7559 (pt0) REVERT: Q 54 TYR cc_start: 0.8490 (m-80) cc_final: 0.8116 (m-80) REVERT: Q 59 GLU cc_start: 0.7400 (pm20) cc_final: 0.7107 (pm20) REVERT: R 77 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8248 (mmtt) REVERT: R 88 TYR cc_start: 0.8173 (m-10) cc_final: 0.7272 (m-80) REVERT: T 39 TYR cc_start: 0.7844 (t80) cc_final: 0.7401 (t80) REVERT: T 61 SER cc_start: 0.8447 (m) cc_final: 0.8171 (p) REVERT: T 65 ASP cc_start: 0.8277 (t70) cc_final: 0.8043 (t0) REVERT: T 68 GLU cc_start: 0.7491 (pt0) cc_final: 0.7175 (pt0) REVERT: T 105 LYS cc_start: 0.8275 (mttt) cc_final: 0.8008 (ttmt) REVERT: T 106 HIS cc_start: 0.7733 (m-70) cc_final: 0.7473 (m-70) REVERT: V 403 ASP cc_start: 0.7647 (m-30) cc_final: 0.7195 (t70) REVERT: V 444 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7747 (tp30) REVERT: V 446 PHE cc_start: 0.6947 (t80) cc_final: 0.6227 (t80) REVERT: V 572 LYS cc_start: 0.7817 (tttt) cc_final: 0.7488 (tptm) REVERT: V 573 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7094 (mt-10) REVERT: V 613 LYS cc_start: 0.8115 (tttt) cc_final: 0.7676 (tppt) REVERT: V 624 LEU cc_start: 0.7960 (tp) cc_final: 0.7686 (tp) REVERT: V 657 HIS cc_start: 0.8460 (t70) cc_final: 0.8247 (t-170) REVERT: Z 560 LEU cc_start: 0.7079 (mt) cc_final: 0.6806 (tp) REVERT: Z 611 ILE cc_start: 0.8126 (mt) cc_final: 0.7811 (tp) REVERT: Z 613 LYS cc_start: 0.7144 (tttt) cc_final: 0.6828 (mmmt) REVERT: Z 626 ILE cc_start: 0.7401 (pt) cc_final: 0.7162 (pt) REVERT: Z 654 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7606 (mp0) REVERT: Z 656 TYR cc_start: 0.8365 (t80) cc_final: 0.7776 (t80) REVERT: Z 657 HIS cc_start: 0.8548 (t70) cc_final: 0.8293 (t70) REVERT: Z 660 ASN cc_start: 0.8588 (m-40) cc_final: 0.8362 (m-40) REVERT: Z 694 LEU cc_start: 0.8611 (mt) cc_final: 0.8328 (mp) REVERT: Z 695 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7093 (tm-30) REVERT: U 653 LEU cc_start: 0.8275 (mt) cc_final: 0.7962 (mt) REVERT: U 656 GLN cc_start: 0.8418 (mt0) cc_final: 0.7929 (mt0) REVERT: U 674 MET cc_start: 0.7674 (mtp) cc_final: 0.7099 (tpt) REVERT: U 694 HIS cc_start: 0.8332 (m170) cc_final: 0.8062 (m90) REVERT: U 711 ASN cc_start: 0.6761 (m-40) cc_final: 0.6464 (m-40) REVERT: U 815 LEU cc_start: 0.8872 (tp) cc_final: 0.8368 (tp) REVERT: U 816 GLN cc_start: 0.8217 (tp40) cc_final: 0.7749 (tp40) REVERT: U 819 LEU cc_start: 0.8485 (mt) cc_final: 0.8265 (mt) REVERT: U 853 ASN cc_start: 0.7678 (m-40) cc_final: 0.6711 (m-40) REVERT: U 866 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7347 (ttm110) REVERT: U 870 PHE cc_start: 0.5638 (m-80) cc_final: 0.4089 (m-80) REVERT: U 875 THR cc_start: 0.8642 (m) cc_final: 0.8135 (p) REVERT: U 883 LEU cc_start: 0.8373 (mt) cc_final: 0.7891 (tp) REVERT: Y 585 MET cc_start: 0.6024 (mmm) cc_final: 0.5312 (ptt) REVERT: Y 621 LYS cc_start: 0.7679 (tttp) cc_final: 0.7361 (tptt) REVERT: Y 656 GLN cc_start: 0.7587 (mt0) cc_final: 0.7099 (mp10) REVERT: Y 674 MET cc_start: 0.8076 (mtp) cc_final: 0.7353 (mtm) REVERT: Y 756 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6112 (tm-30) REVERT: Y 773 LEU cc_start: 0.8723 (mt) cc_final: 0.8467 (mt) REVERT: Y 795 TRP cc_start: 0.7499 (m-90) cc_final: 0.7220 (m-90) REVERT: Y 873 HIS cc_start: 0.8073 (m-70) cc_final: 0.7340 (m-70) REVERT: L 441 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8671 (ttp-110) REVERT: L 481 VAL cc_start: 0.7497 (t) cc_final: 0.6781 (p) REVERT: L 516 LEU cc_start: 0.7950 (tp) cc_final: 0.7698 (pt) REVERT: L 653 PHE cc_start: 0.7887 (m-10) cc_final: 0.7063 (m-10) REVERT: L 655 PHE cc_start: 0.7999 (t80) cc_final: 0.7789 (t80) REVERT: L 656 TYR cc_start: 0.7535 (t80) cc_final: 0.7217 (t80) REVERT: L 688 ARG cc_start: 0.8707 (mtt180) cc_final: 0.7871 (mmm160) REVERT: X 626 ILE cc_start: 0.7494 (pt) cc_final: 0.7288 (mm) REVERT: W 637 LEU cc_start: 0.8344 (tp) cc_final: 0.8018 (tt) REVERT: W 639 LEU cc_start: 0.8701 (mt) cc_final: 0.8285 (pt) REVERT: W 650 LEU cc_start: 0.8493 (mt) cc_final: 0.8228 (mt) REVERT: W 652 ASP cc_start: 0.7014 (m-30) cc_final: 0.6807 (t0) REVERT: W 668 ASP cc_start: 0.8408 (m-30) cc_final: 0.7880 (t0) REVERT: W 693 LYS cc_start: 0.8891 (tttt) cc_final: 0.8412 (mmmt) REVERT: W 724 TYR cc_start: 0.7607 (m-80) cc_final: 0.6316 (m-10) REVERT: W 737 LEU cc_start: 0.8940 (mt) cc_final: 0.8479 (mt) REVERT: W 768 ASP cc_start: 0.8222 (m-30) cc_final: 0.7966 (m-30) REVERT: W 769 ILE cc_start: 0.8849 (mt) cc_final: 0.8585 (pt) REVERT: W 795 TRP cc_start: 0.4689 (m-90) cc_final: 0.4208 (m-90) REVERT: W 864 MET cc_start: 0.8709 (ttm) cc_final: 0.8434 (mtt) REVERT: W 880 MET cc_start: 0.5449 (ptp) cc_final: 0.4591 (ptp) REVERT: W 886 GLN cc_start: 0.8739 (mt0) cc_final: 0.8367 (mm-40) REVERT: W 893 TRP cc_start: 0.6899 (m-10) cc_final: 0.6682 (m-10) outliers start: 0 outliers final: 0 residues processed: 984 average time/residue: 0.3000 time to fit residues: 447.2876 Evaluate side-chains 778 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 778 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0170 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 7.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 79 HIS E 39 HIS E 68 GLN F 25 ASN G 68 ASN H 79 HIS N 93 GLN O 31 HIS O 82 HIS P 106 HIS Q 55 GLN Q 108 ASN S 31 HIS ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 ASN Z 744 GLN ** U 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 847 HIS U 873 HIS Y 612 ASN Y 821 HIS L 660 ASN L 710 HIS X 744 GLN W 739 HIS W 821 HIS K 900 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.148926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.111426 restraints weight = 117103.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112273 restraints weight = 73963.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.113067 restraints weight = 46117.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.113311 restraints weight = 37367.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113559 restraints weight = 36391.922| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 46134 Z= 0.182 Angle : 0.695 14.682 65088 Z= 0.377 Chirality : 0.044 0.265 7176 Planarity : 0.005 0.079 6080 Dihedral : 27.531 176.357 11233 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.14 % Allowed : 6.95 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.54 (0.13), residues: 3738 helix: 0.47 (0.11), residues: 1869 sheet: -0.57 (0.33), residues: 237 loop : -1.25 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG U 767 TYR 0.045 0.002 TYR X 661 PHE 0.038 0.002 PHE W 772 TRP 0.021 0.002 TRP W 753 HIS 0.020 0.002 HIS L 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (46098) covalent geometry : angle 0.67607 / 0.38 (65034) hydrogen bonds : bond 0.05078 / 3.46 ( 2188) hydrogen bonds : angle 3.89786 / 2.87 ( 5631) metal coordination : bond 0.00801 / 0.53 ( 36) metal coordination : angle 5.61499 / 3.96 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 841 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.8669 (tttt) cc_final: 0.8411 (ttpp) REVERT: B 88 TYR cc_start: 0.7976 (m-80) cc_final: 0.7507 (m-80) REVERT: C 77 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7598 (mtt-85) REVERT: D 37 TYR cc_start: 0.8167 (m-80) cc_final: 0.7919 (m-10) REVERT: D 113 LYS cc_start: 0.7982 (tttt) cc_final: 0.7578 (tptt) REVERT: D 117 LYS cc_start: 0.8334 (tptm) cc_final: 0.7949 (tptt) REVERT: E 57 SER cc_start: 0.8146 (p) cc_final: 0.7657 (p) REVERT: E 59 GLU cc_start: 0.7168 (pm20) cc_final: 0.6723 (pm20) REVERT: E 93 GLN cc_start: 0.8617 (tt0) cc_final: 0.8397 (tt0) REVERT: F 91 LYS cc_start: 0.8397 (tttt) cc_final: 0.8141 (tttt) REVERT: G 36 LYS cc_start: 0.8001 (tttt) cc_final: 0.7629 (tttt) REVERT: G 74 LYS cc_start: 0.8589 (mttp) cc_final: 0.8258 (ptpt) REVERT: H 40 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8136 (ttmt) REVERT: H 52 SER cc_start: 0.8697 (p) cc_final: 0.8448 (p) REVERT: M 73 GLU cc_start: 0.7438 (pt0) cc_final: 0.7208 (pt0) REVERT: N 59 LYS cc_start: 0.8765 (tttm) cc_final: 0.8274 (ttpt) REVERT: N 79 LYS cc_start: 0.8582 (mttt) cc_final: 0.8322 (mttp) REVERT: N 84 MET cc_start: 0.8005 (mmm) cc_final: 0.7435 (mmm) REVERT: N 88 TYR cc_start: 0.8596 (m-80) cc_final: 0.6446 (m-80) REVERT: O 15 LYS cc_start: 0.7602 (tppt) cc_final: 0.7144 (tttt) REVERT: O 75 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7832 (mmtp) REVERT: O 85 LEU cc_start: 0.8888 (mt) cc_final: 0.8628 (mt) REVERT: O 89 ASN cc_start: 0.8949 (m-40) cc_final: 0.8716 (m-40) REVERT: P 39 TYR cc_start: 0.7424 (t80) cc_final: 0.7174 (t80) REVERT: P 73 GLU cc_start: 0.7641 (tp30) cc_final: 0.7413 (tp30) REVERT: P 85 THR cc_start: 0.8602 (m) cc_final: 0.8120 (p) REVERT: P 96 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8297 (ttp80) REVERT: P 113 LYS cc_start: 0.7994 (tttt) cc_final: 0.7708 (tttp) REVERT: P 117 LYS cc_start: 0.8512 (tttt) cc_final: 0.8054 (tttt) REVERT: Q 59 GLU cc_start: 0.7537 (pm20) cc_final: 0.7315 (pm20) REVERT: Q 60 LEU cc_start: 0.8228 (mt) cc_final: 0.7954 (mt) REVERT: Q 97 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6764 (mt-10) REVERT: Q 122 LYS cc_start: 0.8409 (ptpt) cc_final: 0.8147 (mtpt) REVERT: R 31 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8734 (tttp) REVERT: R 44 LYS cc_start: 0.8451 (mttt) cc_final: 0.8238 (mttt) REVERT: R 77 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8383 (mmtt) REVERT: R 88 TYR cc_start: 0.7957 (m-10) cc_final: 0.7693 (m-10) REVERT: R 92 ARG cc_start: 0.8713 (ptm-80) cc_final: 0.8485 (ptm-80) REVERT: S 15 LYS cc_start: 0.6821 (tppp) cc_final: 0.6501 (tttt) REVERT: S 74 LYS cc_start: 0.8545 (mttt) cc_final: 0.8282 (mttm) REVERT: S 75 LYS cc_start: 0.8398 (mttm) cc_final: 0.8197 (mttm) REVERT: S 81 ARG cc_start: 0.8991 (tpp-160) cc_final: 0.8586 (tpt170) REVERT: T 39 TYR cc_start: 0.7991 (t80) cc_final: 0.7596 (t80) REVERT: T 61 SER cc_start: 0.8605 (m) cc_final: 0.8245 (p) REVERT: T 65 ASP cc_start: 0.8309 (t70) cc_final: 0.8062 (t0) REVERT: T 68 GLU cc_start: 0.7566 (pt0) cc_final: 0.7265 (pt0) REVERT: T 113 LYS cc_start: 0.8109 (tttt) cc_final: 0.7826 (tttp) REVERT: V 403 ASP cc_start: 0.7501 (m-30) cc_final: 0.7213 (t0) REVERT: V 444 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7958 (tp30) REVERT: V 525 ARG cc_start: 0.8533 (mmt-90) cc_final: 0.8158 (mmm-85) REVERT: V 530 PHE cc_start: 0.7025 (m-80) cc_final: 0.6563 (m-80) REVERT: V 572 LYS cc_start: 0.7859 (tttt) cc_final: 0.7604 (mmmm) REVERT: V 573 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7139 (mt-10) REVERT: V 613 LYS cc_start: 0.8279 (tttt) cc_final: 0.7720 (tppt) REVERT: Z 558 LEU cc_start: 0.7845 (tp) cc_final: 0.7535 (pp) REVERT: Z 610 ASN cc_start: 0.7744 (m110) cc_final: 0.7489 (m110) REVERT: Z 611 ILE cc_start: 0.7895 (mt) cc_final: 0.7576 (tp) REVERT: Z 613 LYS cc_start: 0.7295 (tttt) cc_final: 0.6814 (mmmt) REVERT: Z 656 TYR cc_start: 0.8288 (t80) cc_final: 0.7934 (t80) REVERT: U 656 GLN cc_start: 0.8442 (mt0) cc_final: 0.8001 (mt0) REVERT: U 694 HIS cc_start: 0.8296 (m170) cc_final: 0.7949 (m90) REVERT: U 711 ASN cc_start: 0.6885 (m-40) cc_final: 0.6615 (m-40) REVERT: U 793 TYR cc_start: 0.7268 (m-80) cc_final: 0.6288 (m-80) REVERT: U 815 LEU cc_start: 0.8971 (tp) cc_final: 