Starting phenix.real_space_refine on Mon Sep 30 12:18:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/09_2024/6wrs_21887_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/09_2024/6wrs_21887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/09_2024/6wrs_21887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/09_2024/6wrs_21887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/09_2024/6wrs_21887_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/09_2024/6wrs_21887_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 P 2803 5.49 5 S 56 5.16 5 C 39947 2.51 5 N 15057 2.21 5 O 23251 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 1.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 81115 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 97} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 711 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "G" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "K" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 481 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1472 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1082 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "Y" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "Z" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "1" Number of atoms: 57851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2698, 57851 Inner-chain residues flagged as termini: ['pdbres=" A 1 318 "', 'pdbres=" A 11459 "', 'pdbres=" U 11540 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2698} Modifications used: {'5*END': 5, 'rna2p_pur': 268, 'rna2p_pyr': 139, 'rna3p_pur': 1285, 'rna3p_pyr': 1006} Link IDs: {'rna2p': 407, 'rna3p': 2290} Chain breaks: 6 Chain: "2" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2358 Classifications: {'RNA': 111} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 98} Chain: "I" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "1" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U7V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.63, per 1000 atoms: 0.43 Number of scatterers: 81115 At special positions: 0 Unit cell: (207.48, 237.12, 186.96, 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) S 56 16.00 P 2803 15.00 F 1 9.00 O 23251 8.00 N 15057 7.00 C 39947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.04 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: 13.88 Conformation dependent library (CDL) restraints added in 2.9 seconds 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4852 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 40 sheets defined 23.0% alpha, 20.1% beta 513 base pairs and 1562 stacking pairs defined. Time for finding SS restraints: 28.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.869A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.654A pdb=" N LEU A 105 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.834A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B 201 " --> pdb=" O LEU B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.625A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.972A pdb=" N MET B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 removed outlier: 4.015A pdb=" N LYS B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 4.092A pdb=" N LYS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.901A pdb=" N HIS C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 57 removed outlier: 3.827A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 70 removed outlier: 3.904A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 75 through 87 removed outlier: 3.514A pdb=" N LYS C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 102 through 117 removed outlier: 4.055A pdb=" N PHE C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 25 removed outlier: 4.651A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.710A pdb=" N LYS E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 53 removed outlier: 4.326A pdb=" N LYS E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.536A pdb=" N HIS E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 61' Processing helix chain 'F' and resid 34 through 47 removed outlier: 3.849A pdb=" N VAL F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 removed outlier: 3.528A pdb=" N LEU H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU H 21 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG H 22 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 removed outlier: 3.694A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 24 removed outlier: 3.794A pdb=" N ILE K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 30 removed outlier: 3.501A pdb=" N PHE K 30 " --> pdb=" O ASN K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 61 removed outlier: 3.838A pdb=" N THR K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'M' and resid 16 through 24 removed outlier: 3.532A pdb=" N ARG M 20 " --> pdb=" O PRO M 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS M 21 " --> pdb=" O GLU M 17 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 17 removed outlier: 3.694A pdb=" N ARG N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 20 No H-bonds generated for 'chain 'N' and resid 18 through 20' Processing helix chain 'P' and resid 9 through 15 removed outlier: 3.580A pdb=" N SER P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 23 Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'Q' and resid 37 through 42 removed outlier: 3.518A pdb=" N LYS Q 41 " --> pdb=" O SER Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 58 removed outlier: 3.645A pdb=" N LYS Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 63 removed outlier: 3.837A pdb=" N LEU Q 62 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA Q 63 " --> pdb=" O GLN Q 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 59 through 63' Processing helix chain 'R' and resid 29 through 32 Processing helix chain 'S' and resid 29 through 42 removed outlier: 3.907A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 119 removed outlier: 3.555A pdb=" N SER S 115 " --> pdb=" O ARG S 111 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN S 119 " --> pdb=" O SER S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 146 removed outlier: 3.710A pdb=" N PHE S 139 " --> pdb=" O LYS S 135 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN S 141 " --> pdb=" O LYS S 137 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU S 143 " --> pdb=" O PHE S 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER S 144 " --> pdb=" O LYS S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 166 Processing helix chain 'S' and resid 182 through 189 removed outlier: 3.873A pdb=" N ILE S 186 " --> pdb=" O ASN S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 196 through 206 Processing helix chain 'V' and resid 25 through 34 removed outlier: 3.810A pdb=" N SER V 31 " --> pdb=" O GLY V 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 63 removed outlier: 3.668A pdb=" N ILE V 63 " --> pdb=" O ALA V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 97 Processing helix chain 'V' and resid 97 through 107 removed outlier: 3.647A pdb=" N LEU V 101 " --> pdb=" O ASN V 97 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE V 102 " --> pdb=" O PRO V 98 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS V 107 " --> pdb=" O GLU V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 110 No H-bonds generated for 'chain 'V' and resid 108 through 110' Processing helix chain 'V' and resid 119 through 121 No H-bonds generated for 'chain 'V' and resid 119 through 121' Processing helix chain 'W' and resid 103 through 107 removed outlier: 4.279A pdb=" N ARG W 107 " --> pdb=" O ARG W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'X' and resid 56 through 61 removed outlier: 3.700A pdb=" N ARG X 60 " --> pdb=" O PRO X 56 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU X 61 " --> pdb=" O LEU X 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 56 through 61' Processing helix chain 'X' and resid 78 through 83 Processing helix chain 'X' and resid 92 through 100 Processing helix chain 'X' and resid 129 through 139 removed outlier: 3.679A pdb=" N GLU X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS X 139 " --> pdb=" O ALA X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 58 removed outlier: 4.305A pdb=" N TYR Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET Y 58 " --> pdb=" O MET Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 123 removed outlier: 3.562A pdb=" N SER Y 122 " --> pdb=" O LEU Y 118 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 14 removed outlier: 3.801A pdb=" N LYS Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 28 removed outlier: 3.949A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 52 removed outlier: 3.738A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL Z 44 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU Z 45 " --> pdb=" O ARG Z 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR Z 49 " --> pdb=" O GLU Z 45 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 63 removed outlier: 3.743A pdb=" N ARG Z 59 " --> pdb=" O ASP Z 55 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN Z 61 " --> pdb=" O ALA Z 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 87 Processing helix chain 'Z' and resid 88 through 93 Processing helix chain 'a' and resid 6 through 15 removed outlier: 4.087A pdb=" N VAL a 10 " --> pdb=" O ASP a 6 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 88 removed outlier: 3.804A pdb=" N GLY a 77 " --> pdb=" O ALA a 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY a 88 " --> pdb=" O ALA a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 115 removed outlier: 3.519A pdb=" N ALA a 111 " --> pdb=" O ALA a 107 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG a 113 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU a 114 " --> pdb=" O GLU a 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 removed outlier: 6.914A pdb=" N HIS A 31 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A 86 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A 29 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL A 88 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR A 27 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 75 " --> pdb=" O TYR W 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 105 removed outlier: 4.140A pdb=" N SER B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 95 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL B 78 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.202A pdb=" N LEU B 173 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS B 167 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET B 183 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE B 270 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.490A pdb=" N ILE D 4 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 23 removed outlier: 6.797A pdb=" N TYR D 92 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN D 65 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 94 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR D 59 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 60 " --> pdb=" O PHE D 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.591A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 10 removed outlier: 5.612A pdb=" N LYS E 4 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 107 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL E 6 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE E 105 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG E 8 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE E 103 " --> pdb=" O ARG E 8 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 82 through 87 Processing sheet with id=AB2, first strand: chain 'F' and resid 7 through 10 removed outlier: 6.916A pdb=" N ASP F 28 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR F 26 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS F 77 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE F 55 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE F 79 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 53 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR F 81 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS F 49 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.665A pdb=" N ARG G 32 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR G 26 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL G 34 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN G 8 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU G 71 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU G 70 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 43 removed outlier: 3.591A pdb=" N LYS G 43 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 57 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 82 through 83 Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 8 removed outlier: 7.657A pdb=" N LYS H 5 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP H 44 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LYS H 26 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ILE H 89 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N PHE H 91 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL H 30 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA H 93 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE H 86 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE H 79 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N HIS H 88 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR H 77 " --> pdb=" O HIS H 88 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP H 90 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU H 4 " --> pdb=" O GLY H 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AB8, first strand: chain 'J' and resid 33 through 39 removed outlier: 4.077A pdb=" N ILE J 38 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS J 45 " --> pdb=" O ILE J 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 16 removed outlier: 5.720A pdb=" N LYS L 9 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU L 29 " --> pdb=" O LYS L 9 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY L 11 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL L 194 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL L 188 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU L 196 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU L 184 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE L 116 " --> pdb=" O ASN L 182 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 34 through 39 removed outlier: 6.541A pdb=" N GLN L 50 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS L 38 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA L 48 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG L 89 " --> pdb=" O VAL L 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 34 through 37 Processing sheet with id=AC3, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AC4, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=AC5, first strand: chain 'O' and resid 32 through 36 removed outlier: 3.535A pdb=" N LYS O 41 " --> pdb=" O CYS O 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 23 through 24 removed outlier: 3.836A pdb=" N ARG Q 48 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 2 through 3 removed outlier: 6.740A pdb=" N LYS R 2 " --> pdb=" O ARG R 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'R' and resid 15 through 18 Processing sheet with id=AC9, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.164A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR S 195 " --> pdb=" O LEU S 153 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL S 155 " --> pdb=" O THR S 195 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN S 174 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR S 156 " --> pdb=" O THR S 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 123 through 125 removed outlier: 6.364A pdb=" N TRP V 16 " --> pdb=" O GLU V 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'W' and resid 45 through 46 removed outlier: 6.561A pdb=" N ASN W 45 " --> pdb=" O ARG W 17 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG W 17 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL W 10 " --> pdb=" O ARG W 17 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU W 8 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS W 84 " --> pdb=" O ARG W 7 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS W 9 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE W 86 " --> pdb=" O LYS W 9 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY W 92 " --> pdb=" O ARG W 88 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 45 through 46 removed outlier: 6.561A pdb=" N ASN W 45 " --> pdb=" O ARG W 17 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N THR W 21 " --> pdb=" O THR W 42 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR W 42 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS W 59 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL W 63 " --> pdb=" O ALA W 83 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY W 92 " --> pdb=" O ARG W 88 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 75 through 77 Processing sheet with id=AD6, first strand: chain 'X' and resid 123 through 124 removed outlier: 7.495A pdb=" N VAL X 123 " --> pdb=" O GLU X 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'Y' and resid 32 through 33 removed outlier: 3.608A pdb=" N PHE Y 32 " --> pdb=" O VAL Y 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 40 through 43 removed outlier: 3.589A pdb=" N ILE Y 42 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA Y 89 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR Y 74 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP Y 93 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR Y 72 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 