0.8394 (tp) REVERT: U 816 GLN cc_start: 0.8333 (tp40) cc_final: 0.8125 (tp40) REVERT: U 819 LEU cc_start: 0.8474 (mt) cc_final: 0.8264 (mt) REVERT: U 853 ASN cc_start: 0.7883 (m-40) cc_final: 0.7517 (p0) REVERT: U 875 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8128 (p) REVERT: U 883 LEU cc_start: 0.8530 (mt) cc_final: 0.7889 (tp) REVERT: U 886 GLN cc_start: 0.7705 (mt0) cc_final: 0.7432 (mt0) REVERT: Y 585 MET cc_start: 0.5873 (mmm) cc_final: 0.5531 (mmp) REVERT: Y 621 LYS cc_start: 0.7769 (tttp) cc_final: 0.7473 (tptt) REVERT: Y 656 GLN cc_start: 0.7773 (mt0) cc_final: 0.7247 (mm-40) REVERT: Y 712 ASP cc_start: 0.6207 (m-30) cc_final: 0.5985 (m-30) REVERT: Y 757 ASN cc_start: 0.7268 (t0) cc_final: 0.6768 (t0) REVERT: L 653 PHE cc_start: 0.7399 (m-10) cc_final: 0.6686 (m-10) REVERT: L 656 TYR cc_start: 0.6982 (t80) cc_final: 0.6629 (t80) REVERT: L 657 HIS cc_start: 0.8103 (t-170) cc_final: 0.7762 (t70) REVERT: L 658 LEU cc_start: 0.8265 (mt) cc_final: 0.7865 (mm) REVERT: L 660 ASN cc_start: 0.7675 (m-40) cc_final: 0.7409 (m-40) REVERT: L 688 ARG cc_start: 0.8551 (mtt180) cc_final: 0.7341 (mmm160) REVERT: L 692 ARG cc_start: 0.8210 (mmt180) cc_final: 0.7789 (ptp-110) REVERT: W 637 LEU cc_start: 0.8319 (tp) cc_final: 0.8021 (tt) REVERT: W 639 LEU cc_start: 0.8735 (mt) cc_final: 0.8410 (tp) REVERT: W 650 LEU cc_start: 0.8495 (mt) cc_final: 0.8268 (mt) REVERT: W 724 TYR cc_start: 0.7565 (m-80) cc_final: 0.6577 (m-80) REVERT: W 758 VAL cc_start: 0.6878 (m) cc_final: 0.6553 (p) REVERT: W 761 MET cc_start: 0.2442 (OUTLIER) cc_final: 0.1513 (ppp) REVERT: W 801 MET cc_start: 0.2674 (OUTLIER) cc_final: 0.2465 (ptp) REVERT: K 639 LEU cc_start: 0.8389 (mp) cc_final: 0.7785 (pt) REVERT: K 667 GLU cc_start: 0.7386 (pm20) cc_final: 0.7142 (pm20) outliers start: 70 outliers final: 40 residues processed: 866 average time/residue: 0.3043 time to fit residues: 408.0047 Evaluate side-chains 819 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 776 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 79 HIS Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 700 MET Chi-restraints excluded: chain Z residue 616 ILE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 752 SER Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 775 SER Chi-restraints excluded: chain U residue 858 ILE Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain L residue 504 CYS Chi-restraints excluded: chain L residue 577 LYS Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain K residue 704 VAL Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 188 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 412 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 chunk 360 optimal weight: 0.4980 chunk 214 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 426 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 79 HIS E 68 GLN E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Q 55 GLN T 46 HIS T 60 ASN ** V 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 744 GLN Z 660 ASN ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 612 ASN Y 613 HIS ** Y 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 660 ASN W 739 HIS W 802 ASN K 613 HIS ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110321 restraints weight = 116190.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111759 restraints weight = 69196.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112315 restraints weight = 43593.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112681 restraints weight = 35309.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113075 restraints weight = 35207.426| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 46134 Z= 0.148 Angle : 0.629 15.818 65088 Z= 0.347 Chirality : 0.043 0.259 7176 Planarity : 0.004 0.047 6080 Dihedral : 27.602 176.452 11233 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.14 % Allowed : 10.35 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.06 (0.13), residues: 3738 helix: 1.02 (0.12), residues: 1872 sheet: -0.19 (0.33), residues: 234 loop : -1.07 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 688 TYR 0.040 0.002 TYR P 80 PHE 0.034 0.001 PHE Z 760 TRP 0.035 0.002 TRP Y 860 HIS 0.021 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (46098) covalent geometry : angle 0.61513 / 0.35 (65034) hydrogen bonds : bond 0.04585 / 3.12 ( 2188) hydrogen bonds : angle 3.58753 / 2.63 ( 5631) metal coordination : bond 0.00764 / 0.48 ( 36) metal coordination : angle 4.68105 / 3.10 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 792 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.8675 (tttt) cc_final: 0.8459 (ttpp) REVERT: B 88 TYR cc_start: 0.7964 (m-10) cc_final: 0.7606 (m-80) REVERT: C 32 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7996 (tmm160) REVERT: C 107 VAL cc_start: 0.8705 (m) cc_final: 0.8492 (p) REVERT: D 40 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7946 (ttmm) REVERT: D 113 LYS cc_start: 0.8035 (tttt) cc_final: 0.7694 (tptt) REVERT: D 117 LYS cc_start: 0.8420 (tptm) cc_final: 0.8030 (tptt) REVERT: E 57 SER cc_start: 0.8221 (p) cc_final: 0.7466 (p) REVERT: E 59 GLU cc_start: 0.7188 (pm20) cc_final: 0.6790 (pm20) REVERT: E 93 GLN cc_start: 0.8495 (tt0) cc_final: 0.8187 (tt0) REVERT: F 35 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7986 (mmm-85) REVERT: G 36 LYS cc_start: 0.7986 (tttt) cc_final: 0.7615 (tttt) REVERT: G 74 LYS cc_start: 0.8579 (mttp) cc_final: 0.8297 (ptpt) REVERT: G 101 THR cc_start: 0.8693 (m) cc_final: 0.8369 (p) REVERT: H 52 SER cc_start: 0.8742 (p) cc_final: 0.8424 (p) REVERT: H 56 MET cc_start: 0.8774 (mmm) cc_final: 0.8526 (tpt) REVERT: H 90 GLU cc_start: 0.7548 (mp0) cc_final: 0.7261 (mp0) REVERT: M 52 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7399 (mtp85) REVERT: M 73 GLU cc_start: 0.7456 (pt0) cc_final: 0.7247 (pt0) REVERT: N 35 ARG cc_start: 0.8384 (ttt90) cc_final: 0.8054 (ttt90) REVERT: N 59 LYS cc_start: 0.8713 (tttm) cc_final: 0.8211 (ttpt) REVERT: N 79 LYS cc_start: 0.8626 (mttt) cc_final: 0.8351 (mttp) REVERT: O 15 LYS cc_start: 0.7592 (tppt) cc_final: 0.7201 (tttt) REVERT: O 89 ASN cc_start: 0.8968 (m-40) cc_final: 0.8767 (m-40) REVERT: P 39 TYR cc_start: 0.7417 (t80) cc_final: 0.7185 (t80) REVERT: P 80 TYR cc_start: 0.7154 (t80) cc_final: 0.6855 (t80) REVERT: P 85 THR cc_start: 0.8776 (m) cc_final: 0.8235 (p) REVERT: P 96 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8345 (ttp80) REVERT: P 113 LYS cc_start: 0.8029 (tttt) cc_final: 0.7715 (tttp) REVERT: P 117 LYS cc_start: 0.8618 (tttt) cc_final: 0.8122 (tttt) REVERT: Q 77 ASP cc_start: 0.7531 (t0) cc_final: 0.7291 (t0) REVERT: Q 122 LYS cc_start: 0.8405 (ptpt) cc_final: 0.8203 (mtpt) REVERT: R 31 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8690 (tttp) REVERT: R 44 LYS cc_start: 0.8563 (mttt) cc_final: 0.8336 (mttt) REVERT: R 77 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8356 (mmtt) REVERT: R 92 ARG cc_start: 0.8817 (ptm-80) cc_final: 0.8476 (ptm-80) REVERT: S 15 LYS cc_start: 0.6833 (tppp) cc_final: 0.6495 (tttt) REVERT: S 35 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7715 (mtt90) REVERT: S 74 LYS cc_start: 0.8532 (mttt) cc_final: 0.8180 (mttm) REVERT: T 39 TYR cc_start: 0.7973 (t80) cc_final: 0.7592 (t80) REVERT: T 61 SER cc_start: 0.8584 (m) cc_final: 0.8281 (p) REVERT: T 102 GLU cc_start: 0.6961 (tp30) cc_final: 0.6629 (tp30) REVERT: V 572 LYS cc_start: 0.7863 (tttt) cc_final: 0.7551 (tptm) REVERT: V 573 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7142 (mt-10) REVERT: V 614 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7396 (mmmm) REVERT: V 665 LYS cc_start: 0.7834 (mttt) cc_final: 0.7533 (tttt) REVERT: V 700 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5909 (mmp) REVERT: Z 613 LYS cc_start: 0.7363 (tttt) cc_final: 0.6914 (mmmt) REVERT: Z 626 ILE cc_start: 0.7560 (tp) cc_final: 0.7342 (tp) REVERT: U 656 GLN cc_start: 0.8439 (mt0) cc_final: 0.7994 (mt0) REVERT: U 694 HIS cc_start: 0.8306 (m170) cc_final: 0.8088 (m90) REVERT: U 701 PHE cc_start: 0.8524 (m-80) cc_final: 0.8252 (m-80) REVERT: U 711 ASN cc_start: 0.6835 (m-40) cc_final: 0.6588 (m-40) REVERT: U 815 LEU cc_start: 0.8971 (tp) cc_final: 0.8471 (tp) REVERT: U 816 GLN cc_start: 0.8319 (tp40) cc_final: 0.7956 (tp40) REVERT: U 853 ASN cc_start: 0.7958 (m-40) cc_final: 0.7617 (p0) REVERT: U 875 THR cc_start: 0.8539 (m) cc_final: 0.7919 (p) REVERT: U 883 LEU cc_start: 0.8520 (mt) cc_final: 0.7911 (tp) REVERT: U 886 GLN cc_start: 0.7717 (mt0) cc_final: 0.7447 (mt0) REVERT: Y 585 MET cc_start: 0.6059 (mmm) cc_final: 0.5702 (mmp) REVERT: Y 621 LYS cc_start: 0.7799 (tttp) cc_final: 0.7491 (tptt) REVERT: Y 623 TYR cc_start: 0.6428 (m-80) cc_final: 0.5963 (m-80) REVERT: Y 656 GLN cc_start: 0.7765 (mt0) cc_final: 0.7373 (mp10) REVERT: Y 756 GLU cc_start: 0.6270 (tm-30) cc_final: 0.6055 (tm-30) REVERT: Y 757 ASN cc_start: 0.7535 (t0) cc_final: 0.7268 (t0) REVERT: L 444 GLU cc_start: 0.8290 (pt0) cc_final: 0.7459 (tp30) REVERT: L 653 PHE cc_start: 0.7296 (m-10) cc_final: 0.6593 (m-10) REVERT: L 656 TYR cc_start: 0.6937 (t80) cc_final: 0.6533 (t80) REVERT: L 658 LEU cc_start: 0.8282 (mt) cc_final: 0.7956 (mm) REVERT: L 660 ASN cc_start: 0.7475 (m-40) cc_final: 0.7171 (m-40) REVERT: L 688 ARG cc_start: 0.8534 (mtt180) cc_final: 0.7292 (mmm160) REVERT: L 692 ARG cc_start: 0.8165 (mmt180) cc_final: 0.7784 (ptp-110) REVERT: W 637 LEU cc_start: 0.8397 (tp) cc_final: 0.8108 (tt) REVERT: W 639 LEU cc_start: 0.8667 (mt) cc_final: 0.8369 (pt) REVERT: W 645 THR cc_start: 0.7851 (p) cc_final: 0.7594 (p) REVERT: W 650 LEU cc_start: 0.8461 (mt) cc_final: 0.8224 (mt) REVERT: W 688 ARG cc_start: 0.7630 (ptp90) cc_final: 0.7395 (mpp80) REVERT: W 724 TYR cc_start: 0.7445 (m-80) cc_final: 0.6423 (m-80) REVERT: W 758 VAL cc_start: 0.7102 (m) cc_final: 0.6414 (p) REVERT: W 761 MET cc_start: 0.2297 (OUTLIER) cc_final: 0.1876 (ppp) REVERT: W 801 MET cc_start: 0.2842 (OUTLIER) cc_final: 0.2512 (ptp) REVERT: W 864 MET cc_start: 0.8526 (mtt) cc_final: 0.8214 (ptp) REVERT: W 875 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6704 (p) REVERT: K 667 GLU cc_start: 0.7342 (pm20) cc_final: 0.7121 (pm20) REVERT: K 772 PHE cc_start: 0.6208 (m-80) cc_final: 0.5938 (m-80) REVERT: K 793 TYR cc_start: 0.6530 (m-10) cc_final: 0.6235 (m-10) REVERT: K 883 LEU cc_start: 0.8712 (mt) cc_final: 0.8473 (mm) outliers start: 70 outliers final: 38 residues processed: 815 average time/residue: 0.3049 time to fit residues: 387.4389 Evaluate side-chains 794 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 752 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 700 MET Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 773 LEU Chi-restraints excluded: chain Y residue 671 THR Chi-restraints excluded: chain Y residue 864 MET Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain X residue 661 TYR Chi-restraints excluded: chain W residue 658 ASP Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 801 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 704 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 173 optimal weight: 9.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 378 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 239 optimal weight: 50.0000 chunk 408 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 234 optimal weight: 40.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN E 125 GLN F 27 GLN G 31 HIS H 79 HIS Q 55 GLN T 81 ASN V 510 GLN U 612 ASN ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 612 ASN ** Y 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 739 HIS W 757 ASN W 802 ASN K 789 HIS ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107772 restraints weight = 114940.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108670 restraints weight = 69014.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108956 restraints weight = 44155.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109388 restraints weight = 39520.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109561 restraints weight = 36001.218| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 46134 Z= 0.190 Angle : 0.662 11.800 65088 Z= 0.360 Chirality : 0.043 0.256 7176 Planarity : 0.005 0.060 6080 Dihedral : 27.723 176.439 11233 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.45 % Allowed : 11.11 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.37 (0.13), residues: 3738 helix: 1.27 (0.12), residues: 1872 sheet: -0.21 (0.33), residues: 233 loop : -0.89 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG V 525 TYR 0.038 0.002 TYR W 735 PHE 0.042 0.002 PHE Z 760 TRP 0.024 0.002 TRP Z 674 HIS 0.020 0.001 HIS W 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (46098) covalent geometry : angle 0.65149 / 0.36 (65034) hydrogen bonds : bond 0.04754 / 3.23 ( 2188) hydrogen bonds : angle 3.51053 / 2.57 ( 5631) metal coordination : bond 0.00655 / 0.39 ( 36) metal coordination : angle 4.20085 / 2.74 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 785 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8657 (tt0) cc_final: 0.8327 (tt0) REVERT: B 85 ASP cc_start: 0.7710 (m-30) cc_final: 0.7485 (m-30) REVERT: B 88 TYR cc_start: 0.8130 (m-10) cc_final: 0.7587 (m-80) REVERT: C 76 THR cc_start: 0.8965 (m) cc_final: 0.8688 (p) REVERT: C 107 VAL cc_start: 0.8821 (m) cc_final: 0.8605 (t) REVERT: D 40 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7935 (ttmm) REVERT: D 113 LYS cc_start: 0.8261 (tttt) cc_final: 0.7888 (tptt) REVERT: D 117 LYS cc_start: 0.8473 (tptm) cc_final: 0.8087 (tptt) REVERT: E 57 SER cc_start: 0.8193 (p) cc_final: 0.7324 (p) REVERT: E 59 GLU cc_start: 0.7276 (pm20) cc_final: 0.6882 (pm20) REVERT: E 87 SER cc_start: 0.8617 (p) cc_final: 0.8394 (m) REVERT: E 120 MET cc_start: 0.7496 (mmm) cc_final: 0.7245 (mtt) REVERT: F 35 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8206 (mmm-85) REVERT: G 36 LYS cc_start: 0.8001 (tttt) cc_final: 0.7697 (tttt) REVERT: G 101 THR cc_start: 0.8910 (m) cc_final: 0.8575 (p) REVERT: H 56 MET cc_start: 0.8659 (mmm) cc_final: 0.8060 (tpt) REVERT: H 57 SER cc_start: 0.8669 (m) cc_final: 0.8279 (t) REVERT: H 85 THR cc_start: 0.8943 (m) cc_final: 0.8585 (m) REVERT: H 90 GLU cc_start: 0.7514 (mp0) cc_final: 0.7163 (mp0) REVERT: M 52 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7541 (mtp85) REVERT: M 94 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7430 (mm-30) REVERT: N 35 ARG cc_start: 0.8405 (ttt90) cc_final: 0.8046 (ttt90) REVERT: N 51 TYR cc_start: 0.8622 (m-10) cc_final: 0.8284 (m-10) REVERT: N 59 LYS cc_start: 0.8687 (tttm) cc_final: 0.8227 (ttpt) REVERT: N 88 TYR cc_start: 0.7840 (m-10) cc_final: 0.7622 (m-10) REVERT: O 15 LYS cc_start: 0.7683 (tppt) cc_final: 0.7266 (tttt) REVERT: O 74 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8280 (mmmt) REVERT: P 80 TYR cc_start: 0.7286 (t80) cc_final: 0.7041 (t80) REVERT: P 85 THR cc_start: 0.8878 (m) cc_final: 0.8442 (p) REVERT: P 113 LYS cc_start: 0.8185 (tttt) cc_final: 0.7943 (tttp) REVERT: P 117 LYS cc_start: 0.8770 (tttt) cc_final: 0.8262 (tttt) REVERT: Q 59 GLU cc_start: 0.7502 (pm20) cc_final: 0.7193 (pm20) REVERT: Q 77 ASP cc_start: 0.7519 (t0) cc_final: 0.7260 (t0) REVERT: R 44 LYS cc_start: 0.8567 (mttt) cc_final: 0.8346 (mttt) REVERT: S 15 LYS cc_start: 0.6809 (tppp) cc_final: 0.6494 (tttt) REVERT: S 35 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7787 (mtt90) REVERT: S 50 TYR cc_start: 0.8566 (t80) cc_final: 0.7904 (t80) REVERT: S 74 LYS cc_start: 0.8537 (mttt) cc_final: 0.8195 (mttm) REVERT: S 81 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8718 (tpt170) REVERT: T 39 TYR cc_start: 0.8045 (t80) cc_final: 0.7629 (t80) REVERT: T 61 SER cc_start: 0.8501 (m) cc_final: 0.8279 (p) REVERT: T 102 GLU cc_start: 0.7006 (tp30) cc_final: 0.6785 (tp30) REVERT: V 444 GLU cc_start: 0.8014 (pt0) cc_final: 0.7656 (tp30) REVERT: V 572 LYS cc_start: 0.7766 (tttt) cc_final: 0.7477 (tptm) REVERT: V 573 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7161 (mt-10) REVERT: V 614 LYS cc_start: 0.7861 (mmtm) cc_final: 0.7441 (mmmm) REVERT: V 661 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: V 665 LYS cc_start: 0.7968 (mttt) cc_final: 0.7554 (tttt) REVERT: V 700 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5510 (mtt) REVERT: Z 611 ILE cc_start: 0.8122 (pt) cc_final: 0.7878 (mp) REVERT: Z 613 LYS cc_start: 0.7448 (tttt) cc_final: 0.7001 (mmmt) REVERT: Z 715 PHE cc_start: 0.5456 (OUTLIER) cc_final: 0.3772 (t80) REVERT: Z 759 LEU cc_start: 0.8490 (pp) cc_final: 0.8056 (mt) REVERT: U 641 ASP cc_start: 0.7152 (t0) cc_final: 0.6947 (t0) REVERT: U 656 GLN cc_start: 0.8465 (mt0) cc_final: 0.8017 (mt0) REVERT: U 684 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8700 (m) REVERT: U 692 GLN cc_start: 0.7180 (pp30) cc_final: 0.6762 (tm-30) REVERT: U 701 PHE cc_start: 0.8581 (m-80) cc_final: 0.8329 (m-80) REVERT: U 711 ASN cc_start: 0.7045 (m-40) cc_final: 0.6803 (m-40) REVERT: U 748 ASP cc_start: 0.7098 (p0) cc_final: 0.6636 (m-30) REVERT: U 815 LEU cc_start: 0.9012 (tp) cc_final: 0.8579 (tp) REVERT: U 816 GLN cc_start: 0.8377 (tp40) cc_final: 0.7958 (tp40) REVERT: U 853 ASN cc_start: 0.8058 (m-40) cc_final: 0.7739 (p0) REVERT: U 875 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.7985 (p) REVERT: U 883 LEU cc_start: 0.8513 (mt) cc_final: 0.8052 (tp) REVERT: Y 585 MET cc_start: 0.6199 (mmm) cc_final: 0.5879 (mmp) REVERT: Y 621 LYS cc_start: 0.7858 (tttp) cc_final: 0.7545 (tptt) REVERT: Y 623 TYR cc_start: 0.6464 (m-80) cc_final: 0.6080 (m-80) REVERT: Y 656 GLN cc_start: 0.7855 (mt0) cc_final: 0.7468 (mp10) REVERT: Y 732 PHE cc_start: 0.8324 (m-80) cc_final: 0.7740 (m-80) REVERT: Y 757 ASN cc_start: 0.7595 (t0) cc_final: 0.7079 (t0) REVERT: Y 779 MET cc_start: 0.7927 (tpp) cc_final: 0.7708 (tpp) REVERT: Y 795 TRP cc_start: 0.7680 (m-90) cc_final: 0.7477 (m-90) REVERT: Y 880 MET cc_start: 0.6931 (ppp) cc_final: 0.6720 (tmm) REVERT: L 444 GLU cc_start: 0.8229 (pt0) cc_final: 0.7377 (tp30) REVERT: L 653 PHE cc_start: 0.7306 (m-10) cc_final: 0.6596 (m-10) REVERT: L 656 TYR cc_start: 0.6931 (t80) cc_final: 0.6537 (t80) REVERT: L 658 LEU cc_start: 0.8273 (mt) cc_final: 0.7904 (mm) REVERT: L 688 ARG cc_start: 0.8550 (mtt180) cc_final: 0.7804 (mmm160) REVERT: L 692 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7856 (ptp-110) REVERT: W 637 LEU cc_start: 0.8358 (tp) cc_final: 0.8073 (tt) REVERT: W 645 THR cc_start: 0.7919 (p) cc_final: 0.7664 (p) REVERT: W 650 LEU cc_start: 0.8481 (mt) cc_final: 0.8226 (mt) REVERT: W 683 TYR cc_start: 0.6519 (m-10) cc_final: 0.6100 (m-10) REVERT: W 688 ARG cc_start: 0.7635 (ptp90) cc_final: 0.7267 (ptp-170) REVERT: W 693 LYS cc_start: 0.8762 (tttt) cc_final: 0.8470 (mmmt) REVERT: W 724 TYR cc_start: 0.7476 (m-80) cc_final: 0.6439 (m-10) REVERT: W 732 PHE cc_start: 0.7555 (m-80) cc_final: 0.7347 (m-80) REVERT: W 758 VAL cc_start: 0.7024 (m) cc_final: 0.5253 (p) REVERT: W 761 MET cc_start: 0.2141 (OUTLIER) cc_final: 0.1629 (pmm) REVERT: W 801 MET cc_start: 0.3078 (ptp) cc_final: 0.2777 (ptp) REVERT: W 875 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6857 (p) REVERT: K 667 GLU cc_start: 0.7352 (pm20) cc_final: 0.7134 (pm20) REVERT: K 772 PHE cc_start: 0.6369 (m-80) cc_final: 0.6096 (m-80) REVERT: K 793 TYR cc_start: 0.6617 (m-10) cc_final: 0.5938 (m-10) outliers start: 80 outliers final: 50 residues processed: 810 average time/residue: 0.2964 time to fit residues: 372.9675 Evaluate side-chains 815 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 758 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 661 TYR Chi-restraints excluded: chain V residue 700 MET Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 775 SER Chi-restraints excluded: chain U residue 779 MET Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain Y residue 671 THR Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain W residue 658 ASP Chi-restraints excluded: chain W residue 735 TYR Chi-restraints excluded: chain W residue 757 ASN Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 769 ILE Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 231 optimal weight: 30.0000 chunk 114 optimal weight: 0.5980 chunk 304 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 88 optimal weight: 0.0070 chunk 424 optimal weight: 5.9990 chunk 368 optimal weight: 3.9990 chunk 358 optimal weight: 8.9990 chunk 226 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 415 optimal weight: 0.8980 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN P 81 ASN Q 55 GLN T 81 ASN V 657 HIS ** V 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 789 HIS ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 873 HIS ** X 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 802 ASN W 886 GLN K 886 GLN ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.145623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107001 restraints weight = 114202.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108362 restraints weight = 66622.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109541 restraints weight = 40067.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109726 restraints weight = 34677.