29 through 33 removed outlier: 4.036A pdb=" N GLY Z 107 " --> pdb=" O SER Z 116 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE Z 118 " --> pdb=" O LYS Z 105 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS Z 105 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU Z 120 " --> pdb=" O ILE Z 103 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE Z 103 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 70 through 71 Processing sheet with id=AE2, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.725A pdb=" N ILE a 44 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA a 42 " --> pdb=" O GLN a 55 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR a 34 " --> pdb=" O TYR a 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.701A pdb=" N ILE I 44 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA I 69 " --> pdb=" O ILE I 44 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR I 46 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE I 68 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.767A pdb=" N GLY I 73 " --> pdb=" O VAL I 39 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR I 54 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N VAL I 89 " --> pdb=" O TYR I 54 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1204 hydrogen bonds 1954 hydrogen bond angles 0 basepair planarities 513 basepair parallelities 1562 stacking parallelities Total time for adding SS restraints: 123.45 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7583 1.31 - 1.44: 39951 1.44 - 1.56: 35366 1.56 - 1.69: 5600 1.69 - 1.82: 98 Bond restraints: 88598 Sorted by residual: bond pdb=" C23 U7V 13001 " pdb=" O22 U7V 13001 " ideal model delta sigma weight residual 1.334 1.434 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C23 U7V 13001 " pdb=" N19 U7V 13001 " ideal model delta sigma weight residual 1.368 1.456 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C PHE C 57 " pdb=" N ARG C 58 " ideal model delta sigma weight residual 1.334 1.391 -0.057 1.43e-02 4.89e+03 1.56e+01 bond pdb=" CG ASN K 8 " pdb=" ND2 ASN K 8 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.47e+01 bond pdb=" N05 U7V 13001 " pdb=" N06 U7V 13001 " ideal model delta sigma weight residual 1.292 1.362 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 88593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 130210 2.68 - 5.36: 2866 5.36 - 8.03: 295 8.03 - 10.71: 66 10.71 - 13.39: 20 Bond angle restraints: 133457 Sorted by residual: angle pdb=" N ARG L 86 " pdb=" CA ARG L 86 " pdb=" C ARG L 86 " ideal model delta sigma weight residual 111.36 123.23 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" O2' C 1 674 " pdb=" C2' C 1 674 " pdb=" C1' C 1 674 " ideal model delta sigma weight residual 108.40 95.01 13.39 1.50e+00 4.44e-01 7.97e+01 angle pdb=" N GLU Z 74 " pdb=" CA GLU Z 74 " pdb=" C GLU Z 74 " ideal model delta sigma weight residual 110.50 98.11 12.39 1.41e+00 5.03e-01 7.72e+01 angle pdb=" O3' A 1 224 " pdb=" C3' A 1 224 " pdb=" C2' A 1 224 " ideal model delta sigma weight residual 109.50 97.37 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N VAL J 7 " pdb=" CA VAL J 7 " pdb=" C VAL J 7 " ideal model delta sigma weight residual 110.72 118.77 -8.05 1.01e+00 9.80e-01 6.36e+01 ... (remaining 133452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 49571 35.79 - 71.57: 6299 71.57 - 107.36: 703 107.36 - 143.14: 16 143.14 - 178.93: 33 Dihedral angle restraints: 56622 sinusoidal: 49069 harmonic: 7553 Sorted by residual: dihedral pdb=" CB CYS N 33 " pdb=" SG CYS N 33 " pdb=" SG CYS N 43 " pdb=" CB CYS N 43 " ideal model delta sinusoidal sigma weight residual -86.00 -170.52 84.52 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" O4' U 12655 " pdb=" C1' U 12655 " pdb=" N1 U 12655 " pdb=" C2 U 12655 " ideal model delta sinusoidal sigma weight residual 200.00 28.46 171.54 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C 1 402 " pdb=" C1' C 1 402 " pdb=" N1 C 1 402 " pdb=" C2 C 1 402 " ideal model delta sinusoidal sigma weight residual 200.00 28.47 171.53 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 56619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 16801 0.170 - 0.339: 355 0.339 - 0.509: 37 0.509 - 0.678: 5 0.678 - 0.848: 2 Chirality restraints: 17200 Sorted by residual: chirality pdb=" CA ARG L 86 " pdb=" N ARG L 86 " pdb=" C ARG L 86 " pdb=" CB ARG L 86 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA PHE X 50 " pdb=" N PHE X 50 " pdb=" C PHE X 50 " pdb=" CB PHE X 50 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3' G 11761 " pdb=" C4' G 11761 " pdb=" O3' G 11761 " pdb=" C2' G 11761 " both_signs ideal model delta sigma weight residual False -2.48 -1.87 -0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 17197 not shown) Planarity restraints: 6443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 518 " -0.051 2.00e-02 2.50e+03 2.60e-02 1.86e+01 pdb=" N9 A 1 518 " 0.068 2.00e-02 2.50e+03 pdb=" C8 A 1 518 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 518 " -0.007 2.00e-02 2.50e+03 pdb=" C5 A 1 518 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 1 518 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A 1 518 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 1 518 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 518 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 1 518 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 1 518 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 257 " -0.039 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G 1 257 " 0.062 2.00e-02 2.50e+03 pdb=" C8 G 1 257 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G 1 257 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G 1 257 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G 1 257 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 1 257 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G 1 257 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G 1 257 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G 1 257 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 257 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G 1 257 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 515 " -0.038 2.00e-02 2.50e+03 2.10e-02 1.32e+01 pdb=" N9 G 1 515 " 0.061 2.00e-02 2.50e+03 pdb=" C8 G 1 515 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 1 515 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 1 515 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G 1 515 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 1 515 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G 1 515 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G 1 515 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 1 515 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 515 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G 1 515 " -0.006 2.00e-02 2.50e+03 ... (remaining 6440 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 4519 2.66 - 3.22: 61821 3.22 - 3.78: 141350 3.78 - 4.34: 209971 4.34 - 4.90: 279584 Nonbonded interactions: 697245 Sorted by model distance: nonbonded pdb=" O2' U 1 661 " pdb=" OP2 G 1 662 " model vdw 2.100 3.040 nonbonded pdb=" O2' G 12432 " pdb=" OP2 C 12433 " model vdw 2.121 3.040 nonbonded pdb=" O2' G 11631 " pdb=" O5' A 11632 " model vdw 2.148 3.040 nonbonded pdb=" O2 C 11895 " pdb=" N2 G 11900 " model vdw 2.149 3.120 nonbonded pdb=" O2' A 1 10 " pdb=" OP1 U 1 11 " model vdw 2.161 3.040 ... (remaining 697240 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.120 Extract box with map and model: 2.680 Check model and map are aligned: 0.490 Set scattering table: 0.620 Process input model: 241.120 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.008 0.100 88598 Z= 0.459 Angle : 0.916 13.391 133457 Z= 0.599 Chirality : 0.059 0.848 17200 Planarity : 0.005 0.068 6443 Dihedral : 24.021 178.929 51764 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.63 % Allowed : 8.79 % Favored : 87.58 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.14), residues: 2617 helix: -2.60 (0.19), residues: 575 sheet: -1.77 (0.21), residues: 523 loop : -2.53 (0.13), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 213 HIS 0.008 0.001 HIS S 49 PHE 0.018 0.002 PHE X 50 TYR 0.028 0.002 TYR H 77 ARG 0.006 0.001 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 497 time to evaluate : 3.290 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8639 (pttt) cc_final: 0.8345 (ptmt) REVERT: A 65 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7799 (ptmt) REVERT: A 85 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7820 (ptmt) REVERT: A 111 ARG cc_start: 0.6494 (ptt180) cc_final: 0.6260 (mtm110) REVERT: B 5 LYS cc_start: 0.7546 (tttt) cc_final: 0.7333 (mptt) REVERT: B 74 ILE cc_start: 0.7713 (mm) cc_final: 0.7506 (mt) REVERT: B 139 THR cc_start: 0.7988 (m) cc_final: 0.7498 (t) REVERT: B 147 LYS cc_start: 0.7272 (mttt) cc_final: 0.7034 (mttp) REVERT: B 167 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5819 (ptmt) REVERT: C 11 ARG cc_start: 0.8107 (tpt170) cc_final: 0.7481 (ttp-110) REVERT: C 80 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7544 (mmm) REVERT: C 104 LYS cc_start: 0.6362 (tttt) cc_final: 0.5688 (mttt) REVERT: D 37 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7708 (mmtt) REVERT: D 67 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7516 (mtm180) REVERT: E 4 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8071 (ptpp) REVERT: E 37 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7836 (mttm) REVERT: E 72 LYS cc_start: 0.7405 (tttt) cc_final: 0.7143 (tttm) REVERT: F 49 LYS cc_start: 0.8016 (mmtm) cc_final: 0.6719 (tttt) REVERT: F 90 PHE cc_start: 0.3940 (OUTLIER) cc_final: 0.2299 (p90) REVERT: G 58 GLU cc_start: 0.5971 (pt0) cc_final: 0.5499 (tt0) REVERT: G 69 GLN cc_start: 0.8494 (mt0) cc_final: 0.8278 (mt0) REVERT: J 3 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6302 (mtpt) REVERT: J 28 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: J 35 LYS cc_start: 0.8240 (tppt) cc_final: 0.7741 (tttt) REVERT: J 41 ASP cc_start: 0.3413 (OUTLIER) cc_final: 0.2824 (m-30) REVERT: L 3 LYS cc_start: 0.7099 (ptpp) cc_final: 0.6351 (ptpt) REVERT: L 14 GLN cc_start: 0.8649 (pt0) cc_final: 0.8332 (pt0) REVERT: L 55 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5728 (t0) REVERT: L 71 LYS cc_start: 0.8092 (mttp) cc_final: 0.7794 (mttt) REVERT: M 24 GLU cc_start: 0.7787 (pp20) cc_final: 0.6407 (mm-30) REVERT: M 34 SER cc_start: 0.8023 (m) cc_final: 0.7753 (m) REVERT: N 27 MET cc_start: 0.7983 (pmm) cc_final: 0.7613 (pmm) REVERT: O 28 GLU cc_start: 0.4939 (pt0) cc_final: 0.4303 (mm-30) REVERT: O 38 ARG cc_start: 0.6226 (ptp-170) cc_final: 0.5854 (ptm-80) REVERT: P 37 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7847 (ttp-170) REVERT: R 18 LYS cc_start: 0.7831 (tttt) cc_final: 0.7554 (tttt) REVERT: R 24 MET cc_start: 0.8123 (ptm) cc_final: 0.7809 (ptp) REVERT: S 100 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7868 (mmtt) REVERT: V 15 LYS cc_start: 0.8283 (mttm) cc_final: 0.7993 (mttt) REVERT: V 38 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7839 (ttt180) REVERT: V 76 TYR cc_start: 0.8637 (m-80) cc_final: 0.8179 (m-80) REVERT: V 121 LYS cc_start: 0.8300 (mttm) cc_final: 0.7911 (mmtp) REVERT: V 126 TYR cc_start: 0.7682 (m-80) cc_final: 0.7272 (m-80) REVERT: V 139 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6882 (tt0) REVERT: V 142 GLU cc_start: 0.6982 (tp30) cc_final: 0.6623 (mt-10) REVERT: W 17 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7407 (mpt180) REVERT: W 66 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7395 (mtpt) REVERT: W 76 TYR cc_start: 0.8994 (m-80) cc_final: 0.8378 (m-80) REVERT: X 10 GLU cc_start: 0.7034 (tp30) cc_final: 0.6773 (tp30) REVERT: X 16 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7864 (ptp-170) REVERT: X 98 GLU cc_start: 0.4949 (mt-10) cc_final: 0.4438 (tp30) REVERT: X 136 ILE cc_start: 0.7394 (mm) cc_final: 0.7163 (mp) REVERT: Y 59 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6814 (mmmt) REVERT: Y 76 LYS cc_start: 0.8134 (tttp) cc_final: 0.7567 (mttp) REVERT: Y 136 GLU cc_start: 0.2976 (OUTLIER) cc_final: 0.2298 (mt-10) REVERT: Z 64 LYS cc_start: 0.8104 (mttt) cc_final: 0.7728 (mttt) REVERT: Z 101 THR cc_start: 0.8281 (m) cc_final: 0.7937 (p) REVERT: Z 106 GLN cc_start: 0.8269 (mm110) cc_final: 0.7689 (mt0) REVERT: a 22 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6785 (tt) outliers start: 81 outliers final: 18 residues processed: 555 average time/residue: 0.9035 time to fit residues: 808.8468 Evaluate side-chains 445 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 418 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 102 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 453 optimal weight: 6.9990 chunk 407 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 420 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 487 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN B 53 HIS B 54 HIS D 63 ASN D 90 GLN F 54 ASN G 67 ASN J 30 ASN J 34 GLN L 143 HIS N 50 ASN O 40 ASN Q 35 ASN Q 43 GLN R 36 GLN S 119 GLN S 158 ASN S 174 GLN V 59 ASN V 78 HIS X 54 GLN Y 25 ASN a 15 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 88598 Z= 0.318 Angle : 0.760 11.784 133457 Z= 0.384 Chirality : 0.044 0.337 17200 Planarity : 0.006 0.081 6443 Dihedral : 23.743 179.221 46431 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 4.03 % Allowed : 13.58 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.14), residues: 2617 helix: -2.39 (0.18), residues: 608 sheet: -1.39 (0.21), residues: 554 loop : -2.29 (0.14), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 213 HIS 0.008 0.002 HIS V 48 PHE 0.020 0.002 PHE X 50 TYR 0.029 0.002 TYR F 68 ARG 0.010 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 397 time to evaluate : 3.298 Fit side-chains REVERT: A 51 LYS cc_start: 0.8622 (pttt) cc_final: 0.8328 (ptpt) REVERT: A 65 LYS cc_start: 0.7925 (ptmm) cc_final: 0.7641 (ptmt) REVERT: B 5 LYS cc_start: 0.7617 (tttt) cc_final: 0.7346 (mptt) REVERT: B 102 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7630 (mtt90) REVERT: B 108 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7966 (ttpp) REVERT: C 11 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7437 (ttp-110) REVERT: C 49 ASP cc_start: 0.7983 (m-30) cc_final: 0.7703 (m-30) REVERT: C 84 LYS cc_start: 0.7524 (ttpt) cc_final: 0.7242 (ttpp) REVERT: D 37 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7907 (mmtt) REVERT: E 4 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8105 (ptpp) REVERT: E 52 MET cc_start: 0.6942 (mmm) cc_final: 0.6385 (mmt) REVERT: E 72 LYS cc_start: 0.7522 (tttt) cc_final: 0.7276 (tttm) REVERT: F 69 GLN cc_start: 0.6805 (mm110) cc_final: 0.6395 (mm-40) REVERT: G 58 GLU cc_start: 0.5732 (pt0) cc_final: 0.5325 (tt0) REVERT: J 3 LYS cc_start: 0.7219 (pttm) cc_final: 0.6055 (mtpt) REVERT: J 35 LYS cc_start: 0.8619 (tppt) cc_final: 0.7652 (tttp) REVERT: J 41 ASP cc_start: 0.3664 (OUTLIER) cc_final: 0.2256 (m-30) REVERT: L 14 GLN cc_start: 0.8575 (pt0) cc_final: 0.8261 (pt0) REVERT: M 5 GLN cc_start: 0.7599 (tt0) cc_final: 0.7335 (tt0) REVERT: M 24 GLU cc_start: 0.7602 (pp20) cc_final: 0.6459 (mm-30) REVERT: N 18 THR cc_start: 0.8615 (m) cc_final: 0.8415 (m) REVERT: N 27 MET cc_start: 0.8135 (pmm) cc_final: 0.7611 (pmm) REVERT: O 1 MET cc_start: 0.4989 (ptm) cc_final: 0.4587 (ptp) REVERT: O 4 ASN cc_start: 0.7059 (m-40) cc_final: 0.6733 (m-40) REVERT: O 20 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7922 (m) REVERT: O 38 ARG cc_start: 0.6225 (ptp-170) cc_final: 0.5802 (ptm-80) REVERT: P 37 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7723 (ttp-170) REVERT: R 24 MET cc_start: 0.7891 (ptm) cc_final: 0.7568 (ptp) REVERT: R 36 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: S 31 SER cc_start: 0.8758 (m) cc_final: 0.8417 (p) REVERT: S 148 GLN cc_start: 0.5237 (mm-40) cc_final: 0.4940 (mm-40) REVERT: V 15 LYS cc_start: 0.8018 (mttm) cc_final: 0.7785 (mttt) REVERT: V 50 ASP cc_start: 0.7927 (t0) cc_final: 0.7579 (t0) REVERT: W 3 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7943 (mm-40) REVERT: W 17 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7017 (mtm-85) REVERT: W 53 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6915 (mttt) REVERT: W 114 ILE cc_start: 0.7845 (mm) cc_final: 0.7618 (mt) REVERT: X 85 PHE cc_start: 0.6309 (OUTLIER) cc_final: 0.6004 (m-10) REVERT: Y 59 LYS cc_start: 0.7216 (mmmt) cc_final: 0.6966 (mmmt) REVERT: Y 76 LYS cc_start: 0.8249 (tttp) cc_final: 0.7546 (mttp) REVERT: Y 136 GLU cc_start: 0.2734 (OUTLIER) cc_final: 0.2275 (pt0) REVERT: Z 29 ARG cc_start: 0.7433 (ttm110) cc_final: 0.7105 (ttt180) REVERT: Z 61 ASN cc_start: 0.8126 (m-40) cc_final: 0.7804 (m-40) REVERT: Z 64 LYS cc_start: 0.8098 (mttt) cc_final: 0.7737 (mttt) REVERT: Z 106 GLN cc_start: 0.8251 (mm110) cc_final: 0.7698 (mt0) REVERT: a 17 ARG cc_start: 0.7379 (mtt180) cc_final: 0.7116 (mtt-85) REVERT: a 28 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.4714 (pttp) REVERT: a 102 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6236 (p-80) outliers start: 90 outliers final: 58 residues processed: 450 average time/residue: 0.8553 time to fit residues: 638.7090 Evaluate side-chains 437 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 371 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 85 PHE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 271 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 405 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 134 optimal weight: 0.0670 chunk 488 optimal weight: 7.9990 chunk 527 optimal weight: 8.9990 chunk 435 optimal weight: 7.9990 chunk 484 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 391 optimal weight: 10.0000 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN E 40 ASN E 61 ASN H 38 ASN L 182 ASN N 45 ASN V 48 HIS W 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 