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110058 restraints weight = 32286.763| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46134 Z= 0.147 Angle : 0.624 11.197 65088 Z= 0.341 Chirality : 0.042 0.285 7176 Planarity : 0.004 0.051 6080 Dihedral : 27.759 175.763 11233 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.39 % Allowed : 12.58 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.60 (0.13), residues: 3738 helix: 1.50 (0.12), residues: 1874 sheet: -0.18 (0.33), residues: 233 loop : -0.80 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 767 TYR 0.021 0.001 TYR W 683 PHE 0.042 0.001 PHE V 530 TRP 0.027 0.002 TRP Z 674 HIS 0.018 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (46098) covalent geometry : angle 0.61471 / 0.34 (65034) hydrogen bonds : bond 0.04333 / 2.95 ( 2188) hydrogen bonds : angle 3.37594 / 2.48 ( 5631) metal coordination : bond 0.00498 / 0.33 ( 36) metal coordination : angle 3.84875 / 2.46 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 757 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.8739 (m-80) cc_final: 0.8115 (m-80) REVERT: A 93 GLN cc_start: 0.8560 (tt0) cc_final: 0.8333 (tt0) REVERT: B 63 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 88 TYR cc_start: 0.8000 (m-10) cc_final: 0.7547 (m-80) REVERT: D 85 THR cc_start: 0.8538 (m) cc_final: 0.7968 (p) REVERT: D 113 LYS cc_start: 0.8274 (tttt) cc_final: 0.7932 (tptt) REVERT: D 117 LYS cc_start: 0.8475 (tptm) cc_final: 0.8100 (tptt) REVERT: E 57 SER cc_start: 0.8196 (p) cc_final: 0.7040 (t) REVERT: E 58 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8254 (p) REVERT: E 59 GLU cc_start: 0.7262 (pm20) cc_final: 0.6321 (pm20) REVERT: E 120 MET cc_start: 0.7479 (mmm) cc_final: 0.7230 (mtt) REVERT: F 35 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8209 (mmm-85) REVERT: F 77 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7882 (mmtt) REVERT: G 36 LYS cc_start: 0.8017 (tttt) cc_final: 0.7722 (tttt) REVERT: G 101 THR cc_start: 0.8890 (m) cc_final: 0.8522 (p) REVERT: H 56 MET cc_start: 0.8604 (mmm) cc_final: 0.7981 (tpt) REVERT: H 57 SER cc_start: 0.8654 (m) cc_final: 0.8264 (t) REVERT: H 85 THR cc_start: 0.8934 (m) cc_final: 0.8617 (m) REVERT: H 90 GLU cc_start: 0.7510 (mp0) cc_final: 0.7101 (mp0) REVERT: M 52 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7566 (mtp85) REVERT: M 94 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7410 (mm-30) REVERT: N 59 LYS cc_start: 0.8716 (tttm) cc_final: 0.8203 (ttpt) REVERT: N 88 TYR cc_start: 0.7921 (m-10) cc_final: 0.7623 (m-10) REVERT: O 15 LYS cc_start: 0.7670 (tppt) cc_final: 0.7239 (tttt) REVERT: O 75 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7851 (mmtp) REVERT: P 39 TYR cc_start: 0.7169 (t80) cc_final: 0.6868 (t80) REVERT: P 85 THR cc_start: 0.8930 (m) cc_final: 0.8467 (p) REVERT: P 113 LYS cc_start: 0.8227 (tttt) cc_final: 0.7945 (tttp) REVERT: P 117 LYS cc_start: 0.8736 (tttt) cc_final: 0.8239 (tttt) REVERT: Q 59 GLU cc_start: 0.7556 (pm20) cc_final: 0.7225 (pm20) REVERT: Q 77 ASP cc_start: 0.7549 (t0) cc_final: 0.7328 (t0) REVERT: R 43 VAL cc_start: 0.9335 (t) cc_final: 0.9058 (m) REVERT: R 44 LYS cc_start: 0.8594 (mttt) cc_final: 0.8390 (mttt) REVERT: R 91 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8046 (tttt) REVERT: S 15 LYS cc_start: 0.6763 (tppp) cc_final: 0.6481 (tttt) REVERT: S 24 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7722 (mm-40) REVERT: S 35 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7815 (mtt90) REVERT: S 50 TYR cc_start: 0.8491 (t80) cc_final: 0.7674 (t80) REVERT: S 74 LYS cc_start: 0.8550 (mttt) cc_final: 0.8203 (mttm) REVERT: S 81 ARG cc_start: 0.8928 (tpp-160) cc_final: 0.8723 (tpt170) REVERT: T 39 TYR cc_start: 0.8031 (t80) cc_final: 0.7609 (t80) REVERT: T 56 MET cc_start: 0.8409 (tpp) cc_final: 0.7872 (tpp) REVERT: T 61 SER cc_start: 0.8523 (m) cc_final: 0.8286 (p) REVERT: T 105 LYS cc_start: 0.8454 (tttt) cc_final: 0.8053 (tptp) REVERT: V 572 LYS cc_start: 0.7785 (tttt) cc_final: 0.7469 (tptm) REVERT: V 573 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7220 (mt-10) REVERT: V 614 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7426 (mmmm) REVERT: V 661 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: V 665 LYS cc_start: 0.7930 (mttt) cc_final: 0.7374 (tttt) REVERT: V 692 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7634 (ptp90) REVERT: V 722 MET cc_start: 0.6567 (mtt) cc_final: 0.5602 (mpp) REVERT: Z 611 ILE cc_start: 0.8214 (pt) cc_final: 0.7947 (mp) REVERT: Z 613 LYS cc_start: 0.7426 (tttt) cc_final: 0.6893 (mmmt) REVERT: Z 625 VAL cc_start: 0.5336 (p) cc_final: 0.5032 (m) REVERT: Z 674 TRP cc_start: 0.6612 (p90) cc_final: 0.6226 (p90) REVERT: Z 715 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.4923 (t80) REVERT: Z 759 LEU cc_start: 0.8445 (pp) cc_final: 0.8177 (tp) REVERT: U 656 GLN cc_start: 0.8471 (mt0) cc_final: 0.8035 (mt0) REVERT: U 661 ILE cc_start: 0.8886 (tt) cc_final: 0.8603 (pt) REVERT: U 692 GLN cc_start: 0.7328 (pp30) cc_final: 0.7121 (tm-30) REVERT: U 701 PHE cc_start: 0.8575 (m-80) cc_final: 0.8345 (m-80) REVERT: U 711 ASN cc_start: 0.7025 (m-40) cc_final: 0.6772 (m-40) REVERT: U 748 ASP cc_start: 0.7042 (p0) cc_final: 0.6600 (m-30) REVERT: U 815 LEU cc_start: 0.8996 (tp) cc_final: 0.8566 (tp) REVERT: U 816 GLN cc_start: 0.8380 (tp40) cc_final: 0.7911 (tp40) REVERT: U 853 ASN cc_start: 0.8087 (m-40) cc_final: 0.7762 (p0) REVERT: U 875 THR cc_start: 0.8572 (m) cc_final: 0.7911 (p) REVERT: U 883 LEU cc_start: 0.8455 (mt) cc_final: 0.8010 (tp) REVERT: Y 585 MET cc_start: 0.6358 (mmm) cc_final: 0.6025 (mmp) REVERT: Y 621 LYS cc_start: 0.7902 (tttp) cc_final: 0.7552 (tptt) REVERT: Y 623 TYR cc_start: 0.6394 (m-80) cc_final: 0.6108 (m-80) REVERT: Y 653 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8674 (mm) REVERT: Y 656 GLN cc_start: 0.7834 (mt0) cc_final: 0.7434 (mp10) REVERT: Y 732 PHE cc_start: 0.8325 (m-80) cc_final: 0.7989 (m-80) REVERT: Y 795 TRP cc_start: 0.7714 (m-90) cc_final: 0.7468 (m-90) REVERT: Y 864 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: Y 887 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7742 (ptp90) REVERT: L 516 LEU cc_start: 0.8134 (pt) cc_final: 0.7850 (tp) REVERT: L 653 PHE cc_start: 0.7382 (m-10) cc_final: 0.6732 (m-10) REVERT: L 655 PHE cc_start: 0.7531 (t80) cc_final: 0.7143 (t80) REVERT: L 658 LEU cc_start: 0.8235 (mt) cc_final: 0.7992 (mm) REVERT: L 688 ARG cc_start: 0.8615 (mtt180) cc_final: 0.7925 (mmm160) REVERT: L 692 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7891 (tpt170) REVERT: W 637 LEU cc_start: 0.8411 (tp) cc_final: 0.8119 (tt) REVERT: W 645 THR cc_start: 0.7907 (p) cc_final: 0.7646 (p) REVERT: W 650 LEU cc_start: 0.8467 (mt) cc_final: 0.8209 (mt) REVERT: W 683 TYR cc_start: 0.6571 (m-10) cc_final: 0.4807 (m-10) REVERT: W 688 ARG cc_start: 0.7699 (ptp90) cc_final: 0.6794 (ptp-170) REVERT: W 693 LYS cc_start: 0.8828 (tttt) cc_final: 0.8328 (mmmt) REVERT: W 724 TYR cc_start: 0.7489 (m-80) cc_final: 0.6480 (m-80) REVERT: W 732 PHE cc_start: 0.7720 (m-80) cc_final: 0.7501 (m-80) REVERT: W 757 ASN cc_start: 0.6792 (OUTLIER) cc_final: 0.6586 (m-40) REVERT: W 758 VAL cc_start: 0.7009 (m) cc_final: 0.6295 (p) REVERT: W 761 MET cc_start: 0.2098 (OUTLIER) cc_final: 0.1829 (ppp) REVERT: W 801 MET cc_start: 0.3046 (ptp) cc_final: 0.2762 (ptp) REVERT: W 864 MET cc_start: 0.8607 (ptp) cc_final: 0.8242 (ptp) REVERT: W 875 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6832 (p) REVERT: K 667 GLU cc_start: 0.7421 (pm20) cc_final: 0.7201 (pm20) REVERT: K 682 MET cc_start: 0.4884 (tpp) cc_final: 0.4523 (tpp) REVERT: K 735 TYR cc_start: 0.6435 (t80) cc_final: 0.5475 (t80) REVERT: K 793 TYR cc_start: 0.6280 (m-10) cc_final: 0.5862 (m-10) outliers start: 78 outliers final: 43 residues processed: 783 average time/residue: 0.3121 time to fit residues: 378.8458 Evaluate side-chains 794 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 741 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 40 LYS Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 661 TYR Chi-restraints excluded: chain V residue 692 ARG Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 674 MET Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 775 SER Chi-restraints excluded: chain Y residue 653 LEU Chi-restraints excluded: chain Y residue 864 MET Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain L residue 657 HIS Chi-restraints excluded: chain W residue 658 ASP Chi-restraints excluded: chain W residue 757 ASN Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 129 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 427 optimal weight: 40.0000 chunk 364 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 404 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 431 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 68 GLN F 27 GLN F 75 HIS P 46 HIS Q 55 GLN T 60 ASN V 657 HIS U 789 HIS ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 873 HIS ** L 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 660 ASN ** X 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 757 ASN K 873 HIS ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.144844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105962 restraints weight = 114299.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107586 restraints weight = 70811.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108019 restraints weight = 44584.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108718 restraints weight = 35905.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108866 restraints weight = 33294.279| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46134 Z= 0.154 Angle : 0.624 10.028 65088 Z= 0.340 Chirality : 0.042 0.254 7176 Planarity : 0.004 0.052 6080 Dihedral : 27.797 175.431 11233 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.33 % Allowed : 13.78 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.73 (0.13), residues: 3738 helix: 1.61 (0.12), residues: 1874 sheet: -0.23 (0.33), residues: 232 loop : -0.73 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 67 TYR 0.038 0.002 TYR W 683 PHE 0.040 0.001 PHE Z 760 TRP 0.023 0.001 TRP L 674 HIS 0.021 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (46098) covalent geometry : angle 0.61525 / 0.34 (65034) hydrogen bonds : bond 0.04291 / 2.92 ( 2188) hydrogen bonds : angle 3.32264 / 2.43 ( 5631) metal coordination : bond 0.00511 / 0.32 ( 36) metal coordination : angle 3.60348 / 2.32 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 755 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7505 (pm20) cc_final: 0.7115 (pm20) REVERT: A 78 PHE cc_start: 0.8774 (m-80) cc_final: 0.8185 (m-80) REVERT: B 35 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8304 (mmm-85) REVERT: B 63 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 88 TYR cc_start: 0.8066 (m-10) cc_final: 0.7684 (m-80) REVERT: C 24 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7663 (mm-40) REVERT: D 76 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7209 (mtt-85) REVERT: D 85 THR cc_start: 0.8641 (m) cc_final: 0.8051 (p) REVERT: D 113 LYS cc_start: 0.8298 (tttt) cc_final: 0.7956 (tptt) REVERT: D 117 LYS cc_start: 0.8472 (tptm) cc_final: 0.8103 (tptt) REVERT: E 57 SER cc_start: 0.8207 (p) cc_final: 0.7057 (t) REVERT: E 58 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8265 (p) REVERT: E 59 GLU cc_start: 0.7272 (pm20) cc_final: 0.6326 (pm20) REVERT: E 120 MET cc_start: 0.7488 (mmm) cc_final: 0.7277 (mtt) REVERT: F 35 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8212 (mmm-85) REVERT: F 77 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7810 (mmtt) REVERT: G 36 LYS cc_start: 0.8048 (tttt) cc_final: 0.7727 (tttt) REVERT: G 101 THR cc_start: 0.8901 (m) cc_final: 0.8596 (p) REVERT: H 56 MET cc_start: 0.8538 (mmm) cc_final: 0.8155 (tpp) REVERT: H 57 SER cc_start: 0.8632 (m) cc_final: 0.8284 (t) REVERT: H 85 THR cc_start: 0.8969 (m) cc_final: 0.8637 (m) REVERT: H 90 GLU cc_start: 0.7507 (mp0) cc_final: 0.7070 (mp0) REVERT: M 52 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7282 (mtt-85) REVERT: M 94 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7382 (mm-30) REVERT: N 59 LYS cc_start: 0.8699 (tttm) cc_final: 0.8197 (ttpt) REVERT: O 15 LYS cc_start: 0.7668 (tppt) cc_final: 0.7251 (tttt) REVERT: O 75 