88598 Z= 0.494 Angle : 0.912 11.143 133457 Z= 0.448 Chirality : 0.050 0.390 17200 Planarity : 0.007 0.081 6443 Dihedral : 23.964 178.302 46403 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 5.92 % Allowed : 15.96 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.14), residues: 2617 helix: -2.34 (0.18), residues: 599 sheet: -1.32 (0.21), residues: 571 loop : -2.35 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 213 HIS 0.009 0.002 HIS Q 31 PHE 0.024 0.003 PHE X 50 TYR 0.028 0.003 TYR H 77 ARG 0.008 0.001 ARG W 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 384 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: A 51 LYS cc_start: 0.8697 (pttt) cc_final: 0.8364 (ptpt) REVERT: A 65 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7670 (ptmt) REVERT: B 5 LYS cc_start: 0.7712 (tttt) cc_final: 0.7415 (mptt) REVERT: B 108 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7967 (ttpp) REVERT: B 111 GLU cc_start: 0.3406 (OUTLIER) cc_final: 0.1668 (tm-30) REVERT: B 175 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8324 (ttm170) REVERT: B 186 SER cc_start: 0.8228 (m) cc_final: 0.7853 (t) REVERT: C 11 ARG cc_start: 0.7835 (tpt170) cc_final: 0.7442 (ttp-110) REVERT: C 84 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7461 (ttpp) REVERT: D 23 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6514 (mm-30) REVERT: D 37 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7818 (mmtt) REVERT: E 4 LYS cc_start: 0.8722 (ptmt) cc_final: 0.8148 (ptpp) REVERT: E 37 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8000 (mttm) REVERT: E 72 LYS cc_start: 0.7498 (tttt) cc_final: 0.7272 (tttm) REVERT: F 69 GLN cc_start: 0.6818 (mm110) cc_final: 0.6394 (mm-40) REVERT: G 42 LYS cc_start: 0.7399 (ptpp) cc_final: 0.7099 (mtmt) REVERT: G 58 GLU cc_start: 0.5552 (pt0) cc_final: 0.5270 (tt0) REVERT: H 63 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7275 (tt) REVERT: J 3 LYS cc_start: 0.7237 (pttm) cc_final: 0.5933 (mtpt) REVERT: J 35 LYS cc_start: 0.8567 (tppt) cc_final: 0.7782 (tttt) REVERT: J 41 ASP cc_start: 0.3539 (OUTLIER) cc_final: 0.2448 (m-30) REVERT: K 16 GLU cc_start: 0.5541 (mm-30) cc_final: 0.5261 (tp30) REVERT: M 24 GLU cc_start: 0.7841 (pp20) cc_final: 0.6517 (mm-30) REVERT: M 43 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7932 (tp) REVERT: N 27 MET cc_start: 0.8068 (pmm) cc_final: 0.7683 (pmm) REVERT: O 38 ARG cc_start: 0.6209 (ptp-170) cc_final: 0.5822 (ptm-80) REVERT: P 37 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7647 (ttp-170) REVERT: Q 15 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7484 (ptpp) REVERT: R 24 MET cc_start: 0.7948 (ptm) cc_final: 0.7607 (ptp) REVERT: S 148 GLN cc_start: 0.5125 (mm-40) cc_final: 0.4666 (mm110) REVERT: V 50 ASP cc_start: 0.7979 (t0) cc_final: 0.7570 (t0) REVERT: V 61 SER cc_start: 0.8311 (t) cc_final: 0.8052 (p) REVERT: V 137 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.4800 (mp10) REVERT: V 144 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.5366 (ptp-170) REVERT: W 17 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7041 (mtm-85) REVERT: W 53 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6207 (mptt) REVERT: W 114 ILE cc_start: 0.7831 (mm) cc_final: 0.7623 (mt) REVERT: X 70 ASN cc_start: 0.8040 (m-40) cc_final: 0.7708 (m-40) REVERT: Y 76 LYS cc_start: 0.8304 (tttp) cc_final: 0.7596 (mttp) REVERT: Y 136 GLU cc_start: 0.2621 (OUTLIER) cc_final: 0.1945 (mt-10) REVERT: Z 29 ARG cc_start: 0.7515 (ttm110) cc_final: 0.7113 (ttt180) REVERT: Z 64 LYS cc_start: 0.8061 (mttt) cc_final: 0.7656 (mttt) REVERT: Z 106 GLN cc_start: 0.8237 (mm110) cc_final: 0.7637 (mt0) REVERT: a 102 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6720 (p-80) outliers start: 132 outliers final: 100 residues processed: 471 average time/residue: 0.8259 time to fit residues: 651.2047 Evaluate side-chains 481 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 370 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 482 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 328 optimal weight: 5.9990 chunk 490 optimal weight: 5.9990 chunk 519 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 464 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN V 11 ASN a 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 88598 Z= 0.424 Angle : 0.824 10.944 133457 Z= 0.410 Chirality : 0.047 0.373 17200 Planarity : 0.006 0.073 6443 Dihedral : 23.852 179.834 46395 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.45 % Allowed : 17.71 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.14), residues: 2617 helix: -2.23 (0.19), residues: 603 sheet: -1.29 (0.21), residues: 569 loop : -2.29 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 213 HIS 0.007 0.002 HIS B 142 PHE 0.028 0.003 PHE X 50 TYR 0.022 0.003 TYR H 77 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 381 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8624 (pttt) cc_final: 0.8282 (ptpt) REVERT: A 65 LYS cc_start: 0.8015 (ptmm) cc_final: 0.7814 (ptmt) REVERT: B 5 LYS cc_start: 0.7570 (tttt) cc_final: 0.7317 (mptt) REVERT: B 111 GLU cc_start: 0.3347 (OUTLIER) cc_final: 0.1591 (tm-30) REVERT: B 175 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8325 (ttm170) REVERT: B 186 SER cc_start: 0.8456 (m) cc_final: 0.8073 (t) REVERT: C 11 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7419 (ttp-110) REVERT: C 49 ASP cc_start: 0.8243 (m-30) cc_final: 0.7855 (m-30) REVERT: C 84 LYS cc_start: 0.7641 (ttpt) cc_final: 0.7318 (ttpp) REVERT: D 24 LYS cc_start: 0.7457 (tttt) cc_final: 0.6626 (ttmm) REVERT: D 37 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7768 (mmtt) REVERT: E 4 LYS cc_start: 0.8721 (ptmt) cc_final: 0.8158 (ptpp) REVERT: E 37 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7981 (mttm) REVERT: E 52 MET cc_start: 0.7123 (mmm) cc_final: 0.6575 (mmt) REVERT: E 72 LYS cc_start: 0.7390 (tttt) cc_final: 0.7134 (tttm) REVERT: F 69 GLN cc_start: 0.6858 (mm110) cc_final: 0.6419 (mm-40) REVERT: G 58 GLU cc_start: 0.5979 (pt0) cc_final: 0.5588 (tt0) REVERT: H 43 VAL cc_start: 0.7155 (p) cc_final: 0.6631 (m) REVERT: H 63 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7254 (tt) REVERT: J 35 LYS cc_start: 0.8584 (tppt) cc_final: 0.7760 (tttt) REVERT: J 41 ASP cc_start: 0.3653 (OUTLIER) cc_final: 0.2648 (m-30) REVERT: J 45 LYS cc_start: 0.5445 (OUTLIER) cc_final: 0.4260 (ttpt) REVERT: K 16 GLU cc_start: 0.5579 (mm-30) cc_final: 0.5286 (tp30) REVERT: M 24 GLU cc_start: 0.7748 (pp20) cc_final: 0.6420 (mm-30) REVERT: M 43 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7919 (tp) REVERT: N 27 MET cc_start: 0.8078 (pmm) cc_final: 0.7643 (pmm) REVERT: O 38 ARG cc_start: 0.6091 (ptp-170) cc_final: 0.5681 (ptm-80) REVERT: O 39 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: P 37 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7662 (ttp-170) REVERT: R 24 MET cc_start: 0.7881 (ptm) cc_final: 0.7556 (ptp) REVERT: S 148 GLN cc_start: 0.5095 (mm-40) cc_final: 0.4635 (mm110) REVERT: V 50 ASP cc_start: 0.7997 (t0) cc_final: 0.7576 (t0) REVERT: V 61 SER cc_start: 0.8433 (t) cc_final: 0.8207 (p) REVERT: W 17 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.6901 (mtm-85) REVERT: W 53 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6468 (mptt) REVERT: W 114 ILE cc_start: 0.7806 (mm) cc_final: 0.7588 (mt) REVERT: Y 76 LYS cc_start: 0.8251 (tttp) cc_final: 0.7611 (mttp) REVERT: Y 136 GLU cc_start: 0.2648 (OUTLIER) cc_final: 0.2386 (pt0) REVERT: Z 29 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7060 (ttt180) REVERT: Z 61 ASN cc_start: 0.8189 (m-40) cc_final: 0.7875 (m-40) outliers start: 144 outliers final: 120 residues processed: 480 average time/residue: 0.8232 time to fit residues: 665.4789 Evaluate side-chains 500 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 371 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 11 ASN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 432 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 386 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 442 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 465 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN a 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 88598 Z= 0.268 Angle : 0.705 10.731 133457 Z= 0.361 Chirality : 0.042 0.342 17200 Planarity : 0.005 0.067 6443 Dihedral : 23.795 178.218 46393 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 6.28 % Allowed : 18.92 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.15), residues: 2617 helix: -1.97 (0.20), residues: 597 sheet: -1.04 (0.22), residues: 540 loop : -2.23 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 213 HIS 0.006 0.001 HIS Q 31 PHE 0.031 0.002 PHE X 50 TYR 0.019 0.002 TYR F 68 ARG 0.004 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 377 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8626 (pttt) cc_final: 0.8299 (ptpt) REVERT: A 65 LYS cc_start: 0.8016 (ptmm) cc_final: 0.7696 (ptmt) REVERT: A 90 ARG cc_start: 0.6674 (ttm110) cc_final: 0.5931 (ttp-170) REVERT: B 5 LYS cc_start: 0.7541 (tttt) cc_final: 0.7311 (mptt) REVERT: B 111 GLU cc_start: 0.3255 (OUTLIER) cc_final: 0.1537 (tm-30) REVERT: B 186 SER cc_start: 0.8448 (m) cc_final: 0.8039 (t) REVERT: C 11 ARG cc_start: 0.7729 (tpt170) cc_final: 0.7295 (ttp-110) REVERT: C 49 ASP cc_start: 0.8169 (m-30) cc_final: 0.7767 (m-30) REVERT: C 84 LYS cc_start: 0.7585 (ttpt) cc_final: 0.7271 (ttpp) REVERT: D 24 LYS cc_start: 0.7284 (tttt) cc_final: 0.6562 (ttmm) REVERT: D 37 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7758 (mmtt) REVERT: E 4 LYS cc_start: 0.8722 (ptmt) cc_final: 0.8156 (ptpp) REVERT: E 37 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7984 (mttm) REVERT: E 52 MET cc_start: 0.7094 (mmm) cc_final: 0.6564 (mmt) REVERT: E 72 LYS cc_start: 0.7376 (tttt) cc_final: 0.7111 (tttm) REVERT: E 75 TYR cc_start: 0.8470 (p90) cc_final: 0.8206 (p90) REVERT: F 69 GLN cc_start: 0.6879 (mm110) cc_final: 0.6495 (mm-40) REVERT: G 58 GLU cc_start: 0.5827 (pt0) cc_final: 0.5519 (tt0) REVERT: H 43 VAL cc_start: 0.7015 (p) cc_final: 0.6473 (m) REVERT: H 63 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7181 (tt) REVERT: J 35 LYS cc_start: 0.8446 (tppt) cc_final: 0.7620 (tttt) REVERT: J 41 ASP cc_start: 0.3585 (OUTLIER) cc_final: 0.2528 (m-30) REVERT: J 45 LYS cc_start: 0.5413 (OUTLIER) cc_final: 0.4248 (ttpt) REVERT: J 48 TRP cc_start: 0.8125 (m100) cc_final: 0.7348 (m100) REVERT: K 16 GLU cc_start: 0.5463 (mm-30) cc_final: 0.5234 (tp30) REVERT: L 105 VAL cc_start: 0.8202 (t) cc_final: 0.7968 (m) REVERT: M 24 GLU cc_start: 0.7744 (pp20) cc_final: 0.6397 (mm-30) REVERT: M 29 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7030 (mmtt) REVERT: M 43 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7870 (tp) REVERT: N 27 MET cc_start: 0.8050 (pmm) cc_final: 0.7593 (pmm) REVERT: O 38 ARG cc_start: 0.6175 (ptp-170) cc_final: 0.5651 (ptm-80) REVERT: O 39 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: P 37 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7655 (ttp-170) REVERT: R 24 MET cc_start: 0.7857 (ptm) cc_final: 0.7537 (ptp) REVERT: S 148 GLN cc_start: 0.5092 (mm-40) cc_final: 0.4610 (mm110) REVERT: V 50 ASP cc_start: 0.7963 (t0) cc_final: 0.7549 (t0) REVERT: V 61 SER cc_start: 0.8423 (t) cc_final: 0.8211 (p) REVERT: V 137 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.4683 (mp10) REVERT: W 17 ARG cc_start: 0.7557 (mmm-85) cc_final: 0.6898 (mtm-85) REVERT: W 53 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6421 (mptt) REVERT: W 114 ILE cc_start: 0.7801 (mm) cc_final: 0.7597 (mt) REVERT: X 85 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.6098 (m-10) REVERT: X 90 GLU cc_start: 0.5794 (tp30) cc_final: 0.5569 (tp30) REVERT: Y 55 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7202 (m) REVERT: Y 76 LYS cc_start: 0.8245 (tttp) cc_final: 0.7607 (mttp) REVERT: Y 136 GLU cc_start: 0.2647 (OUTLIER) cc_final: 0.2413 (pt0) REVERT: Z 61 ASN cc_start: 0.8216 (m-40) cc_final: 0.7900 (m-40) outliers start: 140 outliers final: 111 residues processed: 469 average time/residue: 0.8199 time to fit residues: 650.4504 Evaluate side-chains 494 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 371 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 85 PHE Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 174 optimal weight: 0.0770 chunk 467 optimal weight: 7.9990 chunk 102 optimal weight: 0.0010 chunk 304 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 519 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 overall best weight: 3.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 GLN a 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 88598 Z= 0.294 Angle : 0.709 11.057 133457 Z= 0.360 Chirality : 0.042 0.344 17200 Planarity : 0.005 0.063 6443 Dihedral : 23.706 177.558 46393 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.95 % Allowed : 19.00 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.15), residues: 2617 helix: -1.85 (0.20), residues: 596 sheet: -1.03 (0.22), residues: 550 loop : -2.09 (0.14), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 213 HIS 0.006 0.001 HIS Q 31 PHE 0.030 0.002 PHE X 50 TYR 0.017 0.002 TYR F 68 ARG 0.005 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 382 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8594 (pttt) cc_final: 0.8314 (ptpt) REVERT: A 65 LYS cc_start: 0.8016 (ptmm) cc_final: 0.7767 (ptmt) REVERT: A 111 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5903 (ptt-90) REVERT: B 5 LYS cc_start: 0.7504 (tttt) cc_final: 0.7275 (mptt) REVERT: B 111 GLU cc_start: 0.3314 (OUTLIER) cc_final: 0.1601 (tm-30) REVERT: B 175 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8268 (ttm170) REVERT: B 186 SER cc_start: 0.8463 (m) cc_final: 0.8029 (t) REVERT: C 11 ARG cc_start: 0.7718 (tpt170) cc_final: 0.7282 (ttp-110) REVERT: C 49 ASP cc_start: 0.8148 (m-30) cc_final: 0.7774 (m-30) REVERT: C 84 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7288 (ttpp) REVERT: D 24 LYS cc_start: 0.7269 (tttt) cc_final: 0.6535 (ttmm) REVERT: D 37 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7815 (mmtt) REVERT: E 4 LYS cc_start: 0.8725 (ptmt) cc_final: 0.8163 (ptpp) REVERT: E 52 MET cc_start: 0.7013 (mmm) cc_final: 0.6516 (mmt) REVERT: E 72 LYS cc_start: 0.7390 (tttt) cc_final: 0.7097 (tttm) REVERT: E 75 TYR cc_start: 0.8464 (p90) cc_final: 0.8205 (p90) REVERT: F 69 GLN cc_start: 0.6932 (mm110) cc_final: 0.6573 (mm-40) REVERT: G 58 GLU cc_start: 0.5550 (pt0) cc_final: 0.5190 (tt0) REVERT: H 43 VAL cc_start: 0.7028 (p) cc_final: 0.6483 (m) REVERT: H 63 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7021 (tt) REVERT: J 35 LYS cc_start: 0.8561 (tppt) cc_final: 0.7717 (tttt) REVERT: J 41 ASP cc_start: 0.4006 (OUTLIER) cc_final: 0.2623 (m-30) REVERT: J 45 LYS cc_start: 0.5355 (OUTLIER) cc_final: 0.4259 (ttpt) REVERT: J 48 TRP cc_start: 0.8181 (m100) cc_final: 0.7371 (m100) REVERT: L 105 VAL cc_start: 0.8200 (t) cc_final: 0.7964 (m) REVERT: M 24 GLU cc_start: 0.7722 (pp20) cc_final: 0.6351 (mm-30) REVERT: M 29 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.6995 (mmtt) REVERT: M 43 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7927 (tp) REVERT: N 27 MET cc_start: 0.8056 (pmm) cc_final: 0.7630 (pmm) REVERT: O 38 ARG cc_start: 0.6181 (ptp-170) cc_final: 0.5660 (ptm-80) REVERT: O 39 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5924 (mp0) REVERT: P 37 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7666 (ttp-170) REVERT: R 24 MET cc_start: 0.7877 (ptm) cc_final: 0.7567 (ptp) REVERT: R 36 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: S 148 GLN cc_start: 0.5094 (mm-40) cc_final: 0.4608 (mm110) REVERT: V 32 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7152 (tm-30) REVERT: V 50 ASP cc_start: 0.7955 (t0) cc_final: 0.7550 (t0) REVERT: V 61 SER cc_start: 0.8428 (t) cc_final: 0.8213 (p) REVERT: V 137 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.4677 (mp10) REVERT: V 144 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5396 (ptp-170) REVERT: W 17 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.6873 (mtm-85) REVERT: W 53 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6437 (mptt) REVERT: W 114 ILE cc_start: 0.7772 (mm) cc_final: 0.7550 (mt) REVERT: X 85 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.6025 (m-10) REVERT: Y 55 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7231 (m) REVERT: Y 76 LYS cc_start: 0.8313 (tttp) cc_final: 0.7608 (mttp) REVERT: Y 136 GLU cc_start: 0.2642 (OUTLIER) cc_final: 0.2213 (pt0) REVERT: Z 41 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8189 (ttm170) REVERT: Z 61 ASN cc_start: 0.8223 (m-40) cc_final: 0.7900 (m-40) REVERT: Z 64 LYS cc_start: 0.7870 (mttt) cc_final: 0.7632 (mttt) REVERT: a 45 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6487 (mm) REVERT: a 102 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6628 (p-80) outliers start: 155 outliers final: 123 residues processed: 487 average time/residue: 0.8181 time to fit residues: 673.1338 Evaluate side-chains 518 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 376 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 85 PHE Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 500 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 296 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 chunk 517 optimal weight: 8.9990 chunk 323 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 ASN E 61 ASN a 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 88598 Z= 0.477 Angle : 0.882 11.083 133457 Z= 0.435 Chirality : 0.049 0.383 17200 Planarity : 0.007 0.074 6443 Dihedral : 23.906 179.368 46393 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 7.31 % Allowed : 19.72 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.14), residues: 2617 helix: -2.08 (0.19), residues: 599 sheet: -1.17 (0.21), residues: 566 loop : -2.25 