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7848 (mmtp) REVERT: P 39 TYR cc_start: 0.7139 (t80) cc_final: 0.6868 (t80) REVERT: P 76 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7388 (mtp85) REVERT: P 85 THR cc_start: 0.8950 (m) cc_final: 0.8531 (p) REVERT: P 113 LYS cc_start: 0.8299 (tttt) cc_final: 0.8006 (tttp) REVERT: P 117 LYS cc_start: 0.8729 (tttt) cc_final: 0.8213 (tttt) REVERT: Q 59 GLU cc_start: 0.7629 (pm20) cc_final: 0.7326 (pm20) REVERT: Q 76 GLN cc_start: 0.8405 (tp40) cc_final: 0.8141 (tp40) REVERT: Q 77 ASP cc_start: 0.7532 (t0) cc_final: 0.7279 (t0) REVERT: R 60 VAL cc_start: 0.9112 (t) cc_final: 0.8769 (p) REVERT: S 15 LYS cc_start: 0.6778 (tppp) cc_final: 0.6483 (tttt) REVERT: S 32 ARG cc_start: 0.8275 (ttp80) cc_final: 0.8067 (ttp-110) REVERT: S 74 LYS cc_start: 0.8545 (mttt) cc_final: 0.8186 (mttm) REVERT: S 81 ARG cc_start: 0.8957 (tpp-160) cc_final: 0.8712 (tpt170) REVERT: T 39 TYR cc_start: 0.8070 (t80) cc_final: 0.7701 (t80) REVERT: T 51 ILE cc_start: 0.8681 (tp) cc_final: 0.8177 (tt) REVERT: T 56 MET cc_start: 0.8422 (tpp) cc_final: 0.7678 (tpp) REVERT: T 105 LYS cc_start: 0.8466 (tttt) cc_final: 0.8026 (tptp) REVERT: V 572 LYS cc_start: 0.7815 (tttt) cc_final: 0.7467 (tptm) REVERT: V 573 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7287 (mt-10) REVERT: V 614 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7554 (mmmm) REVERT: V 661 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: V 665 LYS cc_start: 0.7915 (mttt) cc_final: 0.7456 (tttt) REVERT: V 683 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7851 (mmtt) REVERT: V 722 MET cc_start: 0.6675 (mtt) cc_final: 0.5674 (mpp) REVERT: Z 674 TRP cc_start: 0.6490 (p90) cc_final: 0.5602 (p90) REVERT: Z 759 LEU cc_start: 0.8435 (pp) cc_final: 0.8216 (tp) REVERT: U 656 GLN cc_start: 0.8489 (mt0) cc_final: 0.8032 (mt0) REVERT: U 684 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8602 (m) REVERT: U 692 GLN cc_start: 0.7364 (pp30) cc_final: 0.6832 (tm-30) REVERT: U 701 PHE cc_start: 0.8561 (m-80) cc_final: 0.8325 (m-80) REVERT: U 711 ASN cc_start: 0.7095 (m-40) cc_final: 0.6850 (m-40) REVERT: U 748 ASP cc_start: 0.7098 (p0) cc_final: 0.6652 (m-30) REVERT: U 815 LEU cc_start: 0.9025 (tp) cc_final: 0.8598 (tp) REVERT: U 816 GLN cc_start: 0.8401 (tp40) cc_final: 0.7922 (tp40) REVERT: U 875 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.7974 (p) REVERT: U 883 LEU cc_start: 0.8467 (mt) cc_final: 0.8016 (tp) REVERT: Y 585 MET cc_start: 0.6450 (mmm) cc_final: 0.6130 (mmp) REVERT: Y 621 LYS cc_start: 0.7885 (tttp) cc_final: 0.7572 (tptt) REVERT: Y 623 TYR cc_start: 0.6396 (m-80) cc_final: 0.6126 (m-80) REVERT: Y 656 GLN cc_start: 0.7857 (mt0) cc_final: 0.7436 (mp10) REVERT: Y 732 PHE cc_start: 0.8290 (m-80) cc_final: 0.8090 (m-10) REVERT: Y 795 TRP cc_start: 0.7791 (m-90) cc_final: 0.7549 (m-90) REVERT: Y 864 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: Y 887 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7135 (ptp90) REVERT: L 516 LEU cc_start: 0.8162 (pt) cc_final: 0.7870 (tp) REVERT: L 653 PHE cc_start: 0.7353 (m-10) cc_final: 0.6786 (m-10) REVERT: L 655 PHE cc_start: 0.7428 (t80) cc_final: 0.7046 (t80) REVERT: L 658 LEU cc_start: 0.8246 (mt) cc_final: 0.7976 (mm) REVERT: L 688 ARG cc_start: 0.8626 (mtt180) cc_final: 0.7961 (mmm160) REVERT: L 692 ARG cc_start: 0.8185 (mmt180) cc_final: 0.7820 (tpt170) REVERT: W 637 LEU cc_start: 0.8440 (tp) cc_final: 0.8154 (tt) REVERT: W 645 THR cc_start: 0.7895 (p) cc_final: 0.7663 (p) REVERT: W 650 LEU cc_start: 0.8446 (mt) cc_final: 0.8242 (mt) REVERT: W 688 ARG cc_start: 0.7719 (ptp90) cc_final: 0.6838 (ptp-170) REVERT: W 693 LYS cc_start: 0.8809 (tttt) cc_final: 0.8332 (mmmt) REVERT: W 724 TYR cc_start: 0.7516 (m-80) cc_final: 0.6542 (m-80) REVERT: W 732 PHE cc_start: 0.7784 (m-80) cc_final: 0.7542 (m-80) REVERT: W 758 VAL cc_start: 0.7118 (m) cc_final: 0.5255 (p) REVERT: W 761 MET cc_start: 0.1881 (OUTLIER) cc_final: 0.1505 (pmm) REVERT: W 801 MET cc_start: 0.3054 (ptp) cc_final: 0.2781 (ptp) REVERT: W 864 MET cc_start: 0.8664 (ptp) cc_final: 0.8326 (ptp) REVERT: W 875 THR cc_start: 0.7196 (OUTLIER) cc_final: 0.6910 (p) REVERT: W 887 ARG cc_start: 0.8207 (ppt170) cc_final: 0.7824 (ppt170) REVERT: K 667 GLU cc_start: 0.7468 (pm20) cc_final: 0.7240 (pm20) REVERT: K 793 TYR cc_start: 0.6333 (m-10) cc_final: 0.5905 (m-10) outliers start: 76 outliers final: 51 residues processed: 780 average time/residue: 0.3089 time to fit residues: 375.3259 Evaluate side-chains 799 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 740 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain V residue 441 ARG Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 624 LEU Chi-restraints excluded: chain V residue 661 TYR Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 775 SER Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain Y residue 864 MET Chi-restraints excluded: chain Y residue 889 LEU Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 657 HIS Chi-restraints excluded: chain W residue 658 ASP Chi-restraints excluded: chain W residue 757 ASN Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 77 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 341 optimal weight: 0.9980 chunk 405 optimal weight: 0.2980 chunk 317 optimal weight: 0.9990 chunk 328 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 68 GLN P 46 HIS R 75 HIS T 81 ASN V 657 HIS U 789 HIS Y 873 HIS ** L 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 886 GLN ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105862 restraints weight = 114139.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107378 restraints weight = 69673.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108280 restraints weight = 40711.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108954 restraints weight = 32783.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109106 restraints weight = 32666.264| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46134 Z= 0.136 Angle : 0.617 10.537 65088 Z= 0.337 Chirality : 0.042 0.254 7176 Planarity : 0.004 0.050 6080 Dihedral : 27.830 174.816 11233 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.99 % Allowed : 14.39 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.85 (0.13), residues: 3738 helix: 1.72 (0.12), residues: 1873 sheet: -0.10 (0.34), residues: 212 loop : -0.68 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 67 TYR 0.061 0.001 TYR W 683 PHE 0.042 0.001 PHE Z 760 TRP 0.029 0.002 TRP W 753 HIS 0.020 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (46098) covalent geometry : angle 0.60883 / 0.34 (65034) hydrogen bonds : bond 0.04125 / 2.80 ( 2188) hydrogen bonds : angle 3.26156 / 2.39 ( 5631) metal coordination : bond 0.00479 / 0.31 ( 36) metal coordination : angle 3.56128 / 2.31 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 747 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7414 (pm20) cc_final: 0.7046 (pm20) REVERT: A 78 PHE cc_start: 0.8770 (m-80) cc_final: 0.8111 (m-80) REVERT: B 30 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 35 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8320 (mmm-85) REVERT: B 63 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 88 TYR cc_start: 0.8072 (m-10) cc_final: 0.7696 (m-80) REVERT: C 71 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7315 (ttp-110) REVERT: D 76 ARG cc_start: 0.7389 (mtt-85) cc_final: 0.7161 (mtt-85) REVERT: D 85 THR cc_start: 0.8671 (m) cc_final: 0.8080 (p) REVERT: D 113 LYS cc_start: 0.8305 (tttt) cc_final: 0.7945 (tptt) REVERT: D 117 LYS cc_start: 0.8504 (tptm) cc_final: 0.8087 (tptt) REVERT: E 57 SER cc_start: 0.8239 (p) cc_final: 0.7368 (p) REVERT: E 58 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8413 (p) REVERT: E 59 GLU cc_start: 0.7320 (pm20) cc_final: 0.6935 (pm20) REVERT: E 120 MET cc_start: 0.7497 (mmm) cc_final: 0.7289 (mtt) REVERT: F 35 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8222 (mmm-85) REVERT: F 77 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7850 (mmtt) REVERT: G 36 LYS cc_start: 0.8082 (tttt) cc_final: 0.7743 (tttt) REVERT: G 101 THR cc_start: 0.8896 (m) cc_final: 0.8598 (p) REVERT: H 56 MET cc_start: 0.8507 (mmm) cc_final: 0.8204 (tpp) REVERT: H 57 SER cc_start: 0.8630 (m) cc_final: 0.8288 (t) REVERT: H 85 THR cc_start: 0.8963 (m) cc_final: 0.8605 (m) REVERT: H 90 GLU cc_start: 0.7528 (mp0) cc_final: 0.7049 (mp0) REVERT: M 52 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7629 (mtp85) REVERT: M 94 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7364 (mm-30) REVERT: N 59 LYS cc_start: 0.8673 (tttm) cc_final: 0.8178 (ttpt) REVERT: O 15 LYS cc_start: 0.7696 (tppt) cc_final: 0.7243 (tttt) REVERT: O 75 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7848 (mmtp) REVERT: P 39 TYR cc_start: 0.7161 (t80) cc_final: 0.6850 (t80) REVERT: P 85 THR cc_start: 0.8958 (m) cc_final: 0.8545 (p) REVERT: P 96 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8204 (ttp80) REVERT: P 113 LYS cc_start: 0.8337 (tttt) cc_final: 0.8040 (tttp) REVERT: P 117 LYS cc_start: 0.8726 (tttt) cc_final: 0.8223 (tttt) REVERT: Q 59 GLU cc_start: 0.7623 (pm20) cc_final: 0.7317 (pm20) REVERT: Q 76 GLN cc_start: 0.8380 (tp40) cc_final: 0.8147 (tp40) REVERT: Q 77 ASP cc_start: 0.7586 (t0) cc_final: 0.7331 (t0) REVERT: Q 97 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6984 (tt0) REVERT: S 15 LYS cc_start: 0.6741 (tppp) cc_final: 0.6480 (tttt) REVERT: S 74 LYS cc_start: 0.8550 (mttt) cc_final: 0.8187 (mttm) REVERT: S 81 ARG cc_start: 0.8916 (tpp-160) cc_final: 0.8672 (tpt170) REVERT: T 39 TYR cc_start: 0.8103 (t80) cc_final: 0.7745 (t80) REVERT: T 51 ILE cc_start: 0.8647 (tp) cc_final: 0.8126 (tt) REVERT: T 56 MET cc_start: 0.8382 (tpp) cc_final: 0.7634 (tpp) REVERT: T 105 LYS cc_start: 0.8437 (tttt) cc_final: 0.8024 (tptp) REVERT: V 572 LYS cc_start: 0.7821 (tttt) cc_final: 0.7253 (tppp) REVERT: V 573 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7269 (mt-10) REVERT: V 614 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7415 (mmmm) REVERT: V 661 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: V 665 LYS cc_start: 0.7893 (mttt) cc_final: 0.7409 (tttt) REVERT: V 722 MET cc_start: 0.6731 (mtt) cc_final: 0.5700 (mpp) REVERT: V 759 LEU cc_start: 0.8795 (mt) cc_final: 0.8570 (mt) REVERT: Z 624 LEU cc_start: 0.7581 (tp) cc_final: 0.7356 (tt) REVERT: Z 625 VAL cc_start: 0.5197 (p) cc_final: 0.4840 (m) REVERT: Z 626 ILE cc_start: 0.7138 (tp) cc_final: 0.6916 (tp) REVERT: Z 674 TRP cc_start: 0.6351 (p90) cc_final: 0.5734 (p90) REVERT: Z 759 LEU cc_start: 0.8438 (pp) cc_final: 0.8235 (mt) REVERT: U 656 GLN cc_start: 0.8501 (mt0) cc_final: 0.8033 (mt0) REVERT: U 674 MET cc_start: 0.7885 (mmm) cc_final: 0.7572 (tpt) REVERT: U 682 MET cc_start: 0.7443 (ttm) cc_final: 0.7195 (ttm) REVERT: U 684 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8689 (m) REVERT: U 692 GLN cc_start: 0.7419 (pp30) cc_final: 0.6874 (tm-30) REVERT: U 701 PHE cc_start: 0.8544 (m-80) cc_final: 0.8316 (m-80) REVERT: U 711 ASN cc_start: 0.7143 (m-40) cc_final: 0.6874 (m-40) REVERT: U 748 ASP cc_start: 0.7126 (p0) cc_final: 0.6671 (m-30) REVERT: U 815 LEU cc_start: 0.9046 (tp) cc_final: 0.8701 (tp) REVERT: U 875 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.7987 (p) REVERT: U 883 LEU cc_start: 0.8342 (mt) cc_final: 0.7917 (tp) REVERT: Y 585 MET cc_start: 0.6514 (mmm) cc_final: 0.6204 (mmp) REVERT: Y 621 LYS cc_start: 0.7890 (tttp) cc_final: 0.7563 (tptp) REVERT: Y 653 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8705 (mm) REVERT: Y 656 GLN cc_start: 0.7903 (mt0) cc_final: 0.7453 (mp10) REVERT: Y 732 PHE cc_start: 0.8375 (m-80) cc_final: 0.7981 (m-80) REVERT: Y 761 MET cc_start: 0.7387 (ppp) cc_final: 0.6838 (ppp) REVERT: Y 771 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7313 (ttt90) REVERT: Y 795 TRP cc_start: 0.7809 (m-90) cc_final: 0.7577 (m-90) REVERT: Y 864 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7173 (mpp) REVERT: L 516 LEU cc_start: 0.8140 (pt) cc_final: 0.7845 (tp) REVERT: L 653 PHE cc_start: 0.7460 (m-10) cc_final: 0.6869 (m-10) REVERT: L 658 LEU cc_start: 0.8289 (mt) cc_final: 0.7995 (mm) REVERT: L 688 ARG cc_start: 0.8650 (mtt180) cc_final: 0.7936 (mmm160) REVERT: W 637 LEU cc_start: 0.8445 (tp) cc_final: 0.8171 (tt) REVERT: W 645 THR cc_start: 0.7862 (p) cc_final: 0.7629 (p) REVERT: W 693 LYS cc_start: 0.8755 (tttt) cc_final: 0.8294 (mmmt) REVERT: W 724 TYR cc_start: 0.7470 (m-80) cc_final: 0.6507 (m-80) REVERT: W 732 PHE cc_start: 0.7808 (m-80) cc_final: 0.7543 (m-80) REVERT: W 758 VAL cc_start: 0.7096 (m) cc_final: 0.5382 (p) REVERT: W 761 MET cc_start: 0.1748 (OUTLIER) cc_final: 0.1493 (pmm) REVERT: W 801 MET cc_start: 0.3102 (ptp) cc_final: 0.2772 (ptp) REVERT: W 864 MET cc_start: 0.8671 (ptp) cc_final: 0.8347 (ptp) REVERT: W 875 THR cc_start: 0.7190 (OUTLIER) cc_final: 0.6899 (p) REVERT: K 667 GLU cc_start: 0.7477 (pm20) cc_final: 0.7254 (pm20) REVERT: K 793 TYR cc_start: 0.6342 (m-10) cc_final: 0.5895 (m-10) REVERT: K 880 MET cc_start: 0.7123 (ppp) cc_final: 0.6655 (ppp) outliers start: 65 outliers final: 47 residues processed: 765 average time/residue: 0.3098 time to fit residues: 368.8095 Evaluate side-chains 790 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 733 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 40 LYS Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 661 TYR Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 775 SER Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 879 ASN Chi-restraints excluded: chain Y residue 653 LEU Chi-restraints excluded: chain Y residue 864 MET Chi-restraints excluded: chain Y residue 889 LEU Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain L residue 657 HIS Chi-restraints excluded: chain W residue 658 ASP Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 243 optimal weight: 6.9990 chunk 413 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 chunk 393 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 427 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 27 GLN O 68 ASN P 46 HIS ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 657 HIS ** V 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 789 HIS ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 873 HIS ** L 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 660 ASN ** K 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.144939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106145 restraints weight = 114319.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107680 restraints weight = 68141.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108184 restraints weight = 42578.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108628 restraints weight = 34886.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108809 restraints weight = 33529.989| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 46134 Z= 0.130 Angle : 0.623 15.422 65088 Z= 0.336 Chirality : 0.042 0.282 7176 Planarity : 0.004 0.086 6080 Dihedral : 27.841 174.380 11233 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.11 % Allowed : 14.97 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.96 (0.14), residues: 3738 helix: 1.81 (0.12), residues: 1863 sheet: -0.02 (0.34), residues: 212 loop : -0.61 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 67 TYR 0.036 0.001 TYR W 683 PHE 0.041 0.001 PHE Z 760 TRP 0.029 0.002 TRP L 674 HIS 0.018 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (46098) covalent geometry : angle 0.61417 / 0.34 (65034) hydrogen bonds : bond 0.04036 / 2.74 ( 2188) hydrogen bonds : angle 3.23083 / 2.37 ( 5631) metal coordination : bond 0.00770 / 0.43 ( 36) metal coordination : angle 3.58840 / 2.35 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 740 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7377 (pm20) cc_final: 0.7068 (pm20) REVERT: A 78 PHE cc_start: 0.8789 (m-80) cc_final: 0.8235 (m-80) REVERT: B 30 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 35 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8332 (mmm-85) REVERT: B 63 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 88 TYR cc_start: 0.8154 (m-10) cc_final: 0.7689 (m-80) REVERT: C 71 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7335 (ttp-110) REVERT: D 76 ARG cc_start: 0.7437 (mtt-85) cc_final: 0.7174 (mtt-85) REVERT: D 85 THR cc_start: 0.8665 (m) cc_final: 0.8089 (p) REVERT: D 113 LYS cc_start: 0.8339 (tttt) cc_final: 0.7930 (tptt) REVERT: D 117 LYS cc_start: 0.8485 (tptm) cc_final: 0.8047 (tptt) REVERT: E 57 SER cc_start: 0.8248 (p) cc_final: 0.7452 (p) REVERT: E 58 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8536 (t) REVERT: E 59 GLU cc_start: 0.7327 (pm20) cc_final: 0.6926 (pm20) REVERT: E 120 MET cc_start: 0.7521 (mmm) cc_final: 0.7305 (mtt) REVERT: F 35 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8246 (mmm-85) REVERT: F 77 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7836 (mmtt) REVERT: G 36 LYS cc_start: 0.8102 (tttt) cc_final: 0.7771 (tttt) REVERT: G 101 THR cc_start: 0.8943 (m) cc_final: 0.8630 (p) REVERT: H 39 TYR cc_start: 0.7416 (t80) cc_final: 0.7027 (t80) REVERT: H 56 MET cc_start: 0.8459 (mmm) cc_final: 0.7661 (tpp) REVERT: H 57 SER cc_start: 0.8641 (m) cc_final: 0.8279 (t) REVERT: H 85 THR cc_start: 0.8964 (m) cc_final: 0.8609 (m) REVERT: H 90 GLU cc_start: 0.7560 (mp0) cc_final: 0.7043 (mp0) REVERT: M 52 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7631 (mtp85) REVERT: M 94 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7357 (mm-30) REVERT: N 59 LYS cc_start: 0.8660 (tttm) cc_final: 0.8166 (ttpt) REVERT: O 15 LYS cc_start: 0.7674 (tppt) cc_final: 0.7233 (tttt) REVERT: O 75 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7835 (mmtp) REVERT: P 39 TYR cc_start: 0.7161 (t80) cc_final: 0.6829 (t80) REVERT: P 85 THR cc_start: 0.8962 (m) cc_final: 0.8568 (p) REVERT: P 96 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8223 (ttp80) REVERT: P 113 LYS cc_start: 0.8349 (tttt) cc_final: 0.8059 (tttp) REVERT: P 117 LYS cc_start: 0.8731 (tttt) cc_final: 0.8213 (tttt) REVERT: Q 59 GLU cc_start: 0.7641 (pm20) cc_final: 0.7315 (pm20) REVERT: Q 76 GLN cc_start: 0.8351 (tp40) cc_final: 0.8110 (tp40) REVERT: Q 77 ASP cc_start: 0.7613 (t0) cc_final: 0.7336 (t0) REVERT: Q 90 MET cc_start: 0.7735 (mmp) cc_final: 0.7531 (mmm) REVERT: Q 97 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7008 (tt0) REVERT: S 15 LYS cc_start: 0.6760 (tppp) cc_final: 0.6492 (tttt) REVERT: S 74 LYS cc_start: 0.8562 (mttt) cc_final: 0.8195 (mttm) REVERT: S 81 ARG cc_start: 0.8889 (tpp-160) cc_final: 0.8661 (tpt170) REVERT: T 39 TYR cc_start: 0.8103 (t80) cc_final: 0.7726 (t80) REVERT: T 105 LYS cc_start: 0.8414 (tttt) cc_final: 0.8180 (tmtt) REVERT: V 573 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7300 (mt-10) REVERT: V 614 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7445 (mmmm) REVERT: V 655 PHE cc_start: 0.8650 (t80) cc_final: 0.8322 (t80) REVERT: V 661 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: V 665 LYS cc_start: 0.7931 (mttt) cc_final: 0.7419 (tttt) REVERT: V 722 MET cc_start: 0.6766 (mtt) cc_final: 0.5715 (mpp) REVERT: V 759 LEU cc_start: 0.8792 (mt) cc_final: 0.8548 (mt) REVERT: Z 653 PHE cc_start: 0.7995 (m-80) cc_final: 0.7372 (m-80) REVERT: Z 759 LEU cc_start: 0.8487 (pp) cc_final: 0.8229 (tp) REVERT: U 656 GLN cc_start: 0.8543 (mt0) cc_final: 0.8073 (mt0) REVERT: U 674 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7536 (tpt) REVERT: U 682 MET cc_start: 0.7458 (ttm) cc_final: 0.7253 (ttm) REVERT: U 684 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8702 (m) REVERT: U 692 GLN cc_start: 0.7426 (pp30) cc_final: 0.6897 (tm-30) REVERT: U 701 PHE cc_start: 0.8542 (m-80) cc_final: 0.8325 (m-80) REVERT: U 711 ASN cc_start: 0.7156 (m-40) cc_final: 0.6873 (m-40) REVERT: U 748 ASP cc_start: 0.7216 (p0) cc_final: 0.6793 (m-30) REVERT: U 815 LEU cc_start: 0.9039 (tp) cc_final: 0.8721 (tp) REVERT: U 875 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8032 (p) REVERT: U 883 LEU cc_start: 0.8312 (mt) cc_final: 0.7883 (tp) REVERT: Y 585 MET cc_start: 0.6526 (mmm) cc_final: 0.6219 (mmp) REVERT: Y 621 LYS cc_start: 0.7867 (tttp) cc_final: 0.7515 (tptt) REVERT: Y 653 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8700 (mm) REVERT: Y 656 GLN cc_start: 0.7904 (mt0) cc_final: 0.7425 (mp10) REVERT: Y 732 PHE cc_start: 0.8379 (m-80) cc_final: 0.7593 (m-80) REVERT: Y 771 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7313 (ttt90) REVERT: Y 795 TRP cc_start: 0.7808 (m-90) cc_final: 0.7565 (m-90) REVERT: Y 864 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7204 (mpp) REVERT: Y 887 ARG cc_start: 0.7980 (ptp90) cc_final: 0.7133 (ptp90) REVERT: L 444 GLU cc_start: 0.8331 (pt0) cc_final: 0.8027 (pp20) REVERT: L 516 LEU cc_start: 0.8102 (pt) cc_final: 0.7809 (tp) REVERT: L 653 PHE cc_start: 0.7434 (m-10) cc_final: 0.6869 (m-10) REVERT: L 658 LEU cc_start: 0.8249 (mt) cc_final: 0.7945 (mm) REVERT: L 688 ARG cc_start: 0.8664 (mtt180) cc_final: 0.7932 (mmm160) REVERT: W 637 LEU cc_start: 0.8444 (tp) cc_final: 0.8166 (tt) REVERT: W 645 THR cc_start: 0.7872 (p) cc_final: 0.7671 (p) REVERT: W 688 ARG cc_start: 0.7834 (ptp90) cc_final: 0.7579 (mpp80) REVERT: W 693 LYS cc_start: 0.8759 (tttt) cc_final: 0.8278 (mmmt) REVERT: W 724 TYR cc_start: 0.7462 (m-80) cc_final: 0.6502 (m-80) REVERT: W 732 PHE cc_start: 0.7772 (m-80) cc_final: 0.7507 (m-80) REVERT: W 758 VAL cc_start: 0.7144 (m) cc_final: 0.5230 (p) REVERT: W 761 MET cc_start: 0.1804 (OUTLIER) cc_final: 0.1504 (pmm) REVERT: W 801 MET cc_start: 0.3231 (ptp) cc_final: 0.2952 (ptm) REVERT: W 864 MET cc_start: 0.8675 (ptp) cc_final: 0.8358 (ptp) REVERT: W 874 TYR cc_start: 0.6785 (t80) cc_final: 0.6471 (t80) REVERT: W 875 THR cc_start: 0.7219 (OUTLIER) cc_final: 0.6935 (p) REVERT: K 667 GLU cc_start: 0.7467 (pm20) cc_final: 0.7252 (pm20) REVERT: K 793 TYR cc_start: 0.6337 (m-10) cc_final: 0.5887 (m-10) REVERT: K 860 TRP cc_start: 0.7147 (m-10) cc_final: 0.6870 (m-10) REVERT: K 880 MET cc_start: 0.7148 (ppp) cc_final: 0.6687 (ppp) outliers start: 69 outliers final: 50 residues processed: 758 average time/residue: 0.2913 time to fit residues: 343.8701 Evaluate side-chains 797 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 736 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 40 LYS Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 624 LEU Chi-restraints excluded: chain V residue 661 TYR Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 674 MET Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain U residue 775 SER Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 879 ASN Chi-restraints excluded: chain Y residue 653 LEU Chi-restraints excluded: chain Y residue 862 THR Chi-restraints excluded: chain Y residue 864 MET Chi-restraints excluded: chain Y residue 889 LEU Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain L residue 657 HIS Chi-restraints excluded: chain W residue 658 ASP Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 852 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 299 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 385 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 372 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 368 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN P 46 HIS ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 406 ASN V 657 HIS ** V 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 789 HIS ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 873 HIS ** L 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 694 HIS ** K 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.139810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097604 restraints weight = 111809.