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 213 HIS 0.009 0.002 HIS B 230 PHE 0.028 0.003 PHE X 50 TYR 0.024 0.003 TYR H 77 ARG 0.008 0.001 ARG R 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 374 time to evaluate : 3.279 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8632 (pttt) cc_final: 0.8282 (ptpt) REVERT: A 65 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7783 (ptmt) REVERT: A 111 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5943 (ptt-90) REVERT: B 5 LYS cc_start: 0.7519 (tttt) cc_final: 0.7300 (mptt) REVERT: B 111 GLU cc_start: 0.3390 (OUTLIER) cc_final: 0.1638 (tm-30) REVERT: B 175 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8294 (ttm170) REVERT: B 186 SER cc_start: 0.8512 (m) cc_final: 0.8049 (t) REVERT: C 11 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7413 (ttp-110) REVERT: C 49 ASP cc_start: 0.8272 (m-30) cc_final: 0.7867 (m-30) REVERT: C 84 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7430 (ttpp) REVERT: D 37 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7801 (mmtt) REVERT: E 4 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8186 (ptpp) REVERT: E 52 MET cc_start: 0.7206 (mmm) cc_final: 0.6710 (mmt) REVERT: E 72 LYS cc_start: 0.7397 (tttt) cc_final: 0.7117 (tttm) REVERT: F 69 GLN cc_start: 0.6829 (mm110) cc_final: 0.6439 (mm110) REVERT: G 42 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6509 (mttt) REVERT: G 58 GLU cc_start: 0.5637 (pt0) cc_final: 0.5227 (tt0) REVERT: G 100 GLU cc_start: 0.6722 (mp0) cc_final: 0.6428 (mp0) REVERT: H 63 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7065 (tt) REVERT: J 3 LYS cc_start: 0.7246 (pttm) cc_final: 0.7040 (pttt) REVERT: J 41 ASP cc_start: 0.4310 (OUTLIER) cc_final: 0.3021 (m-30) REVERT: J 45 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.4263 (ttpt) REVERT: J 48 TRP cc_start: 0.8214 (m100) cc_final: 0.7643 (m100) REVERT: M 29 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.6985 (mmtt) REVERT: M 43 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7942 (tp) REVERT: N 27 MET cc_start: 0.8007 (pmm) cc_final: 0.7681 (pmm) REVERT: O 38 ARG cc_start: 0.6045 (ptp-170) cc_final: 0.5669 (ptm-80) REVERT: P 37 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7652 (ttp-170) REVERT: R 24 MET cc_start: 0.7862 (ptm) cc_final: 0.7513 (ptp) REVERT: S 148 GLN cc_start: 0.5095 (mm-40) cc_final: 0.4656 (mm110) REVERT: V 32 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7130 (tm-30) REVERT: V 50 ASP cc_start: 0.7973 (t0) cc_final: 0.7573 (t0) REVERT: V 61 SER cc_start: 0.8459 (t) cc_final: 0.8162 (p) REVERT: V 137 GLN cc_start: 0.6589 (OUTLIER) cc_final: 0.4795 (mp10) REVERT: V 144 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5376 (ptt180) REVERT: W 17 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.6876 (mtm-85) REVERT: W 53 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6407 (mptt) REVERT: W 105 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5561 (mp0) REVERT: W 114 ILE cc_start: 0.7778 (mm) cc_final: 0.7565 (mt) REVERT: Y 76 LYS cc_start: 0.8222 (tttp) cc_final: 0.7573 (mttp) REVERT: Y 136 GLU cc_start: 0.2515 (OUTLIER) cc_final: 0.2289 (pt0) REVERT: Z 29 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7058 (ttt180) REVERT: Z 41 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8217 (ttm170) REVERT: Z 61 ASN cc_start: 0.8243 (m-40) cc_final: 0.7900 (m-40) REVERT: Z 64 LYS cc_start: 0.7923 (mttt) cc_final: 0.7632 (mttt) outliers start: 163 outliers final: 137 residues processed: 490 average time/residue: 0.8241 time to fit residues: 682.4372 Evaluate side-chains 523 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 371 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 320 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 406 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN E 61 ASN M 5 GLN V 11 ASN a 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 88598 Z= 0.313 Angle : 0.749 11.092 133457 Z= 0.380 Chirality : 0.043 0.342 17200 Planarity : 0.006 0.070 6443 Dihedral : 23.850 179.907 46393 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 7.31 % Allowed : 20.39 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.15), residues: 2617 helix: -1.94 (0.19), residues: 595 sheet: -1.05 (0.22), residues: 552 loop : -2.20 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 213 HIS 0.006 0.001 HIS B 142 PHE 0.033 0.002 PHE X 50 TYR 0.020 0.002 TYR S 99 ARG 0.005 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 378 time to evaluate : 3.485 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8627 (pttt) cc_final: 0.8311 (ptpt) REVERT: A 65 LYS cc_start: 0.7992 (ptmm) cc_final: 0.7719 (ptmt) REVERT: A 111 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.5816 (ptt-90) REVERT: B 111 GLU cc_start: 0.3301 (OUTLIER) cc_final: 0.1569 (tm-30) REVERT: B 175 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8291 (ttm170) REVERT: B 182 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8579 (ptm160) REVERT: B 186 SER cc_start: 0.8503 (m) cc_final: 0.8076 (t) REVERT: C 11 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7394 (ttp-110) REVERT: C 84 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7334 (ttpp) REVERT: D 37 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7820 (mmtt) REVERT: E 4 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8187 (ptpp) REVERT: E 52 MET cc_start: 0.7179 (mmm) cc_final: 0.6691 (mmt) REVERT: E 72 LYS cc_start: 0.7392 (tttt) cc_final: 0.7094 (tttm) REVERT: F 69 GLN cc_start: 0.6845 (mm110) cc_final: 0.6452 (mm110) REVERT: G 42 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6445 (mttt) REVERT: G 58 GLU cc_start: 0.5606 (pt0) cc_final: 0.5196 (tt0) REVERT: G 100 GLU cc_start: 0.6678 (mp0) cc_final: 0.6358 (mp0) REVERT: H 63 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7070 (tt) REVERT: J 41 ASP cc_start: 0.3986 (OUTLIER) cc_final: 0.2903 (m-30) REVERT: J 45 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.4171 (ttpt) REVERT: J 48 TRP cc_start: 0.8089 (m100) cc_final: 0.7667 (m100) REVERT: M 5 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6706 (tm130) REVERT: M 29 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.6977 (mmtt) REVERT: M 43 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7869 (tp) REVERT: N 27 MET cc_start: 0.8010 (pmm) cc_final: 0.7663 (pmm) REVERT: O 38 ARG cc_start: 0.6210 (ptp-170) cc_final: 0.5777 (ptm-80) REVERT: P 37 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7649 (ttp-170) REVERT: R 24 MET cc_start: 0.7842 (ptm) cc_final: 0.7490 (ptp) REVERT: S 148 GLN cc_start: 0.5083 (mm-40) cc_final: 0.4631 (mm110) REVERT: V 32 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7088 (tm-30) REVERT: V 50 ASP cc_start: 0.7947 (t0) cc_final: 0.7536 (t0) REVERT: V 61 SER cc_start: 0.8436 (t) cc_final: 0.8214 (p) REVERT: V 137 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.4786 (mp10) REVERT: V 144 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.5482 (ptp-170) REVERT: W 17 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.6866 (mtm-85) REVERT: W 53 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6418 (mptt) REVERT: W 105 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5507 (mp0) REVERT: Y 76 LYS cc_start: 0.8211 (tttp) cc_final: 0.7563 (mttp) REVERT: Y 136 GLU cc_start: 0.2594 (OUTLIER) cc_final: 0.2198 (pt0) REVERT: Z 29 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7086 (ttt180) REVERT: Z 41 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8208 (ttm170) REVERT: Z 61 ASN cc_start: 0.8234 (m-40) cc_final: 0.7909 (m-40) REVERT: Z 64 LYS cc_start: 0.7907 (mttt) cc_final: 0.7647 (mttt) REVERT: a 45 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6489 (mm) outliers start: 163 outliers final: 139 residues processed: 490 average time/residue: 0.8281 time to fit residues: 685.9201 Evaluate side-chains 530 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 373 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 11 ASN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 470 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 452 optimal weight: 8.9990 chunk 482 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 210 optimal weight: 0.6980 chunk 378 optimal weight: 7.9990 chunk 148 optimal weight: 0.1980 chunk 435 optimal weight: 7.9990 chunk 456 optimal weight: 6.9990 chunk 480 optimal weight: 7.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN E 61 ASN a 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 88598 Z= 0.424 Angle : 0.828 11.187 133457 Z= 0.411 Chirality : 0.047 0.378 17200 Planarity : 0.006 0.074 6443 Dihedral : 23.844 179.764 46393 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 7.40 % Allowed : 20.48 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.14), residues: 2617 helix: -2.04 (0.19), residues: 602 sheet: -1.15 (0.22), residues: 539 loop : -2.24 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 213 HIS 0.008 0.002 HIS B 230 PHE 0.030 0.003 PHE X 50 TYR 0.022 0.003 TYR H 77 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 375 time to evaluate : 3.348 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8627 (pttt) cc_final: 0.8294 (ptpt) REVERT: A 65 LYS cc_start: 0.8038 (ptmm) cc_final: 0.7762 (ptmt) REVERT: A 111 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5797 (ptt-90) REVERT: B 111 GLU cc_start: 0.3340 (OUTLIER) cc_final: 0.1583 (tm-30) REVERT: B 175 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8282 (ttm170) REVERT: B 182 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8561 (ptm160) REVERT: B 186 SER cc_start: 0.8516 (m) cc_final: 0.8056 (t) REVERT: C 11 ARG cc_start: 0.7759 (tpt170) cc_final: 0.7296 (ttp-110) REVERT: C 84 LYS cc_start: 0.7734 (ttpt) cc_final: 0.7413 (ttpp) REVERT: D 37 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7855 (mmtt) REVERT: E 4 LYS cc_start: 0.8735 (ptmt) cc_final: 0.8157 (ptpp) REVERT: E 52 MET cc_start: 0.7188 (mmm) cc_final: 0.6696 (mmt) REVERT: E 72 LYS cc_start: 0.7409 (tttt) cc_final: 0.7105 (tttm) REVERT: F 69 GLN cc_start: 0.6808 (mm110) cc_final: 0.6419 (mm110) REVERT: G 42 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6485 (mttt) REVERT: G 58 GLU cc_start: 0.5624 (pt0) cc_final: 0.5212 (tt0) REVERT: H 63 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7064 (tt) REVERT: J 41 ASP cc_start: 0.3990 (OUTLIER) cc_final: 0.2911 (m-30) REVERT: J 45 LYS cc_start: 0.5541 (OUTLIER) cc_final: 0.4147 (ttpt) REVERT: J 48 TRP cc_start: 0.8058 (m100) cc_final: 0.7815 (m100) REVERT: M 29 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.6986 (mmtt) REVERT: M 43 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7934 (tp) REVERT: N 27 MET cc_start: 0.8013 (pmm) cc_final: 0.7675 (pmm) REVERT: O 38 ARG cc_start: 0.6154 (ptp-170) cc_final: 0.5739 (ptm-80) REVERT: P 37 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7651 (ttp-170) REVERT: R 24 MET cc_start: 0.7862 (ptm) cc_final: 0.7510 (ptp) REVERT: S 148 GLN cc_start: 0.5089 (mm-40) cc_final: 0.4645 (mm110) REVERT: V 32 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7097 (tm-30) REVERT: V 50 ASP cc_start: 0.7968 (t0) cc_final: 0.7543 (t0) REVERT: V 61 SER cc_start: 0.8465 (t) cc_final: 0.8177 (p) REVERT: V 137 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.4790 (mp10) REVERT: V 144 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5490 (ptp-170) REVERT: W 17 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.6891 (mtm-85) REVERT: W 53 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6427 (mptt) REVERT: W 105 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5527 (mp0) REVERT: Y 76 LYS cc_start: 0.8168 (tttp) cc_final: 0.7575 (mttp) REVERT: Y 136 GLU cc_start: 0.2579 (OUTLIER) cc_final: 0.2191 (pt0) REVERT: Z 29 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7065 (ttt180) REVERT: Z 41 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8171 (ttm170) REVERT: Z 61 ASN cc_start: 0.8239 (m-40) cc_final: 0.7928 (m-40) REVERT: Z 106 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7669 (mt0) outliers start: 165 outliers final: 146 residues processed: 489 average time/residue: 0.8293 time to fit residues: 686.4845 Evaluate side-chains 537 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 374 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 316 optimal weight: 7.9990 chunk 510 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 534 optimal weight: 3.9990 chunk 492 optimal weight: 5.9990 chunk 426 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN E 61 ASN M 5 GLN a 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 88598 Z= 0.313 Angle : 0.753 11.192 133457 Z= 0.381 Chirality : 0.043 0.343 17200 Planarity : 0.006 0.072 6443 Dihedral : 23.822 179.269 46393 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 7.44 % Allowed : 20.39 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.15), residues: 2617 helix: -1.96 (0.19), residues: 601 sheet: -1.09 (0.22), residues: 544 loop : -2.21 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP J 48 HIS 0.007 0.001 HIS Q 31 PHE 0.032 0.002 PHE X 50 TYR 0.019 0.002 TYR S 99 ARG 0.005 0.001 ARG I 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 373 time to evaluate : 3.321 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8615 (pttt) cc_final: 0.8303 (ptpt) REVERT: A 65 LYS cc_start: 0.7993 (ptmm) cc_final: 0.7712 (ptmt) REVERT: A 111 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.5800 (ptt-90) REVERT: B 111 GLU cc_start: 0.3302 (OUTLIER) cc_final: 0.1557 (tm-30) REVERT: B 175 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8286 (ttm170) REVERT: B 182 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8581 (ptm160) REVERT: B 186 SER cc_start: 0.8514 (m) cc_final: 0.8091 (t) REVERT: C 11 ARG cc_start: 0.7814 (tpt170) cc_final: 0.7379 (ttp-110) REVERT: C 84 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7341 (ttpp) REVERT: D 12 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7946 (mt) REVERT: D 37 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7816 (mmtt) REVERT: E 4 LYS cc_start: 0.8733 (ptmt) cc_final: 0.8158 (ptpp) REVERT: E 52 MET cc_start: 0.7172 (mmm) cc_final: 0.6682 (mmt) REVERT: E 72 LYS cc_start: 0.7399 (tttt) cc_final: 0.7095 (tttm) REVERT: F 69 GLN cc_start: 0.6806 (mm110) cc_final: 0.6416 (mm110) REVERT: G 42 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6453 (mttt) REVERT: G 58 GLU cc_start: 0.5612 (pt0) cc_final: 0.5197 (tt0) REVERT: H 63 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7083 (tt) REVERT: J 35 LYS cc_start: 0.8291 (tppt) cc_final: 0.7942 (tppt) REVERT: J 41 ASP cc_start: 0.3987 (OUTLIER) cc_final: 0.3194 (m-30) REVERT: J 45 LYS cc_start: 0.5581 (OUTLIER) cc_final: 0.4177 (ttpt) REVERT: J 48 TRP cc_start: 0.8091 (m100) cc_final: 0.7725 (m100) REVERT: M 5 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6722 (tm130) REVERT: M 29 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.6979 (mmtt) REVERT: M 43 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7884 (tp) REVERT: N 27 MET cc_start: 0.8012 (pmm) cc_final: 0.7662 (pmm) REVERT: O 38 ARG cc_start: 0.6222 (ptp-170) cc_final: 0.5789 (ptm-80) REVERT: P 37 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7645 (ttp-170) REVERT: R 24 MET cc_start: 0.7884 (ptm) cc_final: 0.7538 (ptp) REVERT: S 148 GLN cc_start: 0.5084 (mm-40) cc_final: 0.4634 (mm110) REVERT: V 32 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7077 (tm-30) REVERT: V 50 ASP cc_start: 0.7953 (t0) cc_final: 0.7547 (t0) REVERT: V 61 SER cc_start: 0.8448 (t) cc_final: 0.8178 (p) REVERT: V 137 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.4775 (mp10) REVERT: V 144 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.5486 (ptp-170) REVERT: W 17 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.6883 (mtm-85) REVERT: W 53 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6419 (mptt) REVERT: W 105 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5504 (mp0) REVERT: Y 76 LYS cc_start: 0.8162 (tttp) cc_final: 0.7570 (mttp) REVERT: Y 136 GLU cc_start: 0.2621 (OUTLIER) cc_final: 0.2222 (pt0) REVERT: Z 29 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7065 (ttt180) REVERT: Z 41 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8156 (ttm170) REVERT: Z 61 ASN cc_start: 0.8232 (m-40) cc_final: 0.7918 (m-40) REVERT: Z 106 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: a 45 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6488 (mm) outliers start: 166 outliers final: 144 residues processed: 484 average time/residue: 0.8178 time to fit residues: 670.1325 Evaluate side-chains 536 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 372 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 338 optimal weight: 7.9990 chunk 453 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 392 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 118 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 438 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN a 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.150156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.129193 restraints weight = 92958.966| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.75 r_work: 0.2882 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 88598 Z= 0.324 Angle : 0.786 59.200 133457 Z= 0.405 Chirality : 0.043 0.346 17200 Planarity : 0.006 0.072 6443 Dihedral : 23.822 179.261 46393 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 7.62 % Allowed : 20.35 % Favored : 72.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.15), residues: 2617 helix: -1.96 (0.19), residues: 601 sheet: -1.09 (0.22), residues: 544 loop : -2.21 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP J 48 HIS 0.007 0.001 HIS Q 31 PHE 0.032 0.002 PHE X 50 TYR 0.019 0.002 TYR S 99 ARG 0.005 0.001 ARG I 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12544.17 seconds wall clock time: 223 minutes 13.17 seconds (13393.17 seconds total)