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100837 restraints weight = 54563.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.102821 restraints weight = 35227.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104019 restraints weight = 27271.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104628 restraints weight = 23541.823| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 46134 Z= 0.350 Angle : 0.818 13.231 65088 Z= 0.432 Chirality : 0.052 0.260 7176 Planarity : 0.005 0.051 6080 Dihedral : 28.155 176.444 11233 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.05 % Allowed : 15.22 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.30 (0.13), residues: 3738 helix: 1.08 (0.12), residues: 1880 sheet: -0.22 (0.32), residues: 226 loop : -0.74 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 35 TYR 0.056 0.002 TYR W 683 PHE 0.041 0.002 PHE Z 760 TRP 0.056 0.003 TRP Z 674 HIS 0.021 0.002 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.35 (46098) covalent geometry : angle 0.81112 / 0.43 (65034) hydrogen bonds : bond 0.06294 / 4.25 ( 2188) hydrogen bonds : angle 3.81944 / 2.79 ( 5631) metal coordination : bond 0.00584 / 0.37 ( 36) metal coordination : angle 3.66163 / 2.46 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 770 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7680 (pm20) cc_final: 0.7262 (pm20) REVERT: B 34 ILE cc_start: 0.8858 (mt) cc_final: 0.8637 (mm) REVERT: B 63 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 88 TYR cc_start: 0.8295 (m-10) cc_final: 0.7950 (m-80) REVERT: C 76 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8622 (t) REVERT: D 39 TYR cc_start: 0.7957 (t80) cc_final: 0.7750 (t80) REVERT: D 113 LYS cc_start: 0.8421 (tttt) cc_final: 0.8019 (tptt) REVERT: D 117 LYS cc_start: 0.8505 (tptm) cc_final: 0.8148 (tptt) REVERT: E 57 SER cc_start: 0.8335 (p) cc_final: 0.7469 (p) REVERT: E 58 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8529 (p) REVERT: E 59 GLU cc_start: 0.7404 (pm20) cc_final: 0.7045 (pm20) REVERT: E 122 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8225 (mtmt) REVERT: F 77 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8113 (mmmt) REVERT: G 36 LYS cc_start: 0.8263 (tttt) cc_final: 0.8005 (tttt) REVERT: G 101 THR cc_start: 0.9002 (m) cc_final: 0.8645 (p) REVERT: H 57 SER cc_start: 0.8796 (m) cc_final: 0.8531 (t) REVERT: H 85 THR cc_start: 0.8998 (m) cc_final: 0.8738 (m) REVERT: H 90 GLU cc_start: 0.7686 (mp0) cc_final: 0.7088 (mp0) REVERT: M 52 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7580 (mtt-85) REVERT: M 94 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7510 (mm-30) REVERT: N 59 LYS cc_start: 0.8697 (tttm) cc_final: 0.8230 (ttpt) REVERT: N 80 THR cc_start: 0.8911 (m) cc_final: 0.8265 (p) REVERT: O 15 LYS cc_start: 0.7834 (tppt) cc_final: 0.7478 (tttt) REVERT: P 39 TYR cc_start: 0.7436 (t80) cc_final: 0.7105 (t80) REVERT: P 85 THR cc_start: 0.9104 (m) cc_final: 0.8650 (p) REVERT: P 96 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8308 (ttp80) REVERT: P 113 LYS cc_start: 0.8537 (tttt) cc_final: 0.7749 (tppt) REVERT: P 117 LYS cc_start: 0.8655 (tttt) cc_final: 0.8191 (tttt) REVERT: Q 58 THR cc_start: 0.9097 (p) cc_final: 0.8879 (p) REVERT: Q 59 GLU cc_start: 0.7704 (pm20) cc_final: 0.7304 (pm20) REVERT: Q 76 GLN cc_start: 0.8427 (tp40) cc_final: 0.8119 (tp40) REVERT: Q 77 ASP cc_start: 0.7665 (t0) cc_final: 0.7295 (t0) REVERT: Q 97 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7114 (tt0) REVERT: R 31 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8718 (tttp) REVERT: R 77 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8386 (mmtm) REVERT: R 91 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8320 (tttt) REVERT: S 74 LYS cc_start: 0.8557 (mttt) cc_final: 0.8218 (mttm) REVERT: T 39 TYR cc_start: 0.8270 (t80) cc_final: 0.7873 (t80) REVERT: T 65 ASP cc_start: 0.8279 (t0) cc_final: 0.8068 (t0) REVERT: T 69 ARG cc_start: 0.8842 (mtt90) cc_final: 0.8538 (mtt180) REVERT: T 79 HIS cc_start: 0.8354 (m-70) cc_final: 0.8111 (m170) REVERT: T 105 LYS cc_start: 0.8487 (tttt) cc_final: 0.8076 (tptp) REVERT: V 572 LYS cc_start: 0.7778 (tttt) cc_final: 0.7233 (tppp) REVERT: V 614 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7714 (mmmm) REVERT: V 665 LYS cc_start: 0.7888 (mttt) cc_final: 0.7434 (tttt) REVERT: V 722 MET cc_start: 0.7088 (mtt) cc_final: 0.6116 (mpp) REVERT: V 758 HIS cc_start: 0.7050 (t70) cc_final: 0.6777 (t-90) REVERT: V 759 LEU cc_start: 0.8863 (mt) cc_final: 0.8629 (mt) REVERT: V 764 LYS cc_start: 0.7464 (tttt) cc_final: 0.6668 (tptt) REVERT: Z 613 LYS cc_start: 0.7528 (tttt) cc_final: 0.6974 (ttpt) REVERT: Z 693 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: Z 715 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.5340 (t80) REVERT: U 656 GLN cc_start: 0.8600 (mt0) cc_final: 0.8159 (mt0) REVERT: U 674 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7607 (tpt) REVERT: U 684 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8813 (m) REVERT: U 692 GLN cc_start: 0.7472 (pp30) cc_final: 0.6948 (tm-30) REVERT: U 701 PHE cc_start: 0.8543 (m-80) cc_final: 0.8287 (m-80) REVERT: U 711 ASN cc_start: 0.7399 (m-40) cc_final: 0.7198 (m-40) REVERT: U 748 ASP cc_start: 0.7153 (p0) cc_final: 0.6918 (m-30) REVERT: U 815 LEU cc_start: 0.9120 (tp) cc_final: 0.8843 (tp) REVERT: U 861 CYS cc_start: 0.8335 (m) cc_final: 0.7948 (p) REVERT: U 875 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8067 (p) REVERT: U 877 VAL cc_start: 0.8908 (t) cc_final: 0.8702 (t) REVERT: U 883 LEU cc_start: 0.8478 (mt) cc_final: 0.8133 (tp) REVERT: U 886 GLN cc_start: 0.7894 (tt0) cc_final: 0.7597 (tp-100) REVERT: Y 585 MET cc_start: 0.6608 (mmm) cc_final: 0.6303 (mmp) REVERT: Y 621 LYS cc_start: 0.8007 (tttp) cc_final: 0.7749 (tptt) REVERT: Y 653 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8752 (mm) REVERT: Y 656 GLN cc_start: 0.8018 (mt0) cc_final: 0.7516 (mp10) REVERT: Y 684 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.7893 (p) REVERT: Y 887 ARG cc_start: 0.8188 (ptp90) cc_final: 0.7422 (ptp90) REVERT: L 516 LEU cc_start: 0.8121 (pt) cc_final: 0.7800 (tp) REVERT: L 653 PHE cc_start: 0.7975 (m-10) cc_final: 0.7232 (m-10) REVERT: L 658 LEU cc_start: 0.8540 (mt) cc_final: 0.8277 (mm) REVERT: L 660 ASN cc_start: 0.8140 (m110) cc_final: 0.6602 (m110) REVERT: L 663 ARG cc_start: 0.7250 (ptp-110) cc_final: 0.6791 (mtt180) REVERT: L 688 ARG cc_start: 0.8822 (mtt180) cc_final: 0.7897 (mmm160) REVERT: L 692 ARG cc_start: 0.8460 (mmt180) cc_final: 0.7528 (tpt170) REVERT: X 653 PHE cc_start: 0.8586 (m-80) cc_final: 0.8266 (m-10) REVERT: W 637 LEU cc_start: 0.8603 (tp) cc_final: 0.8331 (tt) REVERT: W 645 THR cc_start: 0.8362 (p) cc_final: 0.8156 (p) REVERT: W 688 ARG cc_start: 0.8279 (ptp90) cc_final: 0.7660 (mtp85) REVERT: W 693 LYS cc_start: 0.8902 (tttt) cc_final: 0.8379 (mmmt) REVERT: W 724 TYR cc_start: 0.7552 (m-80) cc_final: 0.6491 (m-80) REVERT: W 732 PHE cc_start: 0.8251 (m-80) cc_final: 0.7761 (m-80) REVERT: W 758 VAL cc_start: 0.7307 (m) cc_final: 0.5503 (p) REVERT: W 761 MET cc_start: 0.2027 (OUTLIER) cc_final: 0.1612 (pmm) REVERT: W 864 MET cc_start: 0.8790 (ptp) cc_final: 0.8579 (ptp) REVERT: W 874 TYR cc_start: 0.7465 (t80) cc_final: 0.6983 (t80) REVERT: W 875 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7358 (p) REVERT: W 880 MET cc_start: 0.5851 (ppp) cc_final: 0.4604 (ppp) REVERT: W 893 TRP cc_start: 0.6580 (m100) cc_final: 0.6326 (m100) REVERT: W 902 PHE cc_start: 0.8438 (m-10) cc_final: 0.8227 (m-10) REVERT: K 667 GLU cc_start: 0.7762 (pm20) cc_final: 0.7521 (pm20) REVERT: K 682 MET cc_start: 0.5036 (tpp) cc_final: 0.4818 (tpp) REVERT: K 735 TYR cc_start: 0.6641 (t80) cc_final: 0.5997 (t80) REVERT: K 738 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8241 (pp) REVERT: K 793 TYR cc_start: 0.7047 (m-10) cc_final: 0.6508 (m-10) REVERT: K 860 TRP cc_start: 0.7725 (m-10) cc_final: 0.7351 (m-90) REVERT: K 880 MET cc_start: 0.7400 (ppp) cc_final: 0.7018 (ppp) outliers start: 67 outliers final: 44 residues processed: 790 average time/residue: 0.3099 time to fit residues: 379.0113 Evaluate side-chains 802 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 745 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 624 LEU Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 674 MET Chi-restraints excluded: chain U residue 684 VAL Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 879 ASN Chi-restraints excluded: chain Y residue 513 MET Chi-restraints excluded: chain Y residue 653 LEU Chi-restraints excluded: chain Y residue 671 THR Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 862 THR Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain L residue 657 HIS Chi-restraints excluded: chain X residue 661 TYR Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 429 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 431 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 155 optimal weight: 40.0000 chunk 84 optimal weight: 0.0870 chunk 406 optimal weight: 30.0000 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 27 GLN H 81 ASN P 46 HIS V 406 ASN ** V 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 789 HIS ** U 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 873 HIS ** X 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.141676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102601 restraints weight = 112453.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103692 restraints weight = 68113.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104221 restraints weight = 41508.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104645 restraints weight = 35351.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106013 restraints weight = 32211.960| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 46134 Z= 0.168 Angle : 0.698 19.009 65088 Z= 0.371 Chirality : 0.045 0.275 7176 Planarity : 0.005 0.055 6080 Dihedral : 28.144 174.081 11233 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.53 % Allowed : 16.32 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.67 (0.13), residues: 3738 helix: 1.46 (0.12), residues: 1871 sheet: -0.29 (0.32), residues: 231 loop : -0.61 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG U 823 TYR 0.054 0.002 TYR W 683 PHE 0.040 0.001 PHE Z 760 TRP 0.043 0.002 TRP L 674 HIS 0.018 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (46098) covalent geometry : angle 0.69134 / 0.37 (65034) hydrogen bonds : bond 0.04547 / 3.11 ( 2188) hydrogen bonds : angle 3.49561 / 2.54 ( 5631) metal coordination : bond 0.00486 / 0.31 ( 36) metal coordination : angle 3.37663 / 2.21 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7476 Ramachandran restraints generated. 3738 Oldfield, 0 Emsley, 3738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 749 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.8813 (m-80) cc_final: 0.8205 (m-80) REVERT: B 35 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8380 (mmm-85) REVERT: B 63 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 88 TYR cc_start: 0.8280 (m-10) cc_final: 0.7839 (m-80) REVERT: C 15 LYS cc_start: 0.6769 (mttt) cc_final: 0.6560 (mtmt) REVERT: C 101 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8697 (p) REVERT: D 36 ILE cc_start: 0.8651 (pt) cc_final: 0.8431 (pt) REVERT: D 39 TYR cc_start: 0.7919 (t80) cc_final: 0.7655 (t80) REVERT: D 113 LYS cc_start: 0.8396 (tttt) cc_final: 0.8063 (tptt) REVERT: D 117 LYS cc_start: 0.8527 (tptm) cc_final: 0.8143 (tptt) REVERT: E 57 SER cc_start: 0.8242 (p) cc_final: 0.7477 (p) REVERT: E 58 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8597 (t) REVERT: E 59 GLU cc_start: 0.7355 (pm20) cc_final: 0.6996 (pm20) REVERT: F 35 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8112 (mmm-85) REVERT: F 77 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8013 (mmmt) REVERT: G 36 LYS cc_start: 0.8204 (tttt) cc_final: 0.7955 (tttt) REVERT: G 101 THR cc_start: 0.8982 (m) cc_final: 0.8699 (p) REVERT: H 56 MET cc_start: 0.8515 (mmm) cc_final: 0.7958 (tpp) REVERT: H 57 SER cc_start: 0.8812 (m) cc_final: 0.8479 (t) REVERT: H 85 THR cc_start: 0.8978 (m) cc_final: 0.8721 (m) REVERT: H 90 GLU cc_start: 0.7639 (mp0) cc_final: 0.7006 (mp0) REVERT: H 98 LEU cc_start: 0.8567 (mt) cc_final: 0.8359 (mp) REVERT: M 52 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7540 (mtt-85) REVERT: M 94 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7396 (mm-30) REVERT: N 59 LYS cc_start: 0.8614 (tttm) cc_final: 0.8176 (ttpt) REVERT: O 15 LYS cc_start: 0.7809 (tppt) cc_final: 0.7421 (tttt) REVERT: P 39 TYR cc_start: 0.7337 (t80) cc_final: 0.6984 (t80) REVERT: P 85 THR cc_start: 0.9089 (m) cc_final: 0.8688 (p) REVERT: P 96 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8230 (ttp80) REVERT: P 113 LYS cc_start: 0.8528 (tttt) cc_final: 0.7921 (tppt) REVERT: P 117 LYS cc_start: 0.8700 (tttt) cc_final: 0.8277 (tttt) REVERT: Q 59 GLU cc_start: 0.7746 (pm20) cc_final: 0.7412 (pm20) REVERT: Q 77 ASP cc_start: 0.7642 (t0) cc_final: 0.7292 (t0) REVERT: Q 97 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7049 (tt0) REVERT: R 31 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8706 (tttp) REVERT: R 91 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8205 (tttt) REVERT: S 74 LYS cc_start: 0.8558 (mttt) cc_final: 0.8196 (mttm) REVERT: T 39 TYR cc_start: 0.8173 (t80) cc_final: 0.7764 (t80) REVERT: T 56 MET cc_start: 0.8163 (tpp) cc_final: 0.7738 (tpp) REVERT: T 105 LYS cc_start: 0.8438 (tttt) cc_final: 0.8044 (tptp) REVERT: V 448 MET cc_start: 0.6220 (mmm) cc_final: 0.5840 (ptp) REVERT: V 573 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7364 (mt-10) REVERT: V 614 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7270 (mmmm) REVERT: V 617 GLU cc_start: 0.7549 (pm20) cc_final: 0.6972 (pm20) REVERT: V 665 LYS cc_start: 0.7917 (mttt) cc_final: 0.7447 (tttt) REVERT: V 700 MET cc_start: 0.7818 (tpt) cc_final: 0.7474 (tpt) REVERT: V 722 MET cc_start: 0.7054 (mtt) cc_final: 0.6269 (mpp) REVERT: V 758 HIS cc_start: 0.6888 (t70) cc_final: 0.6664 (t-90) REVERT: V 759 LEU cc_start: 0.8837 (mt) cc_final: 0.8552 (mt) REVERT: V 764 LYS cc_start: 0.7432 (tttt) cc_final: 0.6681 (tptt) REVERT: Z 613 LYS cc_start: 0.7516 (tttt) cc_final: 0.6938 (ttpt) REVERT: Z 653 PHE cc_start: 0.7887 (m-80) cc_final: 0.7665 (m-80) REVERT: Z 675 MET cc_start: 0.6210 (mmm) cc_final: 0.5963 (mmm) REVERT: Z 693 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: Z 759 LEU cc_start: 0.8437 (pp) cc_final: 0.8211 (tp) REVERT: U 656 GLN cc_start: 0.8549 (mt0) cc_final: 0.8097 (mt0) REVERT: U 674 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7392 (tpt) REVERT: U 692 GLN cc_start: 0.7469 (pp30) cc_final: 0.6963 (tm-30) REVERT: U 701 PHE cc_start: 0.8505 (m-80) cc_final: 0.8262 (m-80) REVERT: U 711 ASN cc_start: 0.7404 (m-40) cc_final: 0.7145 (m-40) REVERT: U 748 ASP cc_start: 0.7311 (p0) cc_final: 0.6986 (m-30) REVERT: U 815 LEU cc_start: 0.9113 (tp) cc_final: 0.8847 (tp) REVERT: U 861 CYS cc_start: 0.8302 (m) cc_final: 0.7952 (p) REVERT: U 875 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.7965 (p) REVERT: U 883 LEU cc_start: 0.8389 (mt) cc_final: 0.8037 (tp) REVERT: U 886 GLN cc_start: 0.7866 (tt0) cc_final: 0.7570 (tp-100) REVERT: U 899 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7623 (ptm160) REVERT: Y 585 MET cc_start: 0.6618 (mmm) cc_final: 0.6216 (mmp) REVERT: Y 621 LYS cc_start: 0.7933 (tttp) cc_final: 0.7689 (tptp) REVERT: Y 656 GLN cc_start: 0.8012 (mt0) cc_final: 0.7322 (mp10) REVERT: Y 732 PHE cc_start: 0.8355 (m-80) cc_final: 0.8126 (m-80) REVERT: Y 757 ASN cc_start: 0.7988 (t0) cc_final: 0.7692 (t0) REVERT: Y 761 MET cc_start: 0.7539 (ppp) cc_final: 0.6921 (ppp) REVERT: Y 771 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7383 (ttt90) REVERT: Y 864 MET cc_start: 0.7725 (ttm) cc_final: 0.7188 (mpp) REVERT: Y 887 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7277 (ptp90) REVERT: L 406 ASN cc_start: -0.1984 (OUTLIER) cc_final: -0.4876 (m-40) REVERT: L 448 MET cc_start: 0.5700 (mpp) cc_final: 0.5492 (mpp) REVERT: L 516 LEU cc_start: 0.8088 (pt) cc_final: 0.7819 (tp) REVERT: L 653 PHE cc_start: 0.7598 (m-10) cc_final: 0.7019 (m-10) REVERT: L 658 LEU cc_start: 0.8349 (mt) cc_final: 0.8037 (mm) REVERT: L 682 MET cc_start: 0.2870 (tpp) cc_final: 0.1944 (tmm) REVERT: L 688 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7728 (mmm160) REVERT: L 692 ARG cc_start: 0.8277 (mmt180) cc_final: 0.7240 (tpt170) REVERT: X 653 PHE cc_start: 0.8260 (m-80) cc_final: 0.7902 (m-10) REVERT: W 637 LEU cc_start: 0.8477 (tp) cc_final: 0.8197 (tt) REVERT: W 645 THR cc_start: 0.8124 (p) cc_final: 0.7888 (p) REVERT: W 678 GLN cc_start: 0.8712 (mp10) cc_final: 0.8482 (mp10) REVERT: W 688 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7463 (mtp85) REVERT: W 693 LYS cc_start: 0.8759 (tttt) cc_final: 0.8294 (mmmt) REVERT: W 724 TYR cc_start: 0.7433 (m-80) cc_final: 0.6493 (m-80) REVERT: W 732 PHE cc_start: 0.7845 (m-80) cc_final: 0.7502 (m-80) REVERT: W 758 VAL cc_start: 0.7102 (m) cc_final: 0.5228 (p) REVERT: W 761 MET cc_start: 0.1730 (OUTLIER) cc_final: 0.1435 (pmm) REVERT: W 864 MET cc_start: 0.8698 (ptp) cc_final: 0.8382 (ptp) REVERT: W 874 TYR cc_start: 0.7022 (t80) cc_final: 0.6672 (t80) REVERT: W 875 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7079 (p) REVERT: W 880 MET cc_start: 0.5409 (ppp) cc_final: 0.4240 (ppp) REVERT: W 887 ARG cc_start: 0.8249 (ppt170) cc_final: 0.7835 (ppt170) REVERT: W 893 TRP cc_start: 0.6495 (m100) cc_final: 0.6290 (m100) REVERT: W 902 PHE cc_start: 0.8233 (m-10) cc_final: 0.8009 (m-10) REVERT: K 639 LEU cc_start: 0.8427 (mp) cc_final: 0.7996 (pt) REVERT: K 667 GLU cc_start: 0.7504 (pm20) cc_final: 0.7291 (pm20) REVERT: K 682 MET cc_start: 0.5137 (tpp) cc_final: 0.4909 (tpp) REVERT: K 793 TYR cc_start: 0.6518 (m-10) cc_final: 0.6008 (m-10) REVERT: K 880 MET cc_start: 0.7324 (ppp) cc_final: 0.6782 (tmm) outliers start: 50 outliers final: 37 residues processed: 763 average time/residue: 0.2976 time to fit residues: 351.6549 Evaluate side-chains 781 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 734 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 73 GLU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 90 MET Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 624 LEU Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 693 PHE Chi-restraints excluded: chain Z residue 715 PHE Chi-restraints excluded: chain U residue 674 MET Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 879 ASN Chi-restraints excluded: chain U residue 899 ARG Chi-restraints excluded: chain Y residue 513 MET Chi-restraints excluded: chain Y residue 900 HIS Chi-restraints excluded: chain L residue 406 ASN Chi-restraints excluded: chain L residue 557 VAL Chi-restraints excluded: chain L residue 657 HIS Chi-restraints excluded: chain W residue 761 MET Chi-restraints excluded: chain W residue 821 HIS Chi-restraints excluded: chain W residue 852 MET Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 738 LEU Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 318 optimal weight: 4.9990 chunk 350 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 211 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 367 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 397 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 93 GLN H 81 ASN P 81 ASN U 789 HIS Y 873 HIS ** X 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.142984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104087 restraints weight = 112907.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104994 restraints weight = 67989.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105374 restraints weight = 43388.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106080 restraints weight = 35852.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106177 restraints weight = 33272.839| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46134 Z= 0.131 Angle : 0.660 16.216 65088 Z= 0.352 Chirality : 0.042 0.254 7176 Planarity : 0.004 0.073 6080 Dihedral : 28.061 174.562 11233 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.50 % Allowed : 16.26 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.91 (0.14), residues: 3738 helix: 1.72 (0.12), residues: 1879 sheet: -0.30 (0.31), residues: 236 loop : -0.55 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 823 TYR 0.031 0.001 TYR W 683 PHE 0.043 0.001 PHE Z 760 TRP 0.048 0.002 TRP K 860 HIS 0.017 0.001 HIS X 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (46098) covalent geometry : angle 0.65368 / 0.35 (65034) hydrogen bonds : bond 0.04096 / 2.79 ( 2188) hydrogen bonds : angle 3.33661 / 2.43 ( 5631) metal coordination : bond 0.00462 / 0.30 ( 36) metal coordination : angle 3.17787 / 2.09 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9637.03 seconds wall clock time: 165 minutes 47.27 seconds (9947.